source /etc/profile.d/modules.csh setenv LMOD_ROOT /usr/local/lmod/lmod setenv LMOD_PKG /usr/local/lmod/lmod/8.4.20 setenv LMOD_CMD /usr/local/lmod/lmod/8.4.20/libexec/lmod setenv LMOD_DIR /usr/local/lmod/lmod/8.4.20/libexec setenv MODULESHOME /usr/local/lmod/lmod/8.4.20 setenv MODULEPATH /usr/local/lmod/modulefiles setenv TARG_TITLE_BAR_PAREN setenv LMOD_SETTARG_FULL_SUPPORT no if ( ! 1 ) then groups grep -wq staff set group_check = 1 if ( `id -u` == 0 || 1 == 0 ) then id -u if ( ! 1 ) then set prefix = set midfix = set postfix = set merge = && set histchar = ! if ( 0 ) then if ( 1 ) then alias module eval `$LMOD_CMD tcsh !*` && eval `$LMOD_SETTARG_CMD -s csh` else alias clearMT eval `/usr/local/lmod/lmod/8.4.20/libexec/clearLMOD_cmd --shell csh --simple` alias clearLmod module --force purge && eval `/usr/local/lmod/lmod/8.4.20/libexec/clearLMOD_cmd --shell csh --full !* ` alias ml eval `/usr/local/lmod/lmod/8.4.20/libexec/ml_cmd !*` setenv LMOD_VERSION 8.4.20 unset prefix unset midfix unset postfix unset histchar unset merge set echo_style=both eval `$LMOD_CMD tcsh load afni freesurfer` /usr/local/lmod/lmod/8.4.20/libexec/lmod tcsh load afni freesurfer [-] Unloading AFNI current-openmp ... [+] Loading AFNI current-openmp ... AFNI/current-openmp last updated 2021-10-15 [+] Loading freesurfer 7.1.1 on cn0853 setenv FREESURFER_HOME /usr/local/apps/freesurfer/7.1.1 setenv LD_LIBRARY_PATH /usr/local/lib64 setenv __LMOD_REF_COUNT_LOADEDMODULES afni/current-openmp:1;freesurfer/7.1.1:1 setenv LOADEDMODULES afni/current-openmp:freesurfer/7.1.1 setenv MODULEPATH /usr/local/lmod/modulefiles setenv __LMOD_REF_COUNT_PATH /usr/local/apps/freesurfer/7.1.1/bin:1;/usr/local/apps/afni/current/linux_centos_7_64:1;/usr/local/slurm/bin:4;/usr/local/bin:5;/usr/local/mysql/bin:4;/usr/X11R6/bin:4;/usr/local/jdk/bin:4;/usr/lib64/qt-3.3/bin:1;/usr/bin:1;/home/reynoldr/rbin:4;/opt/ibutils/bin:1 setenv PATH /usr/local/apps/freesurfer/7.1.1/bin:/usr/local/apps/afni/current/linux_centos_7_64:/usr/local/slurm/bin:/usr/local/bin:/usr/local/mysql/bin:/usr/X11R6/bin:/usr/local/jdk/bin:/usr/lib64/qt-3.3/bin:/usr/bin:/home/reynoldr/rbin:/opt/ibutils/bin setenv __LMOD_REF_COUNT__LMFILES_ /usr/local/lmod/modulefiles/afni/current-openmp.lua:1;/usr/local/lmod/modulefiles/freesurfer/7.1.1.lua:1 setenv _LMFILES_ /usr/local/lmod/modulefiles/afni/current-openmp.lua:/usr/local/lmod/modulefiles/freesurfer/7.1.1.lua setenv _ModuleTable001_ 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 setenv _ModuleTable002_ MS5sdWEiLFsiZnVsbE5hbWUiXT0iZnJlZXN1cmZlci83LjEuMSIsWyJsb2FkT3JkZXIiXT0yLHByb3BUPXt9LFsic3RhY2tEZXB0aCJdPTAsWyJzdGF0dXMiXT0iYWN0aXZlIixbInVzZXJOYW1lIl09ImZyZWVzdXJmZXIiLFsid1YiXT0iXjAwMDAwMDA3LjAwMDAwMDAwMS4wMDAwMDAwMDEuKnpmaW5hbCIsfSx9LG1wYXRoQT17Ii91c3IvbG9jYWwvbG1vZC9tb2R1bGVmaWxlcyIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvdXNyL2xvY2FsL2xtb2QvbW9kdWxlZmlsZXMiLH0= setenv _ModuleTable_Sz_ 2 eval `$LMOD_SETTARG_CMD -s csh` : -s csh source /usr/local/apps/freesurfer/7.1.1/SetUpFreeSurfer.csh if ( ! 1 ) then if ( ! 0 ) then setenv SUBJECTS_DIR /usr/local/apps/freesurfer/7.1.1/subjects endif if ( ! 0 ) then setenv FUNCTIONALS_DIR /usr/local/apps/freesurfer/7.1.1/sessions endif source /usr/local/apps/freesurfer/7.1.1/FreeSurferEnv.csh set VERSION = FreeSurferEnv.csh 7.1.1 if ( ( sub-005 == --help ) || ( sub-005 == -help ) ) then set os = `uname -s` uname -s setenv OS Linux if ( 0 ) then set output = 1 endif if ( 1 == 0 || 0 == 0 ) then set output = 0 endif if ( ! 1 ) then if ( ! -e /usr/local/apps/freesurfer/7.1.1 ) then if ( 0 ) then if ( ! 1 ) then if ( ! 0 ) then setenv FS_OVERRIDE 0 endif if ( ! 0 || 0 ) then setenv FSFAST_HOME /usr/local/apps/freesurfer/7.1.1/fsfast endif if ( ! 1 || 0 ) then if ( ( ! 0 ) && ( ! 0 || 0 ) ) then if ( 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/mni/bin ) then setenv MINC_BIN_DIR /usr/local/apps/freesurfer/7.1.1/mni/bin setenv MNI_DIR /usr/local/apps/freesurfer/7.1.1/mni else if ( -e /usr/pubsw/packages/mni/current/bin ) then endif if ( ( ! 0 ) && ( ! 0 || 0 ) ) then if ( 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/mni/lib ) then setenv MINC_LIB_DIR /usr/local/apps/freesurfer/7.1.1/mni/lib else if ( -e /usr/pubsw/packages/mni/current/lib ) then endif if ( ( ! 0 ) && ( ! 0 || 0 ) ) then if ( 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/mni/data ) then setenv MNI_DATAPATH /usr/local/apps/freesurfer/7.1.1/mni/data else if ( -e /usr/pubsw/packages/mni/current/data ) then endif if ( ! 0 || 0 ) then if ( 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/fsl ) then if ( -e /usr/pubsw/packages/fsl/current ) then if ( -e /usr/local/pubsw/packages/fsl/current ) then if ( -e /usr/local/fsl ) then endif setenv FREESURFER_HOME /usr/local/apps/freesurfer/7.1.1 setenv LOCAL_DIR /usr/local/apps/freesurfer/7.1.1/local foreach d ( /usr/local/apps/freesurfer/7.1.1/fsfast /usr/local/apps/freesurfer/7.1.1/subjects ) if ( ! -e /usr/local/apps/freesurfer/7.1.1/fsfast ) then end if ( ! -e /usr/local/apps/freesurfer/7.1.1/subjects ) then end if ( ! 0 ) setenv FSF_OUTPUT_FORMAT nii.gz setenv FSF_OUTPUT_FORMAT nii.gz if ( 0 ) then if ( 0 && 0 ) then if ( ! 0 ) then setenv FMRI_ANALYSIS_DIR /usr/local/apps/freesurfer/7.1.1/fsfast set SUF = ~/matlab/startup.m if ( ! -e /home/reynoldr/matlab/startup.m ) then set tmp1 = `grep FSFAST_HOME $SUF | wc -l` wc -l grep FSFAST_HOME /home/reynoldr/matlab/startup.m set tmp2 = `grep FMRI_ANALYSIS_DIR $SUF | wc -l` wc -l grep FMRI_ANALYSIS_DIR /home/reynoldr/matlab/startup.m set tmp3 = `grep FREESURFER_HOME $SUF | wc -l` wc -l grep FREESURFER_HOME /home/reynoldr/matlab/startup.m if ( 1 == 0 && 0 == 0 && 1 == 0 ) then endif if ( 0 && 1 ) then if ( ! 0 ) then if ( 1 ) then if ( ! -d /usr/local/apps/freesurfer/7.1.1/mni/bin ) then else if ( 1 ) then if ( ! -d /usr/local/apps/freesurfer/7.1.1/mni/lib ) then else if ( ! 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/mni/share/perl5 ) then setenv MNI_PERL5LIB /usr/local/apps/freesurfer/7.1.1/mni/share/perl5 else if ( -e /usr/local/apps/freesurfer/7.1.1/mni/lib/perl5/5.8.8 ) then endif if ( ! 0 ) then setenv PERL5LIB /usr/local/apps/freesurfer/7.1.1/mni/share/perl5 else if ( /usr/local/apps/freesurfer/7.1.1/mni/share/perl5 != /usr/local/apps/freesurfer/7.1.1/mni/share/perl5 ) then endif if ( ! 0 ) then if ( 1 ) then set path = ( /usr/local/apps/freesurfer/7.1.1/mni/bin /usr/local/apps/freesurfer/7.1.1/bin /usr/local/apps/afni/current/linux_centos_7_64 /usr/local/slurm/bin /usr/local/bin /usr/local/mysql/bin /usr/X11R6/bin /usr/local/jdk/bin /usr/lib64/qt-3.3/bin /usr/bin /home/reynoldr/rbin /opt/ibutils/bin ) endif endif if ( -e /usr/local/apps/freesurfer/7.1.1/lib/misc/bin ) then if ( -e /usr/local/apps/freesurfer/7.1.1/lib/misc/lib ) then if ( 0 && 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/bin/freeview.app ) then if ( -e /usr/local/apps/freesurfer/7.1.1/lib/gcc/lib ) then if ( 0 ) then if ( 0 && 0 ) then if ( 0 ) then if ( 0 ) then if ( 0 && 0 ) then if ( -e /usr/local/apps/freesurfer/7.1.1/tktools ) then set path = ( /usr/local/apps/freesurfer/7.1.1/tktools /usr/local/apps/freesurfer/7.1.1/mni/bin /usr/local/apps/freesurfer/7.1.1/bin /usr/local/apps/afni/current/linux_centos_7_64 /usr/local/slurm/bin /usr/local/bin /usr/local/mysql/bin /usr/X11R6/bin /usr/local/jdk/bin /usr/lib64/qt-3.3/bin /usr/bin /home/reynoldr/rbin /opt/ibutils/bin ) endif set path = ( /usr/local/apps/freesurfer/7.1.1/bin /usr/local/apps/freesurfer/7.1.1/fsfast/bin /usr/local/apps/freesurfer/7.1.1/tktools /usr/local/apps/freesurfer/7.1.1/mni/bin /usr/local/apps/freesurfer/7.1.1/bin /usr/local/apps/afni/current/linux_centos_7_64 /usr/local/slurm/bin /usr/local/bin /usr/local/mysql/bin /usr/X11R6/bin /usr/local/jdk/bin /usr/lib64/qt-3.3/bin /usr/bin /home/reynoldr/rbin /opt/ibutils/bin ) setenv FREESURFER /usr/local/apps/freesurfer/7.1.1 setenv FIX_VERTEX_AREA rehash exit 0 setenv OMP_NUM_THREADS 4 set ecode = 0 set subj = sub-005 set ses = ses-01 set template = MNI152_2009_template_SSW.nii.gz set dir_inroot = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo set dir_log = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/logs set dir_basic = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic set dir_fs = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs set dir_ssw = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_13_ssw set dir_physio = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_14_physio set dir_ap_se = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_20_ap_se set dir_ap_me = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_21_ap_me set dir_ap_me_b = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_22_ap_me_b set dir_ap_me_bt = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_23_ap_me_bt set dir_ap_me_bts = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_24_ap_me_bts set sdir_basic = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01 set sdir_epi = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01/func set sdir_fs = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01 set sdir_suma = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01/SUMA set sdir_ssw = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_13_ssw/sub-005/ses-01 set sdir_physio = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_14_physio/sub-005/ses-01 set sdir_ap_se = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_20_ap_se/sub-005/ses-01 set sdir_ap_me = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_21_ap_me/sub-005/ses-01 set sdir_ap_me_b = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_22_ap_me_b/sub-005/ses-01 set sdir_ap_me_bt = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_23_ap_me_bt/sub-005/ses-01 set sdir_ap_me_bts = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_24_ap_me_bts/sub-005/ses-01 set dset_anat_00 = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01/anat/sub-005_ses-01_mprage_run-1_T1w.nii.gz set nthr_avail = `afni_system_check.py -check_all | grep "number of CPUs:" | awk '{print $4}'` afni_system_check.py -check_all awk {print $4} grep number of CPUs: set nthr_using = `afni_check_omp` afni_check_omp echo ++ INFO: Using 72 of available 4 threads ++ INFO: Using 72 of available 4 threads if ( -d /lscratch/25105636 ) then set usetemp = 1 set sdir_BW = /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01 set sdir_fs = /lscratch/25105636/sub-005_ses-01 else mkdir -p /lscratch/25105636/sub-005_ses-01 recon-all -all -3T -parallel -sd /lscratch/25105636/sub-005_ses-01 -subjid sub-005 -i /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01/anat/sub-005_ses-01_mprage_run-1_T1w.nii.gz Subject Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Current Stamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 INFO: SUBJECTS_DIR is /lscratch/25105636/sub-005_ses-01 Actual FREESURFER_HOME /usr/local/apps/freesurfer/7.1.1 Linux cn0853 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/apps/freesurfer/7.1.1/bin/recon-all' -> '/lscratch/25105636/sub-005_ses-01/sub-005/scripts/recon-all.local-copy' /lscratch/25105636/sub-005_ses-01/sub-005 mri_convert /gpfs/gsfs7/users/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01/anat/sub-005_ses-01_mprage_run-1_T1w.nii.gz /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig/001.mgz mri_convert /gpfs/gsfs7/users/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01/anat/sub-005_ses-01_mprage_run-1_T1w.nii.gz /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig/001.mgz reading from /gpfs/gsfs7/users/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_00_basic/sub-005/ses-01/anat/sub-005_ses-01_mprage_run-1_T1w.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) writing to /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig/001.mgz... @#@FSTIME 2021:10:15:11:51:37 mri_convert N 2 e 1.77 S 0.03 U 2.21 P 126% M 25416 F 0 R 6474 W 0 c 12 w 18 I 0 O 16096 L 51.09 52.72 52.39 @#@FSLOADPOST 2021:10:15:11:51:39 mri_convert N 2 51.09 52.72 52.39 #-------------------------------------------- #@# MotionCor Fri Oct 15 11:51:40 EDT 2021 Found 1 runs /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig/001.mgz /lscratch/25105636/sub-005_ses-01/sub-005/mri/rawavg.mgz /lscratch/25105636/sub-005_ses-01/sub-005 mri_convert /lscratch/25105636/sub-005_ses-01/sub-005/mri/rawavg.mgz /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig.mgz --conform mri_convert /lscratch/25105636/sub-005_ses-01/sub-005/mri/rawavg.mgz /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig.mgz --conform reading from /lscratch/25105636/sub-005_ses-01/sub-005/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (1, -0, 0) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 2137 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig.mgz... @#@FSTIME 2021:10:15:11:51:43 mri_convert N 3 e 5.38 S 0.07 U 5.81 P 109% M 36540 F 0 R 28053 W 0 c 26 w 9 I 0 O 9952 L 50.92 52.66 52.37 @#@FSLOADPOST 2021:10:15:11:51:48 mri_convert N 3 50.85 52.62 52.36 mri_add_xform_to_header -c /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms/talairach.xfm /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig.mgz /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2021:10:15:11:51:48 mri_add_xform_to_header N 4 e 0.75 S 0.02 U 1.43 P 193% M 19688 F 0 R 5027 W 0 c 18 w 9 I 0 O 9944 L 50.85 52.62 52.36 @#@FSLOADPOST 2021:10:15:11:51:49 mri_add_xform_to_header N 4 50.85 52.62 52.36 #-------------------------------------------- #@# Talairach Fri Oct 15 11:51:49 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /lscratch/25105636/sub-005_ses-01/sub-005/mri /usr/local/apps/freesurfer/7.1.1/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 Linux cn0853 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Fri Oct 15 11:51:49 EDT 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.15571 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.15571/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.15571/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.15571/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.15571/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Fri Oct 15 11:56:37 EDT 2021 mri_nu_correct.mni done @#@FSTIME 2021:10:15:11:51:49 mri_nu_correct.mni N 12 e 288.37 S 0.60 U 288.51 P 100% M 486232 F 0 R 225853 W 0 c 220 w 154 I 0 O 9592 L 50.85 52.62 52.36 @#@FSLOADPOST 2021:10:15:11:56:37 mri_nu_correct.mni N 12 49.55 50.89 51.70 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Fri Oct 15 11:56:38 EDT 2021 Ended at Fri Oct 15 11:57:07 EDT 2021 talairach_avi done @#@FSTIME 2021:10:15:11:56:38 talairach_avi N 6 e 29.79 S 1.89 U 22.51 P 81% M 253960 F 0 R 573897 W 0 c 1182 w 280 I 131080 O 295296 L 49.55 50.89 51.70 @#@FSLOADPOST 2021:10:15:11:57:07 talairach_avi N 6 49.52 50.77 51.64 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/apps/freesurfer/7.1.1/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.1.1 --src: orig.mgz src image (geometry). --trg: /usr/local/apps/freesurfer/7.1.1/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.01402 -0.06713 -0.02034 3.50977; 0.06990 0.92924 0.27805 -42.77762; -0.01151 -0.18197 1.10365 0.06479; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms /lscratch/25105636/sub-005_ses-01/sub-005/mri /lscratch/25105636/sub-005_ses-01/sub-005/mri #-------------------------------------------- #@# Talairach Failure Detection Fri Oct 15 11:57:10 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6953, pval=0.4932 >= threshold=0.0050) @#@FSTIME 2021:10:15:11:57:10 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 66% M 2152 F 0 R 627 W 0 c 1 w 11 I 0 O 0 L 49.48 50.74 51.62 @#@FSLOADPOST 2021:10:15:11:57:10 talairach_afd N 4 49.48 50.74 51.62 awk -f /usr/local/apps/freesurfer/7.1.1/bin/extract_talairach_avi_QA.awk /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms/talairach_avi.log tal_QC_AZS /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms/talairach_avi.log TalAviQA: 0.96924 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Fri Oct 15 11:57:10 EDT 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 /usr/bin/bc /lscratch/25105636/sub-005_ses-01/sub-005/mri /usr/local/apps/freesurfer/7.1.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 --ants-n4 nIters 1 mri_nu_correct.mni 7.1.1 Linux cn0853 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Fri Oct 15 11:57:10 EDT 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.16360 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz sysname Linux hostname cn0853 machine x86_64 user reynoldr input /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16360/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16360/input.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16360/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16360/input.mean.dat sysname Linux hostname cn0853 machine x86_64 user reynoldr whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.16360/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16360/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16360/output.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.16360/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.16360/output.mean.dat sysname Linux hostname cn0853 machine x86_64 user reynoldr whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.16360/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.16360/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz mul 1.15933699799990135396 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.16360/nu0.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping (10, 139) to ( 3, 110) Fri Oct 15 12:02:29 EDT 2021 mri_nu_correct.mni done @#@FSTIME 2021:10:15:11:57:10 mri_nu_correct.mni N 13 e 319.00 S 1.85 U 322.89 P 101% M 610280 F 2 R 741339 W 0 c 377 w 285 I 5088 O 24120 L 49.48 50.74 51.62 @#@FSLOADPOST 2021:10:15:12:02:29 mri_nu_correct.mni N 13 49.15 49.76 50.93 mri_add_xform_to_header -c /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2021:10:15:12:02:29 mri_add_xform_to_header N 4 e 0.67 S 0.02 U 1.34 P 204% M 19736 F 0 R 5042 W 0 c 7 w 8 I 0 O 8792 L 49.15 49.76 50.93 @#@FSLOADPOST 2021:10:15:12:02:29 mri_add_xform_to_header N 4 49.15 49.76 50.93 #-------------------------------------------- #@# Intensity Normalization Fri Oct 15 12:02:29 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... talairach transform 1.01402 -0.06713 -0.02034 3.50977; 0.06990 0.92924 0.27805 -42.77762; -0.01151 -0.18197 1.10365 0.06479; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 52 (52), valley at 39 (39) csf peak at 26, setting threshold to 43 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 49 (49), valley at 38 (38) csf peak at 25, setting threshold to 41 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 11 seconds. @#@FSTIME 2021:10:15:12:02:29 mri_normalize N 7 e 131.40 S 1.13 U 153.46 P 117% M 578260 F 0 R 517044 W 0 c 218 w 25 I 0 O 8240 L 49.15 49.76 50.93 @#@FSLOADPOST 2021:10:15:12:04:41 mri_normalize N 7 48.85 49.41 50.65 #-------------------------------------------- #@# Skull Stripping Fri Oct 15 12:04:41 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_em_register -skull nu.mgz /usr/local/apps/freesurfer/7.1.1/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/apps/freesurfer/7.1.1/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=15.0 skull bounding box = (49, 43, 38) --> (212, 255, 255) finding center of left hemi white matter using (103, 114, 147) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (83,88,120) --> (123, 140,173) to find MRI wm before smoothing, mri peak at 107 robust fit to distribution - 106 +- 8.7 after smoothing, mri peak at 106, scaling input intensities by 1.019 scaling channel 0 by 1.01887 initial log_p = -4.727 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.351584 @ (-10.526, -10.526, -31.579) max log p = -4.191452 @ (5.263, 5.263, -5.263) max log p = -4.187304 @ (2.632, 2.632, -2.632) max log p = -4.154970 @ (-1.316, -1.316, 6.579) max log p = -4.110816 @ (-1.974, -0.658, 1.974) max log p = -4.110816 @ (0.000, 0.000, 0.000) max log p = -4.110816 @ (0.000, 0.000, 0.000) max log p = -4.110816 @ (0.000, 0.000, 0.000) Found translation: (-5.9, -4.6, -30.9): log p = -4.111 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.019, old_max_log_p =-4.111 (thresh=-4.1) 1.00000 0.00000 0.00000 -5.92106; 0.00000 1.06580 0.14032 -34.19686; 0.00000 -0.14032 1.06580 -19.68448; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 4 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.984, old_max_log_p =-4.019 (thresh=-4.0) 1.00000 0.00000 0.00000 -5.92106; 0.00000 1.11625 0.29910 -56.65902; 0.00000 -0.27823 1.03837 4.44765; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 3 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.966, old_max_log_p =-3.984 (thresh=-4.0) 1.00000 0.00000 0.00000 -5.92106; 0.00000 1.19997 0.32153 -71.56671; 0.00000 -0.25736 0.96049 12.45163; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 2 seconds. **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.963, old_max_log_p =-3.966 (thresh=-4.0) 0.99144 -0.03359 0.12537 -17.68514; 0.00000 1.19997 0.32153 -71.56671; -0.14032 -0.27430 1.02370 24.34046; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 2 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.854, old_max_log_p =-3.963 (thresh=-4.0) 0.99816 0.01731 0.06596 -15.49649; -0.02620 1.16299 0.27525 -58.31635; -0.07096 -0.22352 0.98188 12.11743; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 0 seconds. **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.852, old_max_log_p =-3.854 (thresh=-3.8) 0.97976 -0.02036 0.05585 -8.22657; 0.00647 1.16293 0.27726 -60.93429; -0.07229 -0.22771 1.00029 10.26025; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 0 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.813, old_max_log_p =-3.852 (thresh=-3.8) 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05649 -0.26625 0.99263 14.67613; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 54 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.812, old_max_log_p =-3.813 (thresh=-3.8) 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.812 (old=-4.727) transform before final EM align: 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 0.97966 -0.01600 0.03959 -6.04376; 0.00412 1.15892 0.31093 -65.79138; -0.05636 -0.26563 0.99030 14.90229; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 910448 FSRUNTIME@ mri_em_register 0.1550 hours 4 threads registration took 9 minutes and 18 seconds. @#@FSTIME 2021:10:15:12:04:41 mri_em_register N 4 e 557.96 S 4.51 U 2042.65 P 366% M 625112 F 0 R 1141125 W 0 c 3399 w 144 I 144744 O 24 L 48.85 49.41 50.65 @#@FSLOADPOST 2021:10:15:12:13:59 mri_em_register N 4 51.68 51.83 51.38 mri_watershed -T1 -brain_atlas /usr/local/apps/freesurfer/7.1.1/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=131 y=116 z=137 r=89 first estimation of the main basin volume: 3043114 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=154, y=109, z=102, Imax=255 CSF=16, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9358403759 voxels, voxel volume =1.000 = 9358403759 mmm3 = 9358403.584 cm3 done. PostAnalyze...Basin Prior 321 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=130,y=123, z=135, r=11167 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=22 , nb = 45522 RIGHT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=25 , nb = 2934 LEFT_CER CSF_MIN=0, CSF_intensity=6, CSF_MAX=22 , nb = 2880 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=21 , nb = 19728 LEFT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=19 , nb = 19566 OTHER CSF_MIN=2, CSF_intensity=10, CSF_MAX=35 , nb = 414 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 22, 22, 23, 45 after analyzing : 22, 24, 25, 29 RIGHT_CER before analyzing : 25, 23, 21, 51 after analyzing : 23, 24, 25, 30 LEFT_CER before analyzing : 22, 22, 22, 49 after analyzing : 22, 24, 25, 30 RIGHT_BRAIN before analyzing : 21, 21, 23, 44 after analyzing : 21, 23, 25, 28 LEFT_BRAIN before analyzing : 19, 20, 23, 45 after analyzing : 19, 23, 25, 28 OTHER before analyzing : 35, 28, 23, 45 after analyzing : 23, 28, 28, 32 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.010 curvature mean = 74.163, std = 8.568 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.28, sigma = 3.41 after rotation: sse = 2.28, sigma = 3.41 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.30, its var is 2.66 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...32 iterations mri_strip_skull: done peeling brain Brain Size = 1844372 voxels, voxel volume = 1.000 mm3 = 1844372 mmm3 = 1844.372 cm3 MRImask(): AllowDiffGeom = 1 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 36.105231 mri_watershed stimesec 0.804645 mri_watershed ru_maxrss 815680 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 423450 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 7960 mri_watershed ru_oublock 3080 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 800 mri_watershed ru_nivcsw 219 mri_watershed done @#@FSTIME 2021:10:15:12:13:59 mri_watershed N 6 e 23.57 S 0.90 U 36.10 P 156% M 815680 F 0 R 423476 W 0 c 220 w 801 I 7960 O 3088 L 51.68 51.83 51.38 @#@FSLOADPOST 2021:10:15:12:14:22 mri_watershed N 6 51.20 51.71 51.35 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Oct 15 12:14:23 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (60, 60, 50) --> (202, 195, 230) finding center of left hemi white matter using (107, 105, 140) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (90,88,118) --> (124, 121,162) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 7.3 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.450 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.099010 @ (-10.526, -10.526, -31.579) max log p = -3.873860 @ (5.263, 5.263, 5.263) max log p = -3.773420 @ (2.632, 2.632, -7.895) max log p = -3.773420 @ (0.000, 0.000, 0.000) max log p = -3.741607 @ (-0.658, 0.658, 3.289) max log p = -3.720429 @ (-0.987, -0.987, -2.961) max log p = -3.720429 @ (0.000, 0.000, 0.000) max log p = -3.720429 @ (0.000, 0.000, 0.000) Found translation: (-4.3, -3.0, -33.9): log p = -3.720 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.622, old_max_log_p =-3.720 (thresh=-3.7) 1.00000 0.00000 0.00000 -4.27632; 0.00000 1.06580 0.14032 -30.55136; 0.00000 -0.12074 0.91709 -7.57137; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 56 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.598, old_max_log_p =-3.622 (thresh=-3.6) 0.99144 -0.03378 0.11629 -15.22434; 0.00000 1.11900 0.27823 -56.26603; -0.14032 -0.27585 0.94955 32.76125; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 56 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.598, old_max_log_p =-3.598 (thresh=-3.6) 0.99144 -0.03378 0.11629 -15.22434; 0.00000 1.11900 0.27823 -56.26603; -0.14032 -0.27585 0.94955 32.76125; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 0 minutes and 55 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.417, old_max_log_p =-3.598 (thresh=-3.6) 1.01442 -0.02718 0.08340 -14.59111; 0.00973 1.11411 0.20707 -47.77918; -0.09809 -0.19584 0.93327 17.54665; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 54 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.416, old_max_log_p =-3.417 (thresh=-3.4) 0.99528 0.00930 0.08746 -17.13438; -0.02064 1.14121 0.17685 -41.21400; -0.09955 -0.16226 0.95716 10.37809; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 0 minutes and 54 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.408, old_max_log_p =-3.416 (thresh=-3.4) 0.99784 -0.00930 0.08450 -14.80126; -0.00594 1.13841 0.19386 -45.55157; -0.09885 -0.18032 0.95078 12.87895; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 48 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.382, old_max_log_p =-3.408 (thresh=-3.4) 1.00005 0.02159 0.07375 -17.44477; -0.03037 1.13423 0.19144 -42.43124; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 48 seconds. **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.375, old_max_log_p =-3.382 (thresh=-3.4) 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; iteration took 0 minutes and 48 seconds. **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.375, old_max_log_p =-3.375 (thresh=-3.4) 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.375 (old=-4.450) transform before final EM align: 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 3.9 tol 0.000000 final transform: 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 897892 FSRUNTIME@ mri_em_register 0.1465 hours 4 threads registration took 8 minutes and 47 seconds. @#@FSTIME 2021:10:15:12:14:23 mri_em_register N 7 e 527.39 S 4.51 U 1967.47 P 373% M 612600 F 0 R 1214290 W 0 c 3027 w 183 I 139952 O 16 L 51.02 51.66 51.34 @#@FSLOADPOST 2021:10:15:12:23:11 mri_em_register N 7 52.34 52.58 51.94 #-------------------------------------- #@# CA Normalize Fri Oct 15 12:23:11 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (60, 60, 50) --> (202, 195, 231) finding center of left hemi white matter using (107, 105, 141) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (90,88,119) --> (124, 121,163) to find MRI wm before smoothing, mri peak at 105 robust fit to distribution - 106 +- 7.3 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 246437 sample points... INFO: compute sample coordinates transform 1.00357 0.02167 0.07401 -17.95228; -0.03041 1.13556 0.19166 -42.62075; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 65, 57) --> (198, 165, 228) Left_Cerebral_White_Matter: limiting intensities to 110.0 --> 132.0 6 of 14 (42.9%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 66, 54) --> (133, 165, 226) Right_Cerebral_White_Matter: limiting intensities to 121.0 --> 132.0 12 of 16 (75.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (133, 141, 86) --> (181, 182, 141) Left_Cerebellum_White_Matter: limiting intensities to 119.0 --> 132.0 7 of 8 (87.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 141, 79) --> (133, 180, 139) Right_Cerebellum_White_Matter: limiting intensities to 114.0 --> 132.0 9 of 15 (60.0%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (114, 133, 120) --> (148, 193, 152) Brain_Stem: limiting intensities to 97.0 --> 132.0 8 of 16 (50.0%) samples deleted using 69 total control points for intensity normalization... bias field = 0.795 +- 0.088 0 of 27 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 65, 57) --> (198, 165, 228) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 2 of 121 (1.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 66, 54) --> (133, 165, 226) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 25 of 121 (20.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (133, 141, 86) --> (181, 182, 141) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 33 of 69 (47.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 141, 79) --> (133, 180, 139) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 52 (46.2%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (114, 133, 120) --> (148, 193, 152) Brain_Stem: limiting intensities to 88.0 --> 132.0 59 of 68 (86.8%) samples deleted using 431 total control points for intensity normalization... bias field = 1.052 +- 0.097 0 of 284 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (129, 65, 57) --> (198, 165, 228) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 219 (2.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (67, 66, 54) --> (133, 165, 226) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 8 of 241 (3.3%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (133, 141, 86) --> (181, 182, 141) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 62 of 101 (61.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (88, 141, 79) --> (133, 180, 139) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 26 of 59 (44.1%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (114, 133, 120) --> (148, 193, 152) Brain_Stem: limiting intensities to 88.0 --> 132.0 76 of 85 (89.4%) samples deleted using 705 total control points for intensity normalization... bias field = 1.021 +- 0.071 0 of 525 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 41 seconds. @#@FSTIME 2021:10:15:12:23:11 mri_ca_normalize N 8 e 100.74 S 1.37 U 107.10 P 107% M 672232 F 0 R 689434 W 0 c 199 w 293 I 0 O 4064 L 52.34 52.58 51.94 @#@FSLOADPOST 2021:10:15:12:24:52 mri_ca_normalize N 8 50.59 51.91 51.77 #-------------------------------------- #@# CA Reg Fri Oct 15 12:24:52 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_ca_register for OpenMP = 4 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.913634 #FOTS# QuadFit found better minimum quadopt=(dt=207.512,rms=0.868907) vs oldopt=(dt=92.48,rms=0.881177) #GCMRL# 0 dt 207.511670 rms 0.869 4.895% neg 0 invalid 762 tFOTS 11.7330 tGradient 4.8540 tsec 17.4090 #FOTS# QuadFit found better minimum quadopt=(dt=212.61,rms=0.852889) vs oldopt=(dt=92.48,rms=0.858474) #GCMRL# 1 dt 212.610169 rms 0.853 1.844% neg 0 invalid 762 tFOTS 11.3840 tGradient 4.8720 tsec 17.0640 #FOTS# QuadFit found better minimum quadopt=(dt=239.061,rms=0.843698) vs oldopt=(dt=369.92,rms=0.845695) #GCMRL# 2 dt 239.060578 rms 0.844 1.078% neg 0 invalid 762 tFOTS 11.2880 tGradient 5.0990 tsec 17.1790 #FOTS# QuadFit found better minimum quadopt=(dt=168.585,rms=0.838396) vs oldopt=(dt=92.48,rms=0.839896) #GCMRL# 3 dt 168.585366 rms 0.838 0.628% neg 0 invalid 762 tFOTS 11.1360 tGradient 4.8290 tsec 16.7690 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.830676) vs oldopt=(dt=369.92,rms=0.831431) #GCMRL# 4 dt 517.888000 rms 0.831 0.921% neg 0 invalid 762 tFOTS 11.3080 tGradient 4.7110 tsec 16.8190 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.826985) vs oldopt=(dt=92.48,rms=0.82741) #GCMRL# 5 dt 129.472000 rms 0.827 0.444% neg 0 invalid 762 tFOTS 11.1640 tGradient 4.7440 tsec 16.7230 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.816083) vs oldopt=(dt=1479.68,rms=0.817157) #GCMRL# 6 dt 2071.552000 rms 0.816 1.318% neg 0 invalid 762 tFOTS 11.3240 tGradient 4.9680 tsec 17.1000 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.811151) vs oldopt=(dt=92.48,rms=0.811703) #GCMRL# 7 dt 129.472000 rms 0.811 0.604% neg 0 invalid 762 tFOTS 11.2110 tGradient 4.4760 tsec 16.4880 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.809275) vs oldopt=(dt=369.92,rms=0.80955) #GCMRL# 8 dt 517.888000 rms 0.809 0.000% neg 0 invalid 762 tFOTS 11.3490 tGradient 4.9410 tsec 17.1310 #GCAMreg# pass 0 level1 5 level2 1 tsec 163.768 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.810461 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.807493) vs oldopt=(dt=92.48,rms=0.807836) #GCMRL# 10 dt 129.472000 rms 0.807 0.366% neg 0 invalid 762 tFOTS 11.4570 tGradient 4.9760 tsec 17.2470 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.804949) vs oldopt=(dt=369.92,rms=0.805397) #GCMRL# 11 dt 517.888000 rms 0.805 0.315% neg 0 invalid 762 tFOTS 12.1610 tGradient 4.9790 tsec 17.9520 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.802554) vs oldopt=(dt=369.92,rms=0.803005) #GCMRL# 12 dt 517.888000 rms 0.803 0.297% neg 0 invalid 762 tFOTS 12.2290 tGradient 4.9630 tsec 18.0070 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.801873) vs oldopt=(dt=92.48,rms=0.802005) #GCMRL# 13 dt 129.472000 rms 0.802 0.000% neg 0 invalid 762 tFOTS 11.4150 tGradient 4.9290 tsec 17.1810 #GCMRL# 14 dt 129.472000 rms 0.801 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2870 tsec 6.0920 #GCMRL# 15 dt 129.472000 rms 0.800 0.153% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0130 tsec 5.8120 #GCMRL# 16 dt 129.472000 rms 0.798 0.238% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9740 tsec 5.7840 #GCMRL# 17 dt 129.472000 rms 0.795 0.322% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.0950 tsec 5.9140 #GCMRL# 18 dt 129.472000 rms 0.793 0.267% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1010 tsec 5.9280 #GCMRL# 19 dt 129.472000 rms 0.792 0.170% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9840 tsec 5.8060 #GCMRL# 20 dt 129.472000 rms 0.791 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.1640 tsec 5.9790 #GCMRL# 21 dt 129.472000 rms 0.790 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.2720 tsec 6.0800 #GCMRL# 22 dt 129.472000 rms 0.789 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8330 tsec 5.6510 #GCMRL# 23 dt 129.472000 rms 0.787 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9930 tsec 5.8090 #GCMRL# 24 dt 129.472000 rms 0.786 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9200 tsec 5.7330 #GCMRL# 25 dt 129.472000 rms 0.784 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9010 tsec 5.7180 #GCMRL# 26 dt 129.472000 rms 0.783 0.165% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8170 tsec 5.6270 #GCMRL# 27 dt 129.472000 rms 0.782 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6290 tsec 5.4430 #GCMRL# 28 dt 129.472000 rms 0.781 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8210 tsec 5.6290 #GCMRL# 29 dt 129.472000 rms 0.779 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6820 tsec 5.4900 #GCMRL# 30 dt 129.472000 rms 0.778 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5790 tsec 5.3960 #GCMRL# 31 dt 129.472000 rms 0.777 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7700 tsec 5.5860 #GCMRL# 32 dt 129.472000 rms 0.776 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9690 tsec 5.8040 #GCMRL# 33 dt 129.472000 rms 0.776 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7410 tsec 5.5910 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.775145) vs oldopt=(dt=369.92,rms=0.775172) #GCMRL# 34 dt 517.888000 rms 0.775 0.000% neg 0 invalid 762 tFOTS 12.1300 tGradient 4.7140 tsec 17.6860 #GCMRL# 35 dt 517.888000 rms 0.775 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5480 tsec 5.3680 setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.785009 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.781067) vs oldopt=(dt=103.68,rms=0.781313) #GCMRL# 37 dt 82.944000 rms 0.781 0.502% neg 0 invalid 762 tFOTS 11.3790 tGradient 4.0820 tsec 16.2830 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.775069) vs oldopt=(dt=414.72,rms=0.776686) #GCMRL# 38 dt 248.832000 rms 0.775 0.768% neg 0 invalid 762 tFOTS 10.7460 tGradient 4.2480 tsec 15.7990 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.770137) vs oldopt=(dt=103.68,rms=0.771006) #GCMRL# 39 dt 145.152000 rms 0.770 0.636% neg 0 invalid 762 tFOTS 11.1880 tGradient 4.2920 tsec 16.2930 #FOTS# QuadFit found better minimum quadopt=(dt=99.6073,rms=0.767194) vs oldopt=(dt=103.68,rms=0.767201) #GCMRL# 40 dt 99.607273 rms 0.767 0.382% neg 0 invalid 762 tFOTS 11.3340 tGradient 3.9500 tsec 16.0970 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.76628) vs oldopt=(dt=103.68,rms=0.766627) #GCMRL# 41 dt 62.208000 rms 0.766 0.000% neg 0 invalid 762 tFOTS 11.4100 tGradient 3.8870 tsec 16.1450 #GCMRL# 42 dt 62.208000 rms 0.765 0.143% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0500 tsec 4.8550 #GCMRL# 43 dt 62.208000 rms 0.764 0.205% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2740 tsec 5.0840 #GCMRL# 44 dt 62.208000 rms 0.762 0.266% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9730 tsec 4.7770 #GCMRL# 45 dt 62.208000 rms 0.759 0.298% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9400 tsec 4.7460 #GCMRL# 46 dt 62.208000 rms 0.757 0.306% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8980 tsec 4.6940 #GCMRL# 47 dt 62.208000 rms 0.755 0.299% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9970 tsec 4.8020 #GCMRL# 48 dt 62.208000 rms 0.753 0.256% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8770 tsec 4.6800 #GCMRL# 49 dt 62.208000 rms 0.751 0.210% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7140 tsec 4.5190 #GCMRL# 50 dt 62.208000 rms 0.750 0.177% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9330 tsec 4.7220 #GCMRL# 51 dt 62.208000 rms 0.749 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0650 tsec 4.8550 #GCMRL# 52 dt 62.208000 rms 0.748 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8950 tsec 4.6910 #GCMRL# 53 dt 62.208000 rms 0.747 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9420 tsec 4.7460 #GCMRL# 54 dt 62.208000 rms 0.746 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0450 tsec 4.8830 #FOTS# QuadFit found better minimum quadopt=(dt=0.0006075,rms=0.746103) vs oldopt=(dt=0.0010125,rms=0.746103) #GCAMreg# pass 0 level1 4 level2 1 tsec 168.835 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.747218 #GCMRL# 56 dt 0.000000 rms 0.746 0.149% neg 0 invalid 762 tFOTS 11.2710 tGradient 3.8650 tsec 15.9330 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.777232 #GCMRL# 58 dt 0.000000 rms 0.776 0.138% neg 0 invalid 762 tFOTS 10.0380 tGradient 3.5030 tsec 14.3460 #GCAMreg# pass 0 level1 3 level2 1 tsec 33.687 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.777232 #GCMRL# 60 dt 0.000000 rms 0.776 0.138% neg 0 invalid 762 tFOTS 9.9310 tGradient 3.4730 tsec 14.2080 setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.867639 #FOTS# QuadFit found better minimum quadopt=(dt=2.58929,rms=0.840503) vs oldopt=(dt=2.88,rms=0.840858) #GCMRL# 62 dt 2.589286 rms 0.841 3.127% neg 0 invalid 762 tFOTS 10.5390 tGradient 3.3180 tsec 14.6600 #FOTS# QuadFit found better minimum quadopt=(dt=1.83333,rms=0.836986) vs oldopt=(dt=0.72,rms=0.838233) #GCMRL# 63 dt 1.833333 rms 0.837 0.418% neg 0 invalid 762 tFOTS 10.5500 tGradient 3.3640 tsec 14.7220 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.836399) vs oldopt=(dt=0.72,rms=0.836459) #GCMRL# 64 dt 1.008000 rms 0.836 0.000% neg 0 invalid 762 tFOTS 10.7030 tGradient 3.4070 tsec 14.9610 #GCAMreg# pass 0 level1 2 level2 1 tsec 53.837 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.837303 #GCMRL# 66 dt 0.000000 rms 0.836 0.109% neg 0 invalid 762 tFOTS 10.1400 tGradient 3.4670 tsec 14.4290 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.902892 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.899157) vs oldopt=(dt=0.32,rms=0.899601) #GCMRL# 68 dt 0.448000 rms 0.899 0.414% neg 0 invalid 762 tFOTS 10.7590 tGradient 3.3590 tsec 14.9380 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.89064) vs oldopt=(dt=1.28,rms=0.891299) #GCMRL# 69 dt 1.024000 rms 0.891 0.947% neg 0 invalid 762 tFOTS 10.7900 tGradient 3.3400 tsec 14.9460 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.88803) vs oldopt=(dt=0.32,rms=0.888291) #GCMRL# 70 dt 0.256000 rms 0.888 0.293% neg 0 invalid 762 tFOTS 10.7300 tGradient 3.3540 tsec 14.8910 #GCMRL# 71 dt 0.320000 rms 0.887 0.000% neg 0 invalid 762 tFOTS 10.5820 tGradient 3.2790 tsec 14.7130 #GCMRL# 72 dt 0.320000 rms 0.885 0.243% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3360 tsec 4.2170 #GCMRL# 73 dt 0.320000 rms 0.882 0.302% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3550 tsec 4.1750 #GCMRL# 74 dt 0.320000 rms 0.880 0.249% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3500 tsec 4.1660 #GCMRL# 75 dt 0.320000 rms 0.878 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2130 tsec 4.0850 #GCMRL# 76 dt 0.320000 rms 0.878 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1530 tsec 3.9720 #GCMRL# 77 dt 0.320000 rms 0.878 -0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1620 tsec 4.7110 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.876565) vs oldopt=(dt=0.32,rms=0.876749) #GCMRL# 78 dt 0.448000 rms 0.877 0.117% neg 0 invalid 762 tFOTS 10.7510 tGradient 3.1780 tsec 14.7310 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.875585) vs oldopt=(dt=0.32,rms=0.875613) #GCAMreg# pass 0 level1 1 level2 1 tsec 118.69 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.87645 #FOTS# QuadFit found better minimum quadopt=(dt=0.256,rms=0.874868) vs oldopt=(dt=0.32,rms=0.874955) #GCMRL# 80 dt 0.256000 rms 0.875 0.180% neg 0 invalid 762 tFOTS 10.5810 tGradient 3.1250 tsec 14.5050 #FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.874327) vs oldopt=(dt=0.32,rms=0.874338) #GCMRL# 81 dt 0.384000 rms 0.874 0.000% neg 0 invalid 762 tFOTS 11.2830 tGradient 3.1580 tsec 15.2900 #GCMRL# 82 dt 0.384000 rms 0.874 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2800 tsec 4.0760 #GCMRL# 83 dt 0.384000 rms 0.873 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1720 tsec 3.9780 #GCMRL# 84 dt 0.384000 rms 0.872 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1450 tsec 3.9690 #GCMRL# 85 dt 0.384000 rms 0.872 0.102% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3780 tsec 4.1960 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.850596 #FOTS# QuadFit found better minimum quadopt=(dt=0.260369,rms=0.842079) vs oldopt=(dt=0.32,rms=0.842317) #GCMRL# 87 dt 0.260369 rms 0.842 1.001% neg 0 invalid 762 tFOTS 10.8010 tGradient 2.4490 tsec 14.0770 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.841835) vs oldopt=(dt=0.02,rms=0.841836) #GCMRL# 88 dt 0.024000 rms 0.842 0.000% neg 0 invalid 762 tFOTS 10.7580 tGradient 2.4860 tsec 14.1050 #GCAMreg# pass 0 level1 0 level2 1 tsec 36.767 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.842719 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.841805) vs oldopt=(dt=0.005,rms=0.84181) #GCMRL# 90 dt 0.007000 rms 0.842 0.108% neg 0 invalid 762 tFOTS 10.7510 tGradient 2.4450 tsec 14.0170 #FOTS# QuadFit found better minimum quadopt=(dt=0.00175,rms=0.841804) vs oldopt=(dt=0.00125,rms=0.841805) #GCMRL# 91 dt 0.001750 rms 0.842 0.000% neg 0 invalid 762 tFOTS 10.6330 tGradient 2.5110 tsec 13.9900 GCAMregister done in 16.3661 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.12901 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.35 x + 0.0 (908 voxels, overlap=0.473) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (908 voxels, peak = 6), gca=6.4 gca peak = 0.17690 (16) mri peak = 0.10954 (10) Right_Lateral_Ventricle (43): linear fit = 0.57 x + 0.0 (716 voxels, overlap=0.713) Right_Lateral_Ventricle (43): linear fit = 0.57 x + 0.0 (716 voxels, peak = 9), gca=9.2 gca peak = 0.28275 (96) mri peak = 0.08532 (87) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (589 voxels, overlap=0.823) Right_Pallidum (52): linear fit = 0.92 x + 0.0 (589 voxels, peak = 88), gca=87.8 gca peak = 0.18948 (93) mri peak = 0.08051 (90) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (454 voxels, overlap=0.635) Left_Pallidum (13): linear fit = 0.95 x + 0.0 (454 voxels, peak = 89), gca=88.8 gca peak = 0.20755 (55) mri peak = 0.14304 (50) Right_Hippocampus: unreasonable value (49.2/50.0), not in range [50, 90] - rejecting gca peak = 0.31831 (58) mri peak = 0.18521 (50) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (580 voxels, overlap=0.024) Left_Hippocampus (17): linear fit = 0.92 x + 0.0 (580 voxels, peak = 53), gca=53.1 gca peak = 0.11957 (102) mri peak = 0.06682 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (48761 voxels, overlap=0.915) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (48761 voxels, peak = 105), gca=104.5 gca peak = 0.11429 (102) mri peak = 0.06611 (103) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (52459 voxels, overlap=0.946) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (52459 voxels, peak = 104), gca=103.5 gca peak = 0.14521 (59) mri peak = 0.06257 (45) Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (13597 voxels, overlap=0.150) Left_Cerebral_Cortex (3): linear fit = 0.76 x + 0.0 (13597 voxels, peak = 45), gca=45.1 gca peak = 0.14336 (58) mri peak = 0.06693 (46) Right_Cerebral_Cortex (42): linear fit = 0.76 x + 0.0 (12628 voxels, overlap=0.077) Right_Cerebral_Cortex (42): linear fit = 0.76 x + 0.0 (12628 voxels, peak = 44), gca=44.4 gca peak = 0.13305 (70) mri peak = 0.09794 (51) Right_Caudate (50): linear fit = 0.77 x + 0.0 (674 voxels, overlap=0.037) Right_Caudate (50): linear fit = 0.77 x + 0.0 (674 voxels, peak = 54), gca=54.2 gca peak = 0.15761 (71) mri peak = 0.08927 (52) Left_Caudate (11): linear fit = 0.71 x + 0.0 (817 voxels, overlap=0.016) Left_Caudate (11): linear fit = 0.71 x + 0.0 (817 voxels, peak = 51), gca=50.8 gca peak = 0.13537 (57) mri peak = 0.04044 (45) Left_Cerebellum_Cortex (8): linear fit = 0.82 x + 0.0 (8746 voxels, overlap=0.337) Left_Cerebellum_Cortex (8): linear fit = 0.82 x + 0.0 (8746 voxels, peak = 47), gca=47.0 gca peak = 0.13487 (56) mri peak = 0.04912 (44) Right_Cerebellum_Cortex (47): linear fit = 0.81 x + 0.0 (9288 voxels, overlap=0.153) Right_Cerebellum_Cortex (47): linear fit = 0.81 x + 0.0 (9288 voxels, peak = 45), gca=45.1 gca peak = 0.19040 (84) mri peak = 0.06180 (84) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5955 voxels, overlap=0.939) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5955 voxels, peak = 89), gca=89.5 gca peak = 0.18871 (83) mri peak = 0.06601 (84) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5413 voxels, overlap=0.891) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (5413 voxels, peak = 88), gca=87.6 gca peak = 0.24248 (57) mri peak = 0.13039 (55) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (371 voxels, overlap=0.868) Left_Amygdala (18): linear fit = 0.89 x + 0.0 (371 voxels, peak = 51), gca=51.0 gca peak = 0.35833 (56) mri peak = 0.12910 (52) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (429 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 0.92 x + 0.0 (429 voxels, peak = 51), gca=51.2 gca peak = 0.12897 (85) mri peak = 0.05848 (87) Left_Thalamus (10): linear fit = 0.95 x + 0.0 (3891 voxels, overlap=0.918) Left_Thalamus (10): linear fit = 0.95 x + 0.0 (3891 voxels, peak = 81), gca=81.2 gca peak = 0.13127 (83) mri peak = 0.08672 (79) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (2933 voxels, overlap=0.864) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (2933 voxels, peak = 84), gca=84.2 gca peak = 0.12974 (78) mri peak = 0.06367 (60) Left_Putamen (12): linear fit = 0.82 x + 0.0 (1790 voxels, overlap=0.714) Left_Putamen (12): linear fit = 0.82 x + 0.0 (1790 voxels, peak = 64), gca=64.3 gca peak = 0.17796 (79) mri peak = 0.06353 (69) Right_Putamen (51): linear fit = 0.88 x + 0.0 (2082 voxels, overlap=0.413) Right_Putamen (51): linear fit = 0.88 x + 0.0 (2082 voxels, peak = 69), gca=69.1 gca peak = 0.10999 (80) mri peak = 0.14235 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (7646 voxels, overlap=0.415) Brain_Stem (16): linear fit = 1.05 x + 0.0 (7646 voxels, peak = 84), gca=84.4 gca peak = 0.13215 (88) mri peak = 0.07073 (83) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (625 voxels, overlap=0.663) Right_VentralDC (60): linear fit = 1.04 x + 0.0 (625 voxels, peak = 92), gca=92.0 gca peak = 0.11941 (89) mri peak = 0.08061 (80) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (765 voxels, overlap=0.848) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (765 voxels, peak = 91), gca=91.2 gca peak = 0.20775 (25) mri peak = 0.12500 ( 8) Third_Ventricle (14): linear fit = 0.49 x + 0.0 (104 voxels, overlap=0.219) Third_Ventricle (14): linear fit = 0.49 x + 0.0 (104 voxels, peak = 12), gca=12.1 gca peak = 0.13297 (21) mri peak = 0.10800 (16) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (505 voxels, overlap=0.561) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (505 voxels, peak = 15), gca=14.8 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Hippocampus = 0.20755 (55) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 0.92 x + 0: 53 estimating mean gm scale to be 0.86 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.56 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 5.44722 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.871935 #FOTS# QuadFit found better minimum quadopt=(dt=317.719,rms=0.851769) vs oldopt=(dt=369.92,rms=0.852307) #GCMRL# 93 dt 317.719078 rms 0.852 2.313% neg 0 invalid 762 tFOTS 11.4220 tGradient 4.5980 tsec 16.8370 #FOTS# QuadFit found better minimum quadopt=(dt=265.309,rms=0.841624) vs oldopt=(dt=369.92,rms=0.842868) #GCMRL# 94 dt 265.309091 rms 0.842 1.191% neg 0 invalid 762 tFOTS 11.2030 tGradient 4.4470 tsec 16.4660 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.83678) vs oldopt=(dt=92.48,rms=0.837319) #GCMRL# 95 dt 129.472000 rms 0.837 0.575% neg 0 invalid 762 tFOTS 12.1620 tGradient 4.5940 tsec 17.5680 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.831771) vs oldopt=(dt=369.92,rms=0.83209) #GCMRL# 96 dt 517.888000 rms 0.832 0.599% neg 0 invalid 762 tFOTS 11.5020 tGradient 4.7580 tsec 17.0800 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.827595) vs oldopt=(dt=92.48,rms=0.827868) #GCMRL# 97 dt 129.472000 rms 0.828 0.502% neg 0 invalid 762 tFOTS 11.3670 tGradient 4.6790 tsec 16.8570 #GCMRL# 98 dt 369.920000 rms 0.825 0.334% neg 0 invalid 762 tFOTS 11.3790 tGradient 4.5630 tsec 16.7590 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.822904) vs oldopt=(dt=92.48,rms=0.823045) #GCMRL# 99 dt 129.472000 rms 0.823 0.234% neg 0 invalid 762 tFOTS 12.1350 tGradient 4.6040 tsec 17.5530 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.820444) vs oldopt=(dt=369.92,rms=0.820692) #GCMRL# 100 dt 517.888000 rms 0.820 0.299% neg 0 invalid 762 tFOTS 11.4890 tGradient 4.6190 tsec 16.9230 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.818505) vs oldopt=(dt=92.48,rms=0.818562) #GCMRL# 101 dt 110.976000 rms 0.819 0.236% neg 0 invalid 762 tFOTS 12.2590 tGradient 4.7800 tsec 17.8610 #FOTS# QuadFit found better minimum quadopt=(dt=1775.62,rms=0.812576) vs oldopt=(dt=1479.68,rms=0.812756) #GCMRL# 102 dt 1775.616000 rms 0.813 0.724% neg 0 invalid 762 tFOTS 11.4600 tGradient 4.6090 tsec 16.8920 #GCMRL# 103 dt 92.480000 rms 0.809 0.483% neg 0 invalid 762 tFOTS 11.5330 tGradient 4.6380 tsec 17.0050 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.807997) vs oldopt=(dt=369.92,rms=0.808021) #GCMRL# 104 dt 443.904000 rms 0.808 0.081% neg 0 invalid 762 tFOTS 11.4110 tGradient 4.5630 tsec 16.7810 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.806641) vs oldopt=(dt=92.48,rms=0.806943) #GCMRL# 105 dt 129.472000 rms 0.807 0.168% neg 0 invalid 762 tFOTS 11.3700 tGradient 4.4270 tsec 16.6060 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.805593) vs oldopt=(dt=369.92,rms=0.805762) #GCMRL# 106 dt 517.888000 rms 0.806 0.130% neg 0 invalid 762 tFOTS 11.3980 tGradient 4.8780 tsec 17.0910 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.804539) vs oldopt=(dt=92.48,rms=0.804764) #GCMRL# 107 dt 129.472000 rms 0.805 0.131% neg 0 invalid 762 tFOTS 11.5130 tGradient 4.5110 tsec 16.8420 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.803806) vs oldopt=(dt=369.92,rms=0.8039) #GCMRL# 108 dt 517.888000 rms 0.804 0.091% neg 0 invalid 762 tFOTS 12.0610 tGradient 4.6020 tsec 17.4930 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.802731) vs oldopt=(dt=92.48,rms=0.80298) #GCMRL# 109 dt 129.472000 rms 0.803 0.134% neg 0 invalid 762 tFOTS 11.2890 tGradient 4.4710 tsec 16.5710 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.80197) vs oldopt=(dt=369.92,rms=0.802047) #GCMRL# 110 dt 517.888000 rms 0.802 0.095% neg 0 invalid 762 tFOTS 12.1700 tGradient 4.7390 tsec 17.7260 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.80082) vs oldopt=(dt=92.48,rms=0.801066) #GCMRL# 111 dt 129.472000 rms 0.801 0.143% neg 0 invalid 762 tFOTS 11.4820 tGradient 4.9810 tsec 17.2850 #GCMRL# 112 dt 369.920000 rms 0.800 0.000% neg 0 invalid 762 tFOTS 12.1390 tGradient 4.7170 tsec 17.7170 #GCMRL# 113 dt 369.920000 rms 0.800 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7030 tsec 5.5130 #GCMRL# 114 dt 369.920000 rms 0.799 -0.200% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6790 tsec 6.2580 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.79867) vs oldopt=(dt=92.48,rms=0.798706) #GCMRL# 115 dt 73.984000 rms 0.799 0.097% neg 0 invalid 762 tFOTS 12.2520 tGradient 4.6760 tsec 17.7560 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.798557) vs oldopt=(dt=92.48,rms=0.798567) #GCMRL# 116 dt 129.472000 rms 0.799 0.000% neg 0 invalid 762 tFOTS 11.4190 tGradient 4.6880 tsec 16.9480 #GCMRL# 117 dt 129.472000 rms 0.798 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6270 tsec 5.4190 #GCMRL# 118 dt 129.472000 rms 0.797 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7730 tsec 5.5750 #GCMRL# 119 dt 129.472000 rms 0.797 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6680 tsec 5.4750 #GCMRL# 120 dt 129.472000 rms 0.796 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6160 tsec 5.4340 #GCMRL# 121 dt 129.472000 rms 0.795 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8200 tsec 5.6350 #GCMRL# 122 dt 129.472000 rms 0.793 0.167% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7460 tsec 5.5660 #GCMRL# 123 dt 129.472000 rms 0.792 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6350 tsec 5.4530 #GCMRL# 124 dt 129.472000 rms 0.791 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5490 tsec 5.3640 #GCMRL# 125 dt 129.472000 rms 0.790 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6660 tsec 5.4730 #GCMRL# 126 dt 129.472000 rms 0.789 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4870 tsec 5.3060 #GCMRL# 127 dt 129.472000 rms 0.788 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8110 tsec 5.6340 #GCMRL# 128 dt 129.472000 rms 0.787 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7740 tsec 5.5950 #GCMRL# 129 dt 129.472000 rms 0.786 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7190 tsec 5.5440 #GCMRL# 130 dt 129.472000 rms 0.785 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5970 tsec 5.4090 #GCMRL# 131 dt 129.472000 rms 0.784 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6990 tsec 5.5210 #GCMRL# 132 dt 129.472000 rms 0.783 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5730 tsec 5.3840 #GCMRL# 133 dt 129.472000 rms 0.782 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6920 tsec 5.5030 #GCMRL# 134 dt 129.472000 rms 0.781 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5570 tsec 5.3700 #GCMRL# 135 dt 129.472000 rms 0.780 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6610 tsec 5.4800 #GCMRL# 136 dt 129.472000 rms 0.779 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6600 tsec 5.4750 #GCMRL# 137 dt 129.472000 rms 0.778 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5760 tsec 5.4040 #GCMRL# 138 dt 129.472000 rms 0.777 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5360 tsec 5.3670 #GCMRL# 139 dt 129.472000 rms 0.776 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6160 tsec 5.4360 #GCMRL# 140 dt 129.472000 rms 0.776 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5640 tsec 5.3820 #GCMRL# 141 dt 129.472000 rms 0.775 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6740 tsec 5.4960 #GCMRL# 142 dt 129.472000 rms 0.774 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5480 tsec 5.3680 #GCMRL# 143 dt 129.472000 rms 0.774 0.078% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5810 tsec 5.4050 #GCMRL# 144 dt 129.472000 rms 0.773 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6100 tsec 5.4420 #GCMRL# 145 dt 129.472000 rms 0.773 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7210 tsec 5.5440 #GCMRL# 146 dt 129.472000 rms 0.772 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6000 tsec 5.4240 #GCMRL# 147 dt 129.472000 rms 0.772 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7010 tsec 5.5160 #GCMRL# 148 dt 129.472000 rms 0.771 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6030 tsec 5.4210 #GCMRL# 149 dt 129.472000 rms 0.771 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6440 tsec 5.4590 #GCMRL# 150 dt 129.472000 rms 0.771 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6350 tsec 5.4400 #GCMRL# 151 dt 129.472000 rms 0.770 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6750 tsec 5.4760 #GCMRL# 152 dt 129.472000 rms 0.770 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5360 tsec 5.3460 #GCMRL# 153 dt 129.472000 rms 0.770 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5810 tsec 5.4070 #GCMRL# 154 dt 129.472000 rms 0.769 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6340 tsec 5.4560 #GCMRL# 155 dt 129.472000 rms 0.769 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5760 tsec 5.3850 #GCMRL# 156 dt 129.472000 rms 0.768 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6410 tsec 5.4580 #GCMRL# 157 dt 129.472000 rms 0.768 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7230 tsec 5.5340 #GCMRL# 158 dt 129.472000 rms 0.768 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5400 tsec 5.3500 #GCMRL# 159 dt 129.472000 rms 0.767 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5730 tsec 5.3870 #GCMRL# 160 dt 129.472000 rms 0.767 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5270 tsec 5.3530 #GCMRL# 161 dt 129.472000 rms 0.767 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5340 tsec 5.3430 #GCMRL# 162 dt 129.472000 rms 0.766 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5020 tsec 5.4160 #GCMRL# 163 dt 129.472000 rms 0.766 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4690 tsec 5.3080 #GCMRL# 164 dt 129.472000 rms 0.766 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4990 tsec 5.3120 #GCMRL# 165 dt 129.472000 rms 0.766 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6290 tsec 5.4400 #GCMRL# 166 dt 129.472000 rms 0.765 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5890 tsec 5.4050 #GCMRL# 167 dt 129.472000 rms 0.765 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5750 tsec 5.4000 #GCMRL# 168 dt 129.472000 rms 0.765 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5300 tsec 5.3450 #GCMRL# 169 dt 129.472000 rms 0.764 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5810 tsec 5.4010 #GCMRL# 170 dt 129.472000 rms 0.764 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5450 tsec 5.3730 #GCMRL# 171 dt 129.472000 rms 0.764 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6450 tsec 5.4680 #GCMRL# 172 dt 129.472000 rms 0.764 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6120 tsec 5.4460 #GCMRL# 173 dt 129.472000 rms 0.763 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5770 tsec 5.4010 #GCMRL# 174 dt 129.472000 rms 0.763 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5880 tsec 5.4070 #GCMRL# 175 dt 129.472000 rms 0.763 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5840 tsec 5.4030 #GCMRL# 176 dt 129.472000 rms 0.763 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6230 tsec 5.4610 #GCMRL# 177 dt 129.472000 rms 0.763 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5600 tsec 5.3890 #GCMRL# 178 dt 129.472000 rms 0.762 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6510 tsec 5.4740 #GCMRL# 179 dt 129.472000 rms 0.762 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5380 tsec 5.3640 #GCMRL# 180 dt 129.472000 rms 0.762 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6750 tsec 5.5050 #GCMRL# 181 dt 129.472000 rms 0.762 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5950 tsec 5.4140 #GCMRL# 182 dt 129.472000 rms 0.761 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5780 tsec 5.4010 #GCMRL# 183 dt 129.472000 rms 0.761 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5360 tsec 5.3420 #GCMRL# 184 dt 129.472000 rms 0.761 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4580 tsec 5.2640 #GCMRL# 185 dt 129.472000 rms 0.761 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4970 tsec 5.3020 #GCMRL# 186 dt 129.472000 rms 0.761 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4670 tsec 5.2840 #GCMRL# 187 dt 129.472000 rms 0.760 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.5360 tsec 5.3870 #FOTS# QuadFit found better minimum quadopt=(dt=4734.98,rms=0.760207) vs oldopt=(dt=5918.72,rms=0.760224) #GCMRL# 188 dt 4734.976000 rms 0.760 0.029% neg 0 invalid 762 tFOTS 12.0070 tGradient 4.4910 tsec 17.3070 #GCMRL# 189 dt 92.480000 rms 0.760 0.000% neg 0 invalid 762 tFOTS 11.4690 tGradient 4.4960 tsec 16.8130 #GCMRL# 190 dt 92.480000 rms 0.760 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6260 tsec 5.4220 #GCMRL# 191 dt 92.480000 rms 0.760 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6420 tsec 5.4410 #GCMRL# 192 dt 92.480000 rms 0.760 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6360 tsec 5.4350 #GCAMreg# pass 0 level1 5 level2 1 tsec 834.13 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.760633 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.758416) vs oldopt=(dt=369.92,rms=0.758605) #GCMRL# 194 dt 295.936000 rms 0.758 0.292% neg 0 invalid 762 tFOTS 11.2350 tGradient 4.5450 tsec 16.6010 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.757776) vs oldopt=(dt=92.48,rms=0.75784) #GCMRL# 195 dt 129.472000 rms 0.758 0.084% neg 0 invalid 762 tFOTS 11.2960 tGradient 4.5960 tsec 16.6950 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.756644) vs oldopt=(dt=1479.68,rms=0.756785) #GCMRL# 196 dt 1183.744000 rms 0.757 0.149% neg 0 invalid 762 tFOTS 12.1220 tGradient 4.5290 tsec 17.4730 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.75576) vs oldopt=(dt=92.48,rms=0.755809) #GCMRL# 197 dt 110.976000 rms 0.756 0.117% neg 0 invalid 762 tFOTS 11.4910 tGradient 4.6110 tsec 16.9260 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.755623) vs oldopt=(dt=369.92,rms=0.755635) #GCMRL# 198 dt 517.888000 rms 0.756 0.000% neg 0 invalid 762 tFOTS 12.2030 tGradient 4.6220 tsec 17.6830 #GCMRL# 199 dt 517.888000 rms 0.755 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6480 tsec 5.4650 #GCMRL# 200 dt 517.888000 rms 0.755 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7140 tsec 5.5360 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.758147 #FOTS# QuadFit found better minimum quadopt=(dt=94.883,rms=0.752927) vs oldopt=(dt=103.68,rms=0.752975) #GCMRL# 202 dt 94.882957 rms 0.753 0.688% neg 0 invalid 762 tFOTS 11.3600 tGradient 3.7400 tsec 15.9090 #FOTS# QuadFit found better minimum quadopt=(dt=172.16,rms=0.747313) vs oldopt=(dt=103.68,rms=0.748093) #GCMRL# 203 dt 172.160000 rms 0.747 0.746% neg 0 invalid 762 tFOTS 11.4150 tGradient 3.7190 tsec 15.9540 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.742612) vs oldopt=(dt=103.68,rms=0.743875) #GCMRL# 204 dt 62.208000 rms 0.743 0.629% neg 0 invalid 762 tFOTS 11.4670 tGradient 3.7070 tsec 15.9860 #GCMRL# 205 dt 414.720000 rms 0.735 1.045% neg 0 invalid 762 tFOTS 11.2920 tGradient 3.6870 tsec 15.7860 #FOTS# QuadFit found better minimum quadopt=(dt=69.9259,rms=0.728225) vs oldopt=(dt=25.92,rms=0.730036) #GCMRL# 206 dt 69.925926 rms 0.728 0.901% neg 0 invalid 762 tFOTS 11.2450 tGradient 3.8000 tsec 15.8470 #FOTS# QuadFit found better minimum quadopt=(dt=101.719,rms=0.725443) vs oldopt=(dt=103.68,rms=0.725445) #GCMRL# 207 dt 101.718631 rms 0.725 0.382% neg 0 invalid 762 tFOTS 12.1140 tGradient 3.8380 tsec 16.7750 #FOTS# QuadFit found better minimum quadopt=(dt=66.8319,rms=0.723695) vs oldopt=(dt=103.68,rms=0.724127) #GCMRL# 208 dt 66.831858 rms 0.724 0.241% neg 0 invalid 762 tFOTS 11.3090 tGradient 3.8310 tsec 15.9520 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.72092) vs oldopt=(dt=103.68,rms=0.721433) #GCMRL# 209 dt 145.152000 rms 0.721 0.383% neg 0 invalid 762 tFOTS 11.6180 tGradient 3.7440 tsec 16.1920 #FOTS# QuadFit found better minimum quadopt=(dt=64.4812,rms=0.719597) vs oldopt=(dt=103.68,rms=0.719983) #GCMRL# 210 dt 64.481203 rms 0.720 0.184% neg 0 invalid 762 tFOTS 11.4030 tGradient 3.8140 tsec 16.0270 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.717315) vs oldopt=(dt=103.68,rms=0.717754) #GCMRL# 211 dt 145.152000 rms 0.717 0.317% neg 0 invalid 762 tFOTS 11.3100 tGradient 3.7590 tsec 15.8780 #FOTS# QuadFit found better minimum quadopt=(dt=70.8571,rms=0.716064) vs oldopt=(dt=103.68,rms=0.716301) #GCMRL# 212 dt 70.857143 rms 0.716 0.174% neg 0 invalid 762 tFOTS 11.3350 tGradient 3.7910 tsec 15.9360 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.714386) vs oldopt=(dt=103.68,rms=0.71453) #GCMRL# 213 dt 145.152000 rms 0.714 0.234% neg 0 invalid 762 tFOTS 11.1550 tGradient 3.8830 tsec 15.8410 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.713088) vs oldopt=(dt=25.92,rms=0.713323) #GCMRL# 214 dt 36.288000 rms 0.713 0.182% neg 0 invalid 762 tFOTS 10.7540 tGradient 3.8250 tsec 15.3910 #GCMRL# 215 dt 414.720000 rms 0.710 0.424% neg 0 invalid 762 tFOTS 11.4420 tGradient 3.7810 tsec 16.0340 #FOTS# QuadFit found better minimum quadopt=(dt=77.2683,rms=0.707235) vs oldopt=(dt=25.92,rms=0.708091) #GCMRL# 216 dt 77.268293 rms 0.707 0.399% neg 0 invalid 762 tFOTS 11.4040 tGradient 3.8580 tsec 16.0720 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.706221) vs oldopt=(dt=25.92,rms=0.706367) #GCMRL# 217 dt 36.288000 rms 0.706 0.143% neg 0 invalid 762 tFOTS 10.6880 tGradient 3.8600 tsec 15.3720 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.703414) vs oldopt=(dt=414.72,rms=0.703567) #GCMRL# 218 dt 580.608000 rms 0.703 0.398% neg 0 invalid 762 tFOTS 11.3200 tGradient 3.7760 tsec 15.9060 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.699723) vs oldopt=(dt=103.68,rms=0.701088) #GCMRL# 219 dt 62.208000 rms 0.700 0.525% neg 0 invalid 762 tFOTS 11.4450 tGradient 3.7910 tsec 16.0680 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.699115) vs oldopt=(dt=103.68,rms=0.699173) #GCMRL# 220 dt 82.944000 rms 0.699 0.087% neg 0 invalid 762 tFOTS 11.4700 tGradient 3.9190 tsec 16.2060 #GCMRL# 221 dt 103.680000 rms 0.698 0.122% neg 0 invalid 762 tFOTS 11.4470 tGradient 3.8330 tsec 16.0990 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.69766) vs oldopt=(dt=25.92,rms=0.697756) #GCMRL# 222 dt 36.288000 rms 0.698 0.086% neg 0 invalid 762 tFOTS 11.4850 tGradient 3.8350 tsec 16.1460 #FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.694586) vs oldopt=(dt=414.72,rms=0.69508) #GCMRL# 223 dt 580.608000 rms 0.695 0.441% neg 0 invalid 762 tFOTS 11.3580 tGradient 3.9010 tsec 16.0640 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.693134) vs oldopt=(dt=25.92,rms=0.693418) #GCMRL# 224 dt 36.288000 rms 0.693 0.209% neg 0 invalid 762 tFOTS 11.3480 tGradient 3.8300 tsec 15.9890 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.692363) vs oldopt=(dt=103.68,rms=0.692388) #GCMRL# 225 dt 124.416000 rms 0.692 0.111% neg 0 invalid 762 tFOTS 11.2750 tGradient 3.8660 tsec 15.9550 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.691876) vs oldopt=(dt=25.92,rms=0.691957) #GCMRL# 226 dt 36.288000 rms 0.692 0.070% neg 0 invalid 762 tFOTS 11.5120 tGradient 3.8570 tsec 16.1860 #FOTS# QuadFit found better minimum quadopt=(dt=995.328,rms=0.688856) vs oldopt=(dt=1658.88,rms=0.689391) #GCMRL# 227 dt 995.328000 rms 0.689 0.437% neg 0 invalid 762 tFOTS 11.3470 tGradient 3.7730 tsec 15.9320 #FOTS# QuadFit found better minimum quadopt=(dt=88.6857,rms=0.686094) vs oldopt=(dt=25.92,rms=0.686849) #GCMRL# 228 dt 88.685714 rms 0.686 0.401% neg 0 invalid 762 tFOTS 11.4410 tGradient 3.6850 tsec 15.9450 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.685076) vs oldopt=(dt=25.92,rms=0.685172) #GCMRL# 229 dt 36.288000 rms 0.685 0.148% neg 0 invalid 762 tFOTS 11.3790 tGradient 4.0650 tsec 16.2580 #GCMRL# 230 dt 103.680000 rms 0.685 0.052% neg 0 invalid 762 tFOTS 11.4080 tGradient 3.9810 tsec 16.2140 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.683819) vs oldopt=(dt=103.68,rms=0.683895) #GCMRL# 231 dt 145.152000 rms 0.684 0.132% neg 0 invalid 762 tFOTS 11.5180 tGradient 3.8550 tsec 16.1970 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.683452) vs oldopt=(dt=25.92,rms=0.683494) #GCMRL# 232 dt 36.288000 rms 0.683 0.054% neg 0 invalid 762 tFOTS 11.4390 tGradient 4.1570 tsec 16.4150 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.682938) vs oldopt=(dt=103.68,rms=0.683034) #GCMRL# 233 dt 145.152000 rms 0.683 0.075% neg 0 invalid 762 tFOTS 11.4320 tGradient 3.9640 tsec 16.2210 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.682063) vs oldopt=(dt=103.68,rms=0.682099) #GCMRL# 234 dt 124.416000 rms 0.682 0.128% neg 0 invalid 762 tFOTS 11.4040 tGradient 3.8130 tsec 16.0370 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.681787) vs oldopt=(dt=25.92,rms=0.681833) #GCMRL# 235 dt 36.288000 rms 0.682 0.000% neg 0 invalid 762 tFOTS 12.0780 tGradient 3.9220 tsec 16.8580 #GCMRL# 236 dt 36.288000 rms 0.682 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8950 tsec 4.6940 #GCMRL# 237 dt 36.288000 rms 0.681 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8220 tsec 4.6270 #GCMRL# 238 dt 36.288000 rms 0.681 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8180 tsec 4.6160 #GCMRL# 239 dt 36.288000 rms 0.680 0.103% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7440 tsec 4.5530 #GCMRL# 240 dt 36.288000 rms 0.679 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9860 tsec 4.8360 #GCMRL# 241 dt 36.288000 rms 0.678 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9090 tsec 4.7440 #GCMRL# 242 dt 36.288000 rms 0.677 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8200 tsec 4.6280 #GCMRL# 243 dt 36.288000 rms 0.676 0.158% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9150 tsec 4.7270 #GCMRL# 244 dt 36.288000 rms 0.675 0.161% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8160 tsec 4.6260 #GCMRL# 245 dt 36.288000 rms 0.674 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9530 tsec 4.7640 #GCMRL# 246 dt 36.288000 rms 0.673 0.167% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8990 tsec 4.7100 #GCMRL# 247 dt 36.288000 rms 0.672 0.169% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7710 tsec 4.5770 #GCMRL# 248 dt 36.288000 rms 0.671 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7760 tsec 4.5830 #GCMRL# 249 dt 36.288000 rms 0.670 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9630 tsec 4.7760 #GCMRL# 250 dt 36.288000 rms 0.669 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8920 tsec 4.7020 #GCMRL# 251 dt 36.288000 rms 0.668 0.147% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8740 tsec 4.6870 #GCMRL# 252 dt 36.288000 rms 0.667 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9010 tsec 4.7170 #GCMRL# 253 dt 36.288000 rms 0.666 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7400 tsec 4.5650 #GCMRL# 254 dt 36.288000 rms 0.665 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7780 tsec 4.5870 #GCMRL# 255 dt 36.288000 rms 0.665 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7380 tsec 4.8670 #GCMRL# 256 dt 36.288000 rms 0.665 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8340 tsec 4.6470 #GCMRL# 257 dt 36.288000 rms 0.665 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8450 tsec 4.6620 #GCMRL# 258 dt 36.288000 rms 0.664 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7600 tsec 4.5910 #GCMRL# 259 dt 36.288000 rms 0.664 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8440 tsec 4.6620 #GCMRL# 260 dt 36.288000 rms 0.664 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8330 tsec 4.6360 #GCMRL# 261 dt 36.288000 rms 0.664 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8440 tsec 4.9820 #GCMRL# 262 dt 36.288000 rms 0.664 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7870 tsec 4.9490 #FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.663688) vs oldopt=(dt=1.62,rms=0.66369) #GCMRL# 263 dt 2.268000 rms 0.664 0.000% neg 0 invalid 762 tFOTS 8.6510 tGradient 3.8230 tsec 13.3160 #GCMRL# 264 dt 2.268000 rms 0.664 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7890 tsec 4.5900 #GCMRL# 265 dt 1.134000 rms 0.664 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8020 tsec 5.2110 #GCMRL# 266 dt 0.283500 rms 0.664 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7790 tsec 5.4690 #GCAMreg# pass 0 level1 4 level2 1 tsec 710.775 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.664753 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.660045) vs oldopt=(dt=103.68,rms=0.660659) #GCMRL# 268 dt 145.152000 rms 0.660 0.708% neg 0 invalid 762 tFOTS 10.8480 tGradient 3.7790 tsec 15.4510 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.659329) vs oldopt=(dt=103.68,rms=0.659406) #GCMRL# 269 dt 82.944000 rms 0.659 0.109% neg 0 invalid 762 tFOTS 10.4590 tGradient 3.9070 tsec 15.2590 #GCMRL# 270 dt 103.680000 rms 0.658 0.128% neg 0 invalid 762 tFOTS 11.4390 tGradient 3.8320 tsec 16.0850 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.658021) vs oldopt=(dt=25.92,rms=0.658099) #GCMRL# 271 dt 36.288000 rms 0.658 0.071% neg 0 invalid 762 tFOTS 10.5700 tGradient 3.7360 tsec 15.1100 #GCMRL# 272 dt 414.720000 rms 0.656 0.237% neg 0 invalid 762 tFOTS 10.5520 tGradient 3.7510 tsec 15.1050 #FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.656263) vs oldopt=(dt=6.48,rms=0.656321) #GCMRL# 273 dt 9.072000 rms 0.656 0.000% neg 0 invalid 762 tFOTS 9.2740 tGradient 3.9170 tsec 14.0250 #GCMRL# 274 dt 9.072000 rms 0.656 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7750 tsec 4.5670 #GCMRL# 275 dt 4.536000 rms 0.656 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7120 tsec 5.1110 #GCMRL# 276 dt 2.268000 rms 0.656 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8480 tsec 5.2850 #FOTS# QuadFit found better minimum quadopt=(dt=0.14175,rms=0.656003) vs oldopt=(dt=0.10125,rms=0.656004) setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.666661 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.658077) vs oldopt=(dt=32,rms=0.659371) #GCMRL# 278 dt 44.800000 rms 0.658 1.288% neg 0 invalid 762 tFOTS 10.6310 tGradient 3.4090 tsec 14.8470 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.657884) vs oldopt=(dt=0.5,rms=0.657929) #GCMRL# 279 dt 0.700000 rms 0.658 0.000% neg 0 invalid 762 tFOTS 8.6480 tGradient 3.4310 tsec 12.9270 #GCMRL# 280 dt 0.350000 rms 0.658 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4220 tsec 4.8270 #GCMRL# 281 dt 0.175000 rms 0.658 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4220 tsec 4.8300 #GCMRL# 282 dt 0.087500 rms 0.658 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4210 tsec 4.9100 #FOTS# QuadFit found better minimum quadopt=(dt=0.04375,rms=0.657739) vs oldopt=(dt=0.03125,rms=0.657741) #GCAMreg# pass 0 level1 3 level2 1 tsec 58.647 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.658848 #FOTS# QuadFit found better minimum quadopt=(dt=0.04375,rms=0.657725) vs oldopt=(dt=0.03125,rms=0.657729) #GCMRL# 284 dt 0.043750 rms 0.658 0.170% neg 0 invalid 762 tFOTS 7.5140 tGradient 3.4600 tsec 11.7910 #GCMRL# 285 dt 0.001953 rms 0.658 0.000% neg 0 invalid 762 tFOTS 6.0760 tGradient 3.4500 tsec 10.4380 #GCMRL# 286 dt 0.000122 rms 0.658 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4580 tsec 5.6930 #GCMRL# 287 dt 0.000061 rms 0.658 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3840 tsec 4.7780 #GCMRL# 288 dt 0.000031 rms 0.658 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3930 tsec 4.8130 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.686809 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.683088) vs oldopt=(dt=0.72,rms=0.683839) #GCMRL# 290 dt 1.008000 rms 0.683 0.542% neg 0 invalid 762 tFOTS 9.3940 tGradient 3.2810 tsec 13.4960 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.680582) vs oldopt=(dt=0.72,rms=0.681288) #GCMRL# 291 dt 1.008000 rms 0.681 0.367% neg 0 invalid 762 tFOTS 9.3740 tGradient 3.2800 tsec 13.4650 #FOTS# QuadFit found better minimum quadopt=(dt=0.864,rms=0.678587) vs oldopt=(dt=0.72,rms=0.678918) #GCMRL# 292 dt 0.864000 rms 0.679 0.293% neg 0 invalid 762 tFOTS 9.3900 tGradient 3.2620 tsec 13.4670 #FOTS# QuadFit found better minimum quadopt=(dt=0.01575,rms=0.678545) vs oldopt=(dt=0.01125,rms=0.678555) #GCMRL# 293 dt 0.015750 rms 0.679 0.000% neg 0 invalid 762 tFOTS 7.4310 tGradient 3.2550 tsec 11.5410 #GCMRL# 294 dt 0.015750 rms 0.679 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2430 tsec 4.0480 #GCMRL# 295 dt 0.000984 rms 0.679 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3180 tsec 5.5960 #GCMRL# 296 dt 0.000492 rms 0.679 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2390 tsec 4.6890 #FOTS# QuadFit found better minimum quadopt=(dt=0.000246094,rms=0.678499) vs oldopt=(dt=0.000175781,rms=0.6785) #GCAMreg# pass 0 level1 2 level2 1 tsec 83.752 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.679524 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.670101) vs oldopt=(dt=2.88,rms=0.672373) #GCMRL# 298 dt 4.032000 rms 0.670 1.387% neg 0 invalid 762 tFOTS 10.0780 tGradient 3.2390 tsec 14.1340 #GCMRL# 299 dt 2.880000 rms 0.665 0.697% neg 0 invalid 762 tFOTS 10.1170 tGradient 3.2070 tsec 14.1450 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.660028) vs oldopt=(dt=2.88,rms=0.661517) #GCMRL# 300 dt 4.032000 rms 0.660 0.812% neg 0 invalid 762 tFOTS 10.1130 tGradient 3.3740 tsec 14.3040 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.658922) vs oldopt=(dt=0.72,rms=0.659242) #GCMRL# 301 dt 1.008000 rms 0.659 0.168% neg 0 invalid 762 tFOTS 9.5210 tGradient 3.2160 tsec 13.5600 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.65785) vs oldopt=(dt=0.72,rms=0.658153) #GCMRL# 302 dt 1.008000 rms 0.658 0.163% neg 0 invalid 762 tFOTS 8.8200 tGradient 3.2350 tsec 12.8680 #FOTS# QuadFit found better minimum quadopt=(dt=0.864,rms=0.656982) vs oldopt=(dt=0.72,rms=0.657126) #GCMRL# 303 dt 0.864000 rms 0.657 0.132% neg 0 invalid 762 tFOTS 9.2750 tGradient 3.2740 tsec 13.3530 #FOTS# QuadFit found better minimum quadopt=(dt=0.063,rms=0.656916) vs oldopt=(dt=0.045,rms=0.656933) #GCMRL# 304 dt 0.063000 rms 0.657 0.000% neg 0 invalid 762 tFOTS 7.9550 tGradient 3.1940 tsec 11.9960 #GCMRL# 305 dt 0.063000 rms 0.657 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2330 tsec 4.0430 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.702688 #FOTS# QuadFit found better minimum quadopt=(dt=3.69355,rms=0.693327) vs oldopt=(dt=1.28,rms=0.69767) #GCMRL# 307 dt 3.693548 rms 0.693 1.332% neg 0 invalid 762 tFOTS 10.0400 tGradient 3.1540 tsec 14.0050 #FOTS# QuadFit found better minimum quadopt=(dt=1.792,rms=0.693029) vs oldopt=(dt=1.28,rms=0.693068) #GCMRL# 308 dt 1.792000 rms 0.693 0.000% neg 0 invalid 762 tFOTS 10.1030 tGradient 3.0200 tsec 13.9740 #GCMRL# 309 dt 1.792000 rms 0.693 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.9490 tsec 3.7530 #GCAMreg# pass 0 level1 1 level2 1 tsec 40.882 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.693827 #GCMRL# 311 dt 5.120000 rms 0.689 0.642% neg 0 invalid 762 tFOTS 10.6660 tGradient 2.9570 tsec 14.4350 #GCMRL# 312 dt 0.100000 rms 0.689 0.000% neg 0 invalid 762 tFOTS 9.4340 tGradient 2.9580 tsec 13.2360 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.645131 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.620116) vs oldopt=(dt=0.32,rms=0.626856) #GCMRL# 314 dt 0.448000 rms 0.620 3.877% neg 0 invalid 762 tFOTS 10.1080 tGradient 2.1850 tsec 13.1090 #GCMRL# 315 dt 0.320000 rms 0.614 0.993% neg 0 invalid 762 tFOTS 10.0970 tGradient 2.1870 tsec 13.0970 #GCMRL# 316 dt 0.320000 rms 0.610 0.679% neg 0 invalid 762 tFOTS 10.0900 tGradient 2.1990 tsec 13.0980 #GCMRL# 317 dt 0.320000 rms 0.607 0.487% neg 0 invalid 762 tFOTS 10.1160 tGradient 2.1310 tsec 13.0440 #GCMRL# 318 dt 0.320000 rms 0.605 0.375% neg 0 invalid 762 tFOTS 9.8500 tGradient 2.1030 tsec 12.7610 #GCMRL# 319 dt 0.320000 rms 0.603 0.297% neg 0 invalid 762 tFOTS 9.9030 tGradient 2.1630 tsec 12.8600 #GCMRL# 320 dt 0.320000 rms 0.601 0.251% neg 0 invalid 762 tFOTS 9.8000 tGradient 2.1020 tsec 12.6910 #GCMRL# 321 dt 0.320000 rms 0.600 0.211% neg 0 invalid 762 tFOTS 9.8590 tGradient 2.1030 tsec 12.7580 #GCMRL# 322 dt 0.320000 rms 0.599 0.186% neg 0 invalid 762 tFOTS 9.8620 tGradient 2.1460 tsec 12.8000 #GCMRL# 323 dt 0.320000 rms 0.598 0.157% neg 0 invalid 762 tFOTS 9.9190 tGradient 2.1360 tsec 12.8580 #GCMRL# 324 dt 0.320000 rms 0.597 0.145% neg 0 invalid 762 tFOTS 9.9960 tGradient 2.1070 tsec 12.9050 #GCMRL# 325 dt 0.320000 rms 0.596 0.126% neg 0 invalid 762 tFOTS 10.0180 tGradient 2.1070 tsec 12.9270 #GCMRL# 326 dt 0.320000 rms 0.596 0.116% neg 0 invalid 762 tFOTS 9.9370 tGradient 2.1070 tsec 12.8480 #GCMRL# 327 dt 0.320000 rms 0.595 0.101% neg 0 invalid 762 tFOTS 10.0280 tGradient 2.1130 tsec 12.9490 #GCMRL# 328 dt 0.320000 rms 0.594 0.098% neg 0 invalid 762 tFOTS 10.0530 tGradient 2.1220 tsec 12.9780 #GCMRL# 329 dt 0.320000 rms 0.594 0.086% neg 0 invalid 762 tFOTS 10.0460 tGradient 2.1310 tsec 12.9850 #GCMRL# 330 dt 0.320000 rms 0.593 0.078% neg 0 invalid 762 tFOTS 10.0170 tGradient 2.2200 tsec 13.0450 #GCMRL# 331 dt 0.320000 rms 0.593 0.072% neg 0 invalid 762 tFOTS 10.0520 tGradient 2.1830 tsec 13.0460 #GCMRL# 332 dt 0.320000 rms 0.593 0.067% neg 0 invalid 762 tFOTS 10.1250 tGradient 2.1290 tsec 13.1060 #GCMRL# 333 dt 0.320000 rms 0.592 0.062% neg 0 invalid 762 tFOTS 10.0790 tGradient 2.1370 tsec 13.0210 #GCMRL# 334 dt 0.320000 rms 0.592 0.059% neg 0 invalid 762 tFOTS 9.9640 tGradient 2.1140 tsec 12.8930 #GCMRL# 335 dt 0.320000 rms 0.592 0.053% neg 0 invalid 762 tFOTS 10.0460 tGradient 2.1540 tsec 13.0200 #GCMRL# 336 dt 0.320000 rms 0.591 0.000% neg 0 invalid 762 tFOTS 10.1210 tGradient 2.1940 tsec 13.1760 #GCMRL# 337 dt 0.320000 rms 0.591 0.046% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1500 tsec 2.9640 #GCMRL# 338 dt 0.320000 rms 0.591 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1520 tsec 2.9680 #GCMRL# 339 dt 0.320000 rms 0.590 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1590 tsec 3.3420 #GCMRL# 340 dt 0.320000 rms 0.590 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1870 tsec 2.9990 #GCMRL# 341 dt 0.320000 rms 0.590 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1490 tsec 3.2840 #GCMRL# 342 dt 0.320000 rms 0.589 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1480 tsec 3.2830 #GCMRL# 343 dt 0.320000 rms 0.589 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1830 tsec 2.9960 #GCMRL# 344 dt 0.320000 rms 0.589 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1900 tsec 3.3260 #GCMRL# 345 dt 0.320000 rms 0.589 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2140 tsec 3.0310 #GCMRL# 346 dt 0.320000 rms 0.589 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1470 tsec 3.2770 #GCMRL# 347 dt 0.320000 rms 0.588 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1450 tsec 3.3210 #GCMRL# 348 dt 0.320000 rms 0.588 0.000% neg 0 invalid 762 tFOTS 10.0180 tGradient 2.1900 tsec 13.1050 #GCMRL# 349 dt 0.320000 rms 0.588 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1510 tsec 2.9390 #GCMRL# 350 dt 0.320000 rms 0.588 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1530 tsec 2.9500 #GCMRL# 351 dt 0.160000 rms 0.588 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1590 tsec 3.5560 #GCMRL# 352 dt 0.160000 rms 0.588 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1690 tsec 2.9710 #GCMRL# 353 dt 0.160000 rms 0.588 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1620 tsec 2.9690 #GCMRL# 354 dt 0.160000 rms 0.588 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1300 tsec 3.2850 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.587612) vs oldopt=(dt=0.08,rms=0.587622) #GCMRL# 355 dt 0.112000 rms 0.588 0.000% neg 0 invalid 762 tFOTS 9.2780 tGradient 2.1780 tsec 12.2840 #GCMRL# 356 dt 0.112000 rms 0.588 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1750 tsec 3.0350 #GCMRL# 357 dt 0.112000 rms 0.588 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1630 tsec 2.9660 #GCMRL# 358 dt 0.112000 rms 0.587 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1670 tsec 3.0040 #GCMRL# 359 dt 0.112000 rms 0.587 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1260 tsec 2.9270 #GCMRL# 360 dt 0.112000 rms 0.587 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1340 tsec 2.9570 #GCMRL# 361 dt 0.112000 rms 0.587 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1520 tsec 3.0380 #GCMRL# 362 dt 0.112000 rms 0.587 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1100 tsec 2.9110 #GCMRL# 363 dt 0.112000 rms 0.587 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1120 tsec 2.9170 #GCMRL# 364 dt 0.112000 rms 0.587 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1140 tsec 2.9130 #GCMRL# 365 dt 0.112000 rms 0.587 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1880 tsec 2.9850 #GCMRL# 366 dt 0.112000 rms 0.586 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1450 tsec 2.9470 #GCMRL# 367 dt 0.112000 rms 0.586 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1470 tsec 2.9840 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.58628) vs oldopt=(dt=0.08,rms=0.586283) #GCMRL# 368 dt 0.112000 rms 0.586 0.000% neg 0 invalid 762 tFOTS 9.2190 tGradient 2.1560 tsec 12.2090 #GCMRL# 369 dt 0.112000 rms 0.586 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1060 tsec 2.8970 #GCMRL# 370 dt 0.112000 rms 0.586 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1470 tsec 2.9410 #GCMRL# 371 dt 0.112000 rms 0.586 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1490 tsec 2.9440 #GCMRL# 372 dt 0.112000 rms 0.586 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1440 tsec 2.9390 #GCMRL# 373 dt 0.112000 rms 0.586 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1460 tsec 2.9300 #GCMRL# 374 dt 0.112000 rms 0.586 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1330 tsec 2.9160 #GCMRL# 375 dt 0.112000 rms 0.586 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1260 tsec 2.9130 #GCAMreg# pass 0 level1 0 level2 1 tsec 452.637 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.586883 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.584134) vs oldopt=(dt=0.08,rms=0.584663) #GCMRL# 377 dt 0.112000 rms 0.584 0.468% neg 0 invalid 762 tFOTS 9.1810 tGradient 2.1210 tsec 12.0940 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.582696) vs oldopt=(dt=0.08,rms=0.583106) #GCMRL# 378 dt 0.112000 rms 0.583 0.246% neg 0 invalid 762 tFOTS 9.1750 tGradient 2.2320 tsec 12.2070 #FOTS# QuadFit found better minimum quadopt=(dt=0.179688,rms=0.580938) vs oldopt=(dt=0.08,rms=0.58191) #GCMRL# 379 dt 0.179688 rms 0.581 0.302% neg 0 invalid 762 tFOTS 9.2250 tGradient 2.2260 tsec 12.2590 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.580234) vs oldopt=(dt=0.08,rms=0.580428) #GCMRL# 380 dt 0.112000 rms 0.580 0.121% neg 0 invalid 762 tFOTS 9.3760 tGradient 2.1330 tsec 12.3240 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.579734) vs oldopt=(dt=0.08,rms=0.579881) #GCMRL# 381 dt 0.112000 rms 0.580 0.086% neg 0 invalid 762 tFOTS 9.4430 tGradient 2.1380 tsec 12.3950 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.57934) vs oldopt=(dt=0.08,rms=0.579449) #GCMRL# 382 dt 0.112000 rms 0.579 0.068% neg 0 invalid 762 tFOTS 9.3580 tGradient 2.1390 tsec 12.3120 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.579061) vs oldopt=(dt=0.08,rms=0.579143) #GCMRL# 383 dt 0.112000 rms 0.579 0.000% neg 0 invalid 762 tFOTS 9.3910 tGradient 2.1440 tsec 12.3970 #GCMRL# 384 dt 0.112000 rms 0.579 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1560 tsec 2.9980 #GCMRL# 385 dt 0.112000 rms 0.579 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1600 tsec 2.9810 #GCMRL# 386 dt 0.112000 rms 0.578 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1550 tsec 2.9830 #GCMRL# 387 dt 0.112000 rms 0.578 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1970 tsec 3.0170 #GCMRL# 388 dt 0.112000 rms 0.578 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2040 tsec 3.0630 #GCMRL# 389 dt 0.112000 rms 0.578 -0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1320 tsec 3.6590 #FOTS# QuadFit found better minimum quadopt=(dt=0,rms=0.577802) vs oldopt=(dt=0,rms=0.577802) GCAMregister done in 45.336 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.575101 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.574087) vs oldopt=(dt=23.12,rms=0.574103) #GCMRL# 391 dt 32.368000 rms 0.574 0.176% neg 0 invalid 762 tFOTS 12.9390 tGradient 4.3510 tsec 18.0970 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.574018) vs oldopt=(dt=23.12,rms=0.574031) #GCMRL# 392 dt 32.368000 rms 0.574 0.000% neg 0 invalid 762 tFOTS 12.9040 tGradient 4.3100 tsec 18.0580 #GCMRL# 393 dt 32.368000 rms 0.574 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3670 tsec 5.1830 #GCMRL# 394 dt 32.368000 rms 0.574 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3660 tsec 5.1880 #GCMRL# 395 dt 32.368000 rms 0.574 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3420 tsec 5.1480 #GCAMreg# pass 0 level1 5 level2 1 tsec 61.405 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.57477 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.572542) vs oldopt=(dt=92.48,rms=0.57259) #GCMRL# 397 dt 110.976000 rms 0.573 0.388% neg 0 invalid 762 tFOTS 12.9490 tGradient 4.3300 tsec 18.0900 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.572364) vs oldopt=(dt=23.12,rms=0.572393) #GCMRL# 398 dt 32.368000 rms 0.572 0.000% neg 0 invalid 762 tFOTS 12.8390 tGradient 4.3410 tsec 18.0340 #GCMRL# 399 dt 32.368000 rms 0.572 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3760 tsec 5.1780 #GCMRL# 400 dt 32.368000 rms 0.572 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3310 tsec 5.1470 #GCMRL# 401 dt 32.368000 rms 0.572 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3350 tsec 5.1510 #GCMRL# 402 dt 32.368000 rms 0.572 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3880 tsec 5.2010 #GCMRL# 403 dt 32.368000 rms 0.572 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3720 tsec 5.1870 #GCMRL# 404 dt 32.368000 rms 0.571 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3320 tsec 5.1500 #GCMRL# 405 dt 32.368000 rms 0.571 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3420 tsec 5.1600 #GCMRL# 406 dt 32.368000 rms 0.571 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3360 tsec 5.1950 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.571124) vs oldopt=(dt=5.78,rms=0.571124) setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.572077 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.570034) vs oldopt=(dt=25.92,rms=0.570238) #GCMRL# 408 dt 36.288000 rms 0.570 0.357% neg 0 invalid 762 tFOTS 12.9680 tGradient 3.6400 tsec 17.4330 #FOTS# QuadFit found better minimum quadopt=(dt=71.2911,rms=0.569119) vs oldopt=(dt=103.68,rms=0.569287) #GCMRL# 409 dt 71.291139 rms 0.569 0.000% neg 0 invalid 762 tFOTS 12.9700 tGradient 3.6050 tsec 17.4470 #GCMRL# 410 dt 71.291139 rms 0.569 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5730 tsec 4.3910 #GCMRL# 411 dt 71.291139 rms 0.568 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5940 tsec 4.4210 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 4 level2 1 tsec 55.228 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.569111 #FOTS# QuadFit found better minimum quadopt=(dt=131.681,rms=0.56308) vs oldopt=(dt=103.68,rms=0.563288) #GCMRL# 413 dt 131.680511 rms 0.563 1.060% neg 0 invalid 762 tFOTS 12.9410 tGradient 3.6070 tsec 17.3750 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.562014) vs oldopt=(dt=25.92,rms=0.562159) #GCMRL# 414 dt 36.288000 rms 0.562 0.000% neg 0 invalid 762 tFOTS 12.8170 tGradient 3.6080 tsec 17.2770 #GCMRL# 415 dt 36.288000 rms 0.562 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5800 tsec 4.3910 #GCMRL# 416 dt 36.288000 rms 0.561 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5900 tsec 4.4110 #GCMRL# 417 dt 36.288000 rms 0.560 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6140 tsec 4.4300 #GCMRL# 418 dt 36.288000 rms 0.559 0.166% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6050 tsec 4.4290 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 419 dt 36.288000 rms 0.558 0.182% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5850 tsec 6.1670 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 420 dt 36.288000 rms 0.557 0.163% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5900 tsec 6.1450 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 421 dt 36.288000 rms 0.556 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5800 tsec 6.0870 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 #GCMRL# 422 dt 36.288000 rms 0.556 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5760 tsec 9.7150 #GCMRL# 423 dt 36.288000 rms 0.555 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6120 tsec 4.4640 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.555087) vs oldopt=(dt=103.68,rms=0.555102) #GCMRL# 424 dt 82.944000 rms 0.555 0.000% neg 0 invalid 762 tFOTS 12.0580 tGradient 3.5870 tsec 16.4860 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 425 dt 82.944000 rms 0.555 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6420 tsec 6.7740 #GCMRL# 426 dt 82.944000 rms 0.555 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5790 tsec 4.3930 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 427 dt 82.944000 rms 0.554 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5790 tsec 6.7550 #GCMRL# 428 dt 82.944000 rms 0.554 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5930 tsec 4.4150 iter 0, gcam->neg = 4 after 2 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.555649 iter 0, gcam->neg = 22 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 430 dt 32.000000 rms 0.551 0.881% neg 0 invalid 762 tFOTS 12.8390 tGradient 3.2490 tsec 20.7300 iter 0, gcam->neg = 23 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 431 dt 32.000000 rms 0.548 0.491% neg 0 invalid 762 tFOTS 12.8350 tGradient 3.2850 tsec 24.4430 #FOTS# QuadFit found better minimum quadopt=(dt=23.2727,rms=0.546002) vs oldopt=(dt=32,rms=0.546249) iter 0, gcam->neg = 18 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 432 dt 23.272727 rms 0.546 0.361% neg 0 invalid 762 tFOTS 12.8830 tGradient 3.2970 tsec 21.3530 iter 0, gcam->neg = 29 after 11 iterations, nbhd size=1, neg = 0 #GCMRL# 433 dt 32.000000 rms 0.544 0.299% neg 0 invalid 762 tFOTS 12.5780 tGradient 3.2720 tsec 23.5610 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.543105) vs oldopt=(dt=32,rms=0.54344) iter 0, gcam->neg = 15 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 434 dt 19.200000 rms 0.543 0.000% neg 0 invalid 762 tFOTS 12.7900 tGradient 3.2610 tsec 19.1670 iter 0, gcam->neg = 11 after 8 iterations, nbhd size=0, neg = 0 #GCMRL# 435 dt 19.200000 rms 0.542 0.174% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4790 tsec 9.6620 iter 0, gcam->neg = 31 after 13 iterations, nbhd size=1, neg = 0 #GCMRL# 436 dt 19.200000 rms 0.541 0.302% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2250 tsec 11.9720 iter 0, gcam->neg = 27 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 437 dt 19.200000 rms 0.539 0.318% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2420 tsec 13.6410 iter 0, gcam->neg = 47 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 438 dt 19.200000 rms 0.537 0.345% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3520 tsec 13.1990 iter 0, gcam->neg = 58 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 439 dt 19.200000 rms 0.535 0.290% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2160 tsec 14.1210 iter 0, gcam->neg = 60 after 6 iterations, nbhd size=0, neg = 0 #GCMRL# 440 dt 19.200000 rms 0.534 0.277% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3310 tsec 8.4790 iter 0, gcam->neg = 42 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 441 dt 19.200000 rms 0.533 0.199% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2880 tsec 8.9990 iter 0, gcam->neg = 49 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 442 dt 19.200000 rms 0.532 0.250% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2300 tsec 13.5400 iter 0, gcam->neg = 49 after 24 iterations, nbhd size=1, neg = 0 #GCMRL# 443 dt 19.200000 rms 0.530 0.302% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2280 tsec 17.6760 iter 0, gcam->neg = 42 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 444 dt 19.200000 rms 0.528 0.279% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2530 tsec 13.0840 iter 0, gcam->neg = 71 after 27 iterations, nbhd size=1, neg = 0 #GCMRL# 445 dt 19.200000 rms 0.528 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2400 tsec 19.2880 iter 0, gcam->neg = 26 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 446 dt 19.200000 rms 0.526 0.286% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1820 tsec 12.2230 iter 0, gcam->neg = 75 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 447 dt 19.200000 rms 0.525 0.208% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5260 tsec 13.9020 iter 0, gcam->neg = 98 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 448 dt 19.200000 rms 0.524 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2360 tsec 8.9290 iter 0, gcam->neg = 83 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 449 dt 19.200000 rms 0.524 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2810 tsec 15.8200 iter 0, gcam->neg = 66 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 450 dt 19.200000 rms 0.523 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4110 tsec 13.2630 iter 0, gcam->neg = 131 after 9 iterations, nbhd size=0, neg = 0 #GCMRL# 451 dt 19.200000 rms 0.522 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2460 tsec 10.2060 iter 0, gcam->neg = 133 after 20 iterations, nbhd size=1, neg = 0 #GCMRL# 452 dt 19.200000 rms 0.522 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2310 tsec 15.5210 iter 0, gcam->neg = 108 after 9 iterations, nbhd size=0, neg = 0 #GCMRL# 453 dt 19.200000 rms 0.521 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2170 tsec 9.9170 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.521136) vs oldopt=(dt=8,rms=0.521156) iter 0, gcam->neg = 6 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 454 dt 11.200000 rms 0.521 0.000% neg 0 invalid 762 tFOTS 12.8560 tGradient 3.2280 tsec 26.9590 iter 0, gcam->neg = 7 after 12 iterations, nbhd size=1, neg = 0 #GCMRL# 455 dt 11.200000 rms 0.521 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4270 tsec 11.6710 iter 0, gcam->neg = 10 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 456 dt 11.200000 rms 0.521 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2470 tsec 6.8140 iter 0, gcam->neg = 12 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 457 dt 11.200000 rms 0.521 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2120 tsec 12.4790 iter 0, gcam->neg = 11 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 458 dt 11.200000 rms 0.521 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3050 tsec 9.0650 iter 0, gcam->neg = 16 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 459 dt 11.200000 rms 0.520 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2980 tsec 8.9330 iter 0, gcam->neg = 23 after 6 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 3 level2 1 tsec 441.657 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.521175 #FOTS# QuadFit found better minimum quadopt=(dt=65.641,rms=0.514607) vs oldopt=(dt=32,rms=0.51579) iter 0, gcam->neg = 19 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 461 dt 65.641026 rms 0.515 1.257% neg 0 invalid 762 tFOTS 12.8070 tGradient 3.2810 tsec 20.7090 #FOTS# QuadFit found better minimum quadopt=(dt=25.5375,rms=0.513042) vs oldopt=(dt=32,rms=0.513195) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 462 dt 25.537459 rms 0.513 0.308% neg 0 invalid 762 tFOTS 12.8200 tGradient 3.2470 tsec 18.6090 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.512634) vs oldopt=(dt=8,rms=0.512718) #GCMRL# 463 dt 11.200000 rms 0.513 0.000% neg 0 invalid 762 tFOTS 12.5840 tGradient 3.3630 tsec 16.7840 #GCMRL# 464 dt 11.200000 rms 0.512 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1950 tsec 3.9980 #GCMRL# 465 dt 11.200000 rms 0.512 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.2470 tsec 4.0480 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 466 dt 11.200000 rms 0.512 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1880 tsec 6.1730 iter 0, gcam->neg = 4 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 467 dt 11.200000 rms 0.512 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1960 tsec 6.6830 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=1, neg = 0 #GCMRL# 468 dt 11.200000 rms 0.511 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1830 tsec 10.2130 iter 0, gcam->neg = 6 after 10 iterations, nbhd size=0, neg = 0 #GCMRL# 469 dt 11.200000 rms 0.511 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.1990 tsec 10.3430 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.511225) vs oldopt=(dt=32,rms=0.511252) iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 470 dt 44.800000 rms 0.511 0.043% neg 0 invalid 762 tFOTS 12.1180 tGradient 3.2260 tsec 18.3780 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.511034) vs oldopt=(dt=32,rms=0.511052) iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.522361 #GCMRL# 472 dt 0.000113 rms 0.521 0.194% neg 0 invalid 762 tFOTS 16.1290 tGradient 3.0510 tsec 19.9940 #GCAMreg# pass 0 level1 2 level2 1 tsec 41.415 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.522361 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.521284) vs oldopt=(dt=0.72,rms=0.521294) #GCMRL# 474 dt 1.008000 rms 0.521 0.206% neg 0 invalid 762 tFOTS 12.7030 tGradient 3.0610 tsec 16.5740 #FOTS# QuadFit found better minimum quadopt=(dt=0.576,rms=0.521258) vs oldopt=(dt=0.72,rms=0.52126) #GCMRL# 475 dt 0.576000 rms 0.521 0.000% neg 0 invalid 762 tFOTS 12.8090 tGradient 3.0770 tsec 16.7310 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.542168 iter 0, gcam->neg = 5 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 477 dt 1.280000 rms 0.539 0.575% neg 0 invalid 762 tFOTS 12.7400 tGradient 2.9760 tsec 19.2610 #GCMRL# 478 dt 0.320000 rms 0.539 0.000% neg 0 invalid 762 tFOTS 12.7390 tGradient 2.9320 tsec 16.5160 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 1 level2 1 tsec 46.53 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.539928 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.538313) vs oldopt=(dt=1.28,rms=0.538383) iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 480 dt 1.024000 rms 0.538 0.299% neg 0 invalid 762 tFOTS 12.8450 tGradient 2.9600 tsec 18.3430 #GCMRL# 481 dt 0.320000 rms 0.538 0.000% neg 0 invalid 762 tFOTS 12.6910 tGradient 2.9420 tsec 16.4800 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.520653 #FOTS# QuadFit found better minimum quadopt=(dt=2.55012,rms=0.462839) vs oldopt=(dt=1.28,rms=0.476535) iter 0, gcam->neg = 1718 after 17 iterations, nbhd size=1, neg = 0 #GCMRL# 483 dt 2.550124 rms 0.471 9.564% neg 0 invalid 762 tFOTS 12.8240 tGradient 2.1720 tsec 25.9190 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.469757) vs oldopt=(dt=0.08,rms=0.469961) #GCMRL# 484 dt 0.112000 rms 0.470 0.000% neg 0 invalid 762 tFOTS 12.7230 tGradient 2.1350 tsec 15.6980 #GCMRL# 485 dt 0.112000 rms 0.470 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1970 tsec 2.9880 #GCAMreg# pass 0 level1 0 level2 1 tsec 52.851 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.470985 #FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.469625) vs oldopt=(dt=0.08,rms=0.469639) #GCMRL# 487 dt 0.064000 rms 0.470 0.289% neg 0 invalid 762 tFOTS 12.6740 tGradient 2.1730 tsec 15.6550 #GCMRL# 488 dt 0.050000 rms 0.470 0.000% neg 0 invalid 762 tFOTS 12.0880 tGradient 2.2210 tsec 15.1530 label assignment complete, 0 changed (0.00%) GCAMregister done in 19.8446 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.451553 #GCAMreg# pass 0 level1 5 level2 1 tsec 20.811 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.451553 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.451527) vs oldopt=(dt=23.12,rms=0.451532) #GCMRL# 491 dt 32.368000 rms 0.452 0.006% neg 0 invalid 762 tFOTS 11.9750 tGradient 3.5490 tsec 16.2890 #GCMRL# 492 dt 92.480000 rms 0.451 0.007% neg 0 invalid 762 tFOTS 11.3650 tGradient 3.5210 tsec 15.6930 #GCMRL# 493 dt 369.920000 rms 0.451 0.030% neg 0 invalid 762 tFOTS 11.4630 tGradient 3.5240 tsec 15.7600 #FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.451356) vs oldopt=(dt=5.78,rms=0.451356) #GCMRL# 494 dt 8.092000 rms 0.451 0.000% neg 0 invalid 762 tFOTS 12.0350 tGradient 3.5310 tsec 16.3750 #GCMRL# 495 dt 8.092000 rms 0.451 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5240 tsec 4.2890 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.451584 #FOTS# QuadFit found better minimum quadopt=(dt=3.888,rms=0.451577) vs oldopt=(dt=6.48,rms=0.451578) #GCMRL# 497 dt 3.888000 rms 0.452 0.002% neg 0 invalid 762 tFOTS 12.0180 tGradient 2.7570 tsec 15.5630 #FOTS# QuadFit found better minimum quadopt=(dt=0.972,rms=0.451576) vs oldopt=(dt=1.62,rms=0.451576) #GCMRL# 498 dt 0.972000 rms 0.452 0.000% neg 0 invalid 762 tFOTS 12.1940 tGradient 2.7700 tsec 15.7850 #GCAMreg# pass 0 level1 4 level2 1 tsec 40.038 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.451576 #GCMRL# 500 dt 103.680000 rms 0.451 0.117% neg 0 invalid 762 tFOTS 11.3800 tGradient 2.8540 tsec 15.0010 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.450721) vs oldopt=(dt=103.68,rms=0.450776) #GCMRL# 501 dt 82.944000 rms 0.451 0.000% neg 0 invalid 762 tFOTS 11.4060 tGradient 2.7220 tsec 14.9430 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.451589 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.450817) vs oldopt=(dt=8,rms=0.450959) #GCMRL# 503 dt 11.200000 rms 0.451 0.171% neg 0 invalid 762 tFOTS 12.0460 tGradient 2.3900 tsec 15.2130 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.4506) vs oldopt=(dt=8,rms=0.450621) #GCMRL# 504 dt 11.200000 rms 0.451 0.000% neg 0 invalid 762 tFOTS 12.0590 tGradient 2.3870 tsec 15.2660 #GCMRL# 505 dt 11.200000 rms 0.451 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3840 tsec 3.1550 #GCAMreg# pass 0 level1 3 level2 1 tsec 41.943 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.450586 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.447678) vs oldopt=(dt=32,rms=0.447964) #GCMRL# 507 dt 44.800000 rms 0.448 0.646% neg 0 invalid 762 tFOTS 12.1390 tGradient 2.3940 tsec 15.3090 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 508 dt 32.000000 rms 0.447 0.000% neg 0 invalid 762 tFOTS 12.1160 tGradient 2.3690 tsec 20.1880 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 509 dt 32.000000 rms 0.446 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4030 tsec 8.0400 iter 0, gcam->neg = 14 after 9 iterations, nbhd size=0, neg = 0 #GCMRL# 510 dt 32.000000 rms 0.445 0.233% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4060 tsec 9.0830 iter 0, gcam->neg = 23 after 15 iterations, nbhd size=1, neg = 0 #GCMRL# 511 dt 32.000000 rms 0.444 0.313% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3920 tsec 12.1960 iter 0, gcam->neg = 52 after 8 iterations, nbhd size=0, neg = 0 #GCMRL# 512 dt 32.000000 rms 0.442 0.239% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.3980 tsec 8.5830 iter 0, gcam->neg = 53 after 14 iterations, nbhd size=0, neg = 0 #GCMRL# 513 dt 32.000000 rms 0.442 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4060 tsec 11.7320 iter 0, gcam->neg = 56 after 18 iterations, nbhd size=1, neg = 0 #GCMRL# 514 dt 32.000000 rms 0.441 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4240 tsec 13.8000 iter 0, gcam->neg = 69 after 33 iterations, nbhd size=2, neg = 0 #GCMRL# 515 dt 32.000000 rms 0.441 -0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.4030 tsec 22.0790 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.441195) vs oldopt=(dt=8,rms=0.441215) #GCMRL# 516 dt 11.200000 rms 0.441 0.025% neg 0 invalid 762 tFOTS 12.0640 tGradient 2.3690 tsec 15.2010 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.441169) vs oldopt=(dt=32,rms=0.441176) iter 0, gcam->neg = 1 after 15 iterations, nbhd size=1, neg = 0 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.445794 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.445483) vs oldopt=(dt=2.88,rms=0.445511) iter 0, gcam->neg = 11 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 518 dt 4.032000 rms 0.446 0.057% neg 0 invalid 762 tFOTS 12.1530 tGradient 2.2280 tsec 17.9180 #FOTS# QuadFit found better minimum quadopt=(dt=0.864,rms=0.445533) vs oldopt=(dt=0.72,rms=0.445534) iter 0, gcam->neg = 10 after 4 iterations, nbhd size=0, neg = 0 #GCMRL# 519 dt 0.864000 rms 0.446 0.000% neg 0 invalid 762 tFOTS 12.1520 tGradient 2.2460 tsec 18.4810 iter 0, gcam->neg = 4 after 4 iterations, nbhd size=0, neg = 0 #GCAMreg# pass 0 level1 2 level2 1 tsec 47.828 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.445519 #FOTS# QuadFit found better minimum quadopt=(dt=8.92517,rms=0.444913) vs oldopt=(dt=11.52,rms=0.444981) iter 0, gcam->neg = 38 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 521 dt 8.925170 rms 0.445 0.138% neg 0 invalid 762 tFOTS 12.0880 tGradient 2.2370 tsec 19.9510 #FOTS# QuadFit found better minimum quadopt=(dt=14.4314,rms=0.444315) vs oldopt=(dt=11.52,rms=0.444342) iter 0, gcam->neg = 48 after 5 iterations, nbhd size=0, neg = 0 #GCMRL# 522 dt 14.431373 rms 0.444 0.000% neg 0 invalid 762 tFOTS 12.1260 tGradient 2.2470 tsec 19.0020 iter 0, gcam->neg = 148 after 7 iterations, nbhd size=0, neg = 0 #GCMRL# 523 dt 14.431373 rms 0.444 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2390 tsec 7.8420 iter 0, gcam->neg = 233 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 524 dt 14.431373 rms 0.443 0.258% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2490 tsec 12.6240 iter 0, gcam->neg = 247 after 29 iterations, nbhd size=2, neg = 0 #GCMRL# 525 dt 14.431373 rms 0.443 -0.202% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.2280 tsec 20.1930 #FOTS# QuadFit found better minimum quadopt=(dt=16.128,rms=0.442149) vs oldopt=(dt=11.52,rms=0.442225) iter 0, gcam->neg = 62 after 21 iterations, nbhd size=1, neg = 0 #GCMRL# 526 dt 16.128000 rms 0.443 0.012% neg 0 invalid 762 tFOTS 11.9240 tGradient 2.2420 tsec 26.8830 #FOTS# QuadFit found better minimum quadopt=(dt=13.2923,rms=0.441953) vs oldopt=(dt=11.52,rms=0.441965) iter 0, gcam->neg = 113 after 29 iterations, nbhd size=2, neg = 0 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.449688 #GCMRL# 528 dt 0.000050 rms 0.450 0.000% neg 0 invalid 762 tFOTS 15.2760 tGradient 2.1250 tsec 18.1800 #GCAMreg# pass 0 level1 1 level2 1 tsec 37.705 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.449688 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.437767 #FOTS# QuadFit found better minimum quadopt=(dt=1.6864,rms=0.414799) vs oldopt=(dt=1.28,rms=0.416365) iter 0, gcam->neg = 1303 after 16 iterations, nbhd size=1, neg = 0 #GCMRL# 531 dt 1.686396 rms 0.423 3.364% neg 0 invalid 762 tFOTS 12.1810 tGradient 1.3450 tsec 24.0030 #FOTS# QuadFit found better minimum quadopt=(dt=2.54313e-05,rms=0.423042) vs oldopt=(dt=1.25e-05,rms=0.423042) #GCMRL# 532 dt 0.000025 rms 0.423 0.000% neg 0 invalid 762 tFOTS 15.3700 tGradient 1.4500 tsec 17.6370 #GCAMreg# pass 0 level1 0 level2 1 tsec 48.908 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.423042 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.422676) vs oldopt=(dt=0.08,rms=0.422696) #GCMRL# 534 dt 0.112000 rms 0.423 0.086% neg 0 invalid 762 tFOTS 12.1940 tGradient 1.3460 tsec 14.3280 #FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.422665) vs oldopt=(dt=0.02,rms=0.422665) #GCMRL# 535 dt 0.024000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 12.0350 tGradient 1.3460 tsec 14.1890 GCAMregister done in 11.8002 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4587 tmin = 11.4245 Calls to gcamLabelEnergy 3956 tmin = 2.22963 Calls to gcamJacobianEnergy 4587 tmin = 9.97858 Calls to gcamSmoothnessEnergy 4587 tmin = 11.4658 Calls to gcamLogLikelihoodTerm 537 tmin = 2.33715 Calls to gcamLabelTerm 490 tmin = 8.20628 Calls to gcamJacobianTerm 537 tmin = 5.87027 Calls to gcamSmoothnessTerm 537 tmin = 1.76335 Calls to gcamComputeGradient 537 tmin = 31.757 Calls to gcamComputeMetricProperties 6905 tmin = 9.00728 mri_ca_register took 1 hours, 39 minutes and 7 seconds. #VMPC# mri_ca_register VmPeak 2361904 FSRUNTIME@ mri_ca_register 1.6521 hours 4 threads @#@FSTIME 2021:10:15:12:24:52 mri_ca_register N 9 e 5947.57 S 24.85 U 17029.50 P 286% M 1324956 F 0 R 16897660 W 0 c 43890 w 47129 I 0 O 63128 L 50.59 51.91 51.77 @#@FSLOADPOST 2021:10:15:14:03:59 mri_ca_register N 9 50.66 50.96 51.04 #-------------------------------------- #@# SubCort Seg Fri Oct 15 14:03:59 EDT 2021 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname cn0853 machine x86_64 setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 == Number of threads available to for OpenMP = 4 == reading 1 input volumes reading classifier array from /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.09 Atlas used for the 3D morph was /usr/local/apps/freesurfer/7.1.1/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.13371 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.29 x + 0.0 (1408 voxels, overlap=0.218) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1408 voxels, peak = 6), gca=8.0 gca peak = 0.20380 (13) mri peak = 0.12121 (10) Right_Lateral_Ventricle (43): linear fit = 0.46 x + 0.0 (1084 voxels, overlap=0.607) Right_Lateral_Ventricle (43): linear fit = 0.46 x + 0.0 (1084 voxels, peak = 6), gca=5.9 gca peak = 0.26283 (96) mri peak = 0.09101 (92) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (438 voxels, overlap=0.823) Right_Pallidum (52): linear fit = 0.96 x + 0.0 (438 voxels, peak = 93), gca=92.6 gca peak = 0.15814 (97) mri peak = 0.08000 (95) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (506 voxels, overlap=0.895) Left_Pallidum (13): linear fit = 0.96 x + 0.0 (506 voxels, peak = 94), gca=93.6 gca peak = 0.27624 (56) mri peak = 0.28315 (50) Right_Hippocampus: unreasonable value (49.6/50.0), not in range [50, 90] - rejecting gca peak = 0.28723 (59) mri peak = 0.25009 (50) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (612 voxels, overlap=0.476) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (612 voxels, peak = 52), gca=51.6 gca peak = 0.07623 (103) mri peak = 0.07028 (104) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (40498 voxels, overlap=0.840) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (40498 voxels, peak = 105), gca=104.5 gca peak = 0.07837 (105) mri peak = 0.06829 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41511 voxels, overlap=0.844) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41511 voxels, peak = 106), gca=105.5 gca peak = 0.10165 (58) mri peak = 0.06197 (45) Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (15893 voxels, overlap=0.273) Left_Cerebral_Cortex (3): linear fit = 0.77 x + 0.0 (15893 voxels, peak = 45), gca=44.9 gca peak = 0.11113 (58) mri peak = 0.06098 (46) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15338 voxels, overlap=0.253) Right_Cerebral_Cortex (42): linear fit = 0.80 x + 0.0 (15338 voxels, peak = 46), gca=46.1 gca peak = 0.27796 (67) mri peak = 0.07330 (62) Right_Caudate (50): linear fit = 0.83 x + 0.0 (876 voxels, overlap=0.124) Right_Caudate (50): linear fit = 0.83 x + 0.0 (876 voxels, peak = 56), gca=55.9 gca peak = 0.14473 (69) mri peak = 0.08817 (55) Left_Caudate: unreasonable value (49.3/55.0), not in range [50, 100] - rejecting gca peak = 0.14301 (56) mri peak = 0.05479 (45) Left_Cerebellum_Cortex (8): linear fit = 0.82 x + 0.0 (6946 voxels, overlap=0.496) Left_Cerebellum_Cortex (8): linear fit = 0.82 x + 0.0 (6946 voxels, peak = 46), gca=46.2 gca peak = 0.14610 (55) mri peak = 0.06149 (44) Right_Cerebellum_Cortex (47): linear fit = 0.81 x + 0.0 (7247 voxels, overlap=0.364) Right_Cerebellum_Cortex (47): linear fit = 0.81 x + 0.0 (7247 voxels, peak = 44), gca=44.3 gca peak = 0.16309 (85) mri peak = 0.06497 (85) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4320 voxels, overlap=0.953) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (4320 voxels, peak = 91), gca=90.5 gca peak = 0.15172 (84) mri peak = 0.06724 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4683 voxels, overlap=0.827) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (4683 voxels, peak = 89), gca=89.5 gca peak = 0.30461 (58) mri peak = 0.13831 (55) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (417 voxels, overlap=0.725) Left_Amygdala (18): linear fit = 0.94 x + 0.0 (417 voxels, peak = 55), gca=54.8 gca peak = 0.32293 (57) mri peak = 0.16667 (50) Right_Amygdala: unreasonable value (49.9/50.0), not in range [50, 90] - rejecting gca peak = 0.11083 (90) mri peak = 0.07198 (77) Left_Thalamus (10): linear fit = 0.95 x + 0.0 (3338 voxels, overlap=0.806) Left_Thalamus (10): linear fit = 0.95 x + 0.0 (3338 voxels, peak = 86), gca=85.9 gca peak = 0.11393 (83) mri peak = 0.07552 (79) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (3171 voxels, overlap=0.960) Right_Thalamus (49): linear fit = 0.99 x + 0.0 (3171 voxels, peak = 82), gca=81.8 gca peak = 0.08575 (81) mri peak = 0.05663 (62) Left_Putamen (12): linear fit = 0.87 x + 0.0 (1723 voxels, overlap=0.656) Left_Putamen (12): linear fit = 0.87 x + 0.0 (1723 voxels, peak = 70), gca=70.1 gca peak = 0.08618 (78) mri peak = 0.06295 (72) Right_Putamen (51): linear fit = 0.86 x + 0.0 (2050 voxels, overlap=0.453) Right_Putamen (51): linear fit = 0.86 x + 0.0 (2050 voxels, peak = 67), gca=66.7 gca peak = 0.08005 (78) mri peak = 0.12995 (80) Brain_Stem (16): linear fit = 1.05 x + 0.0 (7238 voxels, overlap=0.491) Brain_Stem (16): linear fit = 1.05 x + 0.0 (7238 voxels, peak = 82), gca=82.3 gca peak = 0.12854 (88) mri peak = 0.06318 (87) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (685 voxels, overlap=0.792) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (685 voxels, peak = 95), gca=95.5 gca peak = 0.15703 (87) mri peak = 0.05970 (82) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (774 voxels, overlap=0.926) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (774 voxels, peak = 93), gca=92.7 gca peak = 0.17522 (25) mri peak = 0.10046 (12) Third_Ventricle (14): linear fit = 0.28 x + 0.0 (219 voxels, overlap=0.212) Third_Ventricle (14): linear fit = 0.28 x + 0.0 (219 voxels, peak = 7), gca=7.1 gca peak = 0.17113 (14) mri peak = 0.10506 (13) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (498 voxels, overlap=0.789) Fourth_Ventricle (15): linear fit = 0.77 x + 0.0 (498 voxels, peak = 11), gca=10.8 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Left_Caudate = 0.14473 (69) gca peak Third_Ventricle = 0.17522 (25) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Hippocampus = 0.27624 (56) gca peak Right_Amygdala = 0.32293 (57) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 0.88 x + 0: 52 setting label Left_Caudate based on Right_Caudate = 0.83 x + 0: 56 setting label Right_Amygdala based on Left_Amygdala = 0.94 x + 0: 55 estimating mean gm scale to be 0.87 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.54 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31708 ( 7) mri peak = 0.13371 ( 7) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1408 voxels, overlap=0.995) Left_Lateral_Ventricle (4): linear fit = 0.81 x + 0.0 (1408 voxels, peak = 6), gca=5.6 gca peak = 0.36474 ( 6) mri peak = 0.12121 (10) Right_Lateral_Ventricle (43): linear fit = 1.45 x + 0.0 (1084 voxels, overlap=0.994) Right_Lateral_Ventricle (43): linear fit = 1.45 x + 0.0 (1084 voxels, peak = 9), gca=8.7 gca peak = 0.24618 (91) mri peak = 0.09101 (92) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (438 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (438 voxels, peak = 90), gca=89.6 gca peak = 0.17988 (93) mri peak = 0.08000 (95) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (506 voxels, overlap=0.831) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (506 voxels, peak = 94), gca=94.4 gca peak = 0.30899 (49) mri peak = 0.28315 (50) Right_Hippocampus: unreasonable value (49.0/50.0), not in range [50, 90] - rejecting gca peak = 0.32231 (52) mri peak = 0.25009 (50) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (612 voxels, overlap=0.986) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (612 voxels, peak = 52), gca=52.0 gca peak = 0.07890 (105) mri peak = 0.07028 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40498 voxels, overlap=0.885) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40498 voxels, peak = 105), gca=105.0 gca peak = 0.07990 (105) mri peak = 0.06829 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41511 voxels, overlap=0.864) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (41511 voxels, peak = 105), gca=105.0 gca peak = 0.12823 (45) mri peak = 0.06197 (45) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15893 voxels, overlap=0.982) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (15893 voxels, peak = 45), gca=45.0 gca peak = 0.14125 (46) mri peak = 0.06098 (46) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (15338 voxels, overlap=0.979) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (15338 voxels, peak = 45), gca=44.9 gca peak = 0.30677 (56) mri peak = 0.07330 (62) Right_Caudate (50): linear fit = 1.04 x + 0.0 (876 voxels, overlap=1.006) Right_Caudate (50): linear fit = 1.04 x + 0.0 (876 voxels, peak = 59), gca=58.5 gca peak = 0.13958 (65) mri peak = 0.08817 (55) Left_Caudate (11): linear fit = 0.86 x + 0.0 (855 voxels, overlap=0.747) Left_Caudate (11): linear fit = 0.86 x + 0.0 (855 voxels, peak = 56), gca=55.6 gca peak = 0.17085 (46) mri peak = 0.05479 (45) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (6946 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (6946 voxels, peak = 45), gca=45.3 gca peak = 0.16730 (44) mri peak = 0.06149 (44) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (7247 voxels, overlap=0.999) Right_Cerebellum_Cortex (47): linear fit = 1.03 x + 0.0 (7247 voxels, peak = 46), gca=45.5 gca peak = 0.15236 (90) mri peak = 0.06497 (85) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (4320 voxels, overlap=0.995) Left_Cerebellum_White_Matter (7): linear fit = 0.98 x + 0.0 (4320 voxels, peak = 88), gca=87.8 gca peak = 0.16978 (90) mri peak = 0.06724 (88) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4683 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (4683 voxels, peak = 89), gca=88.7 gca peak = 0.31004 (54) mri peak = 0.13831 (55) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (417 voxels, overlap=1.007) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (417 voxels, peak = 54), gca=54.0 gca peak = 0.28137 (53) mri peak = 0.16667 (50) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (502 voxels, overlap=1.007) Right_Amygdala (54): linear fit = 0.94 x + 0.0 (502 voxels, peak = 50), gca=50.1 gca peak = 0.12130 (86) mri peak = 0.07198 (77) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3338 voxels, overlap=0.965) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (3338 voxels, peak = 86), gca=85.6 gca peak = 0.10182 (82) mri peak = 0.07552 (79) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3171 voxels, overlap=0.934) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (3171 voxels, peak = 83), gca=83.2 gca peak = 0.09053 (70) mri peak = 0.05663 (62) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1723 voxels, overlap=0.984) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1723 voxels, peak = 72), gca=72.4 gca peak = 0.10622 (66) mri peak = 0.06295 (72) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2050 voxels, overlap=0.985) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2050 voxels, peak = 68), gca=67.7 gca peak = 0.08505 (83) mri peak = 0.12995 (80) Brain_Stem (16): linear fit = 1.00 x + 0.0 (7238 voxels, overlap=0.677) Brain_Stem (16): linear fit = 1.00 x + 0.0 (7238 voxels, peak = 83), gca=82.6 gca peak = 0.11702 (97) mri peak = 0.06318 (87) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (685 voxels, overlap=0.896) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (685 voxels, peak = 95), gca=94.6 gca peak = 0.14018 (91) mri peak = 0.05970 (82) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (774 voxels, overlap=0.975) Left_VentralDC (28): linear fit = 0.94 x + 0.0 (774 voxels, peak = 86), gca=86.0 gca peak = 0.29286 (14) mri peak = 0.10046 (12) Third_Ventricle (14): linear fit = 1.18 x + 0.0 (219 voxels, overlap=1.023) Third_Ventricle (14): linear fit = 1.18 x + 0.0 (219 voxels, peak = 17), gca=16.6 gca peak = 0.23722 (11) mri peak = 0.10506 (13) Fourth_Ventricle (15): linear fit = 1.13 x + 0.0 (498 voxels, overlap=0.918) Fourth_Ventricle (15): linear fit = 1.13 x + 0.0 (498 voxels, peak = 12), gca=12.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.20983 (24) gca peak CSF = 0.28082 (20) gca peak Left_Accumbens_area = 0.92288 (52) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.78302 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.26623 (20) gca peak Right_Hippocampus = 0.30899 (49) gca peak Right_Accumbens_area = 0.41967 (54) gca peak Right_vessel = 0.64601 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60952 (18) gca peak WM_hypointensities = 0.10805 (77) gca peak non_WM_hypointensities = 0.14618 (41) gca peak Optic_Chiasm = 0.51840 (76) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.00 x + 0: 52 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.14 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 81214 voxels changed in iteration 0 of unlikely voxel relabeling 143 voxels changed in iteration 1 of unlikely voxel relabeling 1 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 26674 gm and wm labels changed (%28 to gray, %72 to white out of all changed labels) 286 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 90417 changed. image ll: -2.181, PF=0.500 pass 2: 28162 changed. image ll: -2.181, PF=0.500 pass 3: 9795 changed. pass 4: 3838 changed. 48834 voxels changed in iteration 0 of unlikely voxel relabeling 186 voxels changed in iteration 1 of unlikely voxel relabeling 7 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6294 voxels changed in iteration 0 of unlikely voxel relabeling 121 voxels changed in iteration 1 of unlikely voxel relabeling 3 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5434 voxels changed in iteration 0 of unlikely voxel relabeling 31 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 4949 voxels changed in iteration 0 of unlikely voxel relabeling 17 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 237 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 8173 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 183 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 5 with volume 220 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 6801 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 718 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 4601.488166 mri_ca_label stimesec 14.631478 mri_ca_label ru_maxrss 2205976 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 10638863 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 272 mri_ca_label ru_oublock 800 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 323 mri_ca_label ru_nivcsw 3076 auto-labeling took 74 minutes and 24 seconds. @#@FSTIME 2021:10:15:14:03:59 mri_ca_label N 10 e 4463.91 S 14.91 U 4601.48 P 103% M 2205976 F 0 R 10638893 W 0 c 3076 w 324 I 272 O 800 L 50.66 50.96 51.04 @#@FSLOADPOST 2021:10:15:15:18:23 mri_ca_label N 10 49.79 49.59 49.62 #-------------------------------------- #@# CC Seg Fri Oct 15 15:18:23 EDT 2021 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms/cc_up.lta sub-005 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /lscratch/25105636/sub-005_ses-01/sub-005/mri/transforms/cc_up.lta reading aseg from /lscratch/25105636/sub-005_ses-01/sub-005/mri/aseg.auto_noCCseg.mgz reading norm from /lscratch/25105636/sub-005_ses-01/sub-005/mri/norm.mgz 43974 voxels in left wm, 47101 in right wm, xrange [125, 135] searching rotation angles z=[-6 8], y=[-4 10] searching scale 1 Z rot -6.3 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.7 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.7 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.7 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.7 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.7 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.7 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.7 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.4 global minimum found at slice 130.6, rotations (2.67, 0.66) final transformation (x=130.6, yr=2.673, zr=0.655): 0.99885 -0.01143 0.04664 -6.49857; 0.01142 0.99993 0.00053 15.45510; -0.04664 0.00000 0.99891 19.21468; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 132] in xformed coordinates best xformed slice 128 min_x_fornix = 153 min_x_fornix = 154 min_x_fornix = 156 min_x_fornix = 154 min_x_fornix = 155 cc center is found at 128 111 115 eigenvectors: 0.00041 0.00422 0.99999; -0.02796 -0.99960 0.00423; 0.99961 -0.02796 -0.00030; writing aseg with callosum to /lscratch/25105636/sub-005_ses-01/sub-005/mri/aseg.auto.mgz... corpus callosum segmentation took 1.2 minutes #VMPC# mri_cc VmPeak 560316 mri_cc done @#@FSTIME 2021:10:15:15:18:23 mri_cc N 7 e 69.93 S 0.63 U 70.97 P 102% M 340168 F 0 R 319132 W 0 c 74 w 36 I 0 O 784 L 49.79 49.59 49.62 @#@FSLOADPOST 2021:10:15:15:19:33 mri_cc N 7 49.99 49.69 49.65 #-------------------------------------- #@# Merge ASeg Fri Oct 15 15:19:33 EDT 2021 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Oct 15 15:19:33 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... MRImask(): AllowDiffGeom = 1 Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 4393 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 104 gm peak at 46 (46), valley at 20 (20) csf peak at 23, setting threshold to 38 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 48 (48), valley at 20 (20) csf peak at 24, setting threshold to 40 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 19 seconds. @#@FSTIME 2021:10:15:15:19:33 mri_normalize N 9 e 200.98 S 2.64 U 231.31 P 116% M 1199880 F 0 R 1095549 W 0 c 287 w 49 I 0 O 3112 L 49.99 49.69 49.65 @#@FSLOADPOST 2021:10:15:15:22:54 mri_normalize N 9 50.07 49.79 49.70 #-------------------------------------------- #@# Mask BFS Fri Oct 15 15:22:54 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1797447 voxels in mask (pct= 10.71) MRImask(): AllowDiffGeom = 1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2021:10:15:15:22:54 mri_mask N 5 e 1.42 S 0.06 U 2.75 P 198% M 70572 F 0 R 17748 W 0 c 12 w 16 I 0 O 3064 L 50.07 49.79 49.70 @#@FSLOADPOST 2021:10:15:15:22:56 mri_mask N 5 50.30 49.85 49.72 #-------------------------------------------- #@# WM Segmentation Fri Oct 15 15:22:56 EDT 2021 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2021:10:15:15:22:56 AntsDenoiseImageFs N 4 e 69.22 S 0.40 U 69.35 P 100% M 347524 F 3 R 222513 W 0 c 95 w 20 I 6584 O 3120 L 50.30 49.85 49.72 @#@FSLOADPOST 2021:10:15:15:24:05 AntsDenoiseImageFs N 4 49.75 49.77 49.70 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 WHITE_MATTER_MEAN 110 wsize 13 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm_low 79 wm_hi 125 gray_low 30 gray_hi 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (105.0): 105.5 +- 4.2 [79.0 --> 125.0] CCS GM (63.0) : 62.7 +- 10.7 [30.0 --> 95.0] white_mean 105.513 white_sigma 4.16691 gray_mean 62.6587 gray_sigma 10.6525 setting bottom of white matter range wm_low to 73.3 setting top of gray matter range gray_hi to 84.0 wm_low 73.3112 wm_hi 125 gray_low 30 gray_hi 83.9637 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 73.3112 wm_hi 125 gray_low 30 gray_hi 83.9637 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 83.9637, wm_low = 73.3112 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=83.9637, wmlow=73.3112 96730 voxels processed (0.58%) 43385 voxels white (0.26%) 53345 voxels non-white (0.32%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=68.3112, gray_hi=83.9637, wsize=13 149439 voxels tested (0.89%) 41218 voxels changed (0.25%) 38869 multi-scale searches (0.23%) Recovering bright white MRIrecoverBrightWhite() wm_low 73.3112 wm_hi 125 slack 4.16691 pct_thresh 0.33 intensity_thresh 129.167 nvox_thresh 8.58 54 voxels tested (0.00%) 45 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=68.3112, hithr=83.9637 smoothing input volume with sigma = 0.250 62559 voxels tested (0.37%) 15143 voxels changed (0.09%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 3818 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 2577 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 7779 filled MRIfindBrightNonWM(): 230 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.7 minutes writing output to wm.seg.mgz... @#@FSTIME 2021:10:15:15:24:05 mri_segment N 5 e 100.87 S 0.56 U 102.48 P 102% M 140664 F 0 R 259021 W 0 c 118 w 27 I 0 O 1072 L 49.75 49.77 49.70 @#@FSLOADPOST 2021:10:15:15:25:46 mri_segment N 5 49.56 49.71 49.68 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.66 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 3313 additional wm voxels added 0 additional wm voxels added SEG EDIT: 62688 voxels turned on, 35826 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2021:10:15:15:25:46 mri_edit_wm_with_aseg N 5 e 39.86 S 0.61 U 43.26 P 110% M 473268 F 0 R 330643 W 0 c 80 w 55 I 0 O 1008 L 49.56 49.71 49.68 @#@FSLOADPOST 2021:10:15:15:26:26 mri_edit_wm_with_aseg N 5 49.77 49.75 49.69 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 22 found - 22 modified | TOTAL: 22 pass 2 (xy+): 0 found - 22 modified | TOTAL: 22 pass 1 (xy-): 30 found - 30 modified | TOTAL: 52 pass 2 (xy-): 0 found - 30 modified | TOTAL: 52 pass 1 (yz+): 43 found - 43 modified | TOTAL: 95 pass 2 (yz+): 0 found - 43 modified | TOTAL: 95 pass 1 (yz-): 26 found - 26 modified | TOTAL: 121 pass 2 (yz-): 0 found - 26 modified | TOTAL: 121 pass 1 (xz+): 39 found - 39 modified | TOTAL: 160 pass 2 (xz+): 0 found - 39 modified | TOTAL: 160 pass 1 (xz-): 34 found - 34 modified | TOTAL: 194 pass 2 (xz-): 0 found - 34 modified | TOTAL: 194 Iteration Number : 1 pass 1 (+++): 28 found - 28 modified | TOTAL: 28 pass 2 (+++): 0 found - 28 modified | TOTAL: 28 pass 1 (+++): 8 found - 8 modified | TOTAL: 36 pass 2 (+++): 0 found - 8 modified | TOTAL: 36 pass 1 (+++): 10 found - 10 modified | TOTAL: 46 pass 2 (+++): 0 found - 10 modified | TOTAL: 46 pass 1 (+++): 21 found - 21 modified | TOTAL: 67 pass 2 (+++): 0 found - 21 modified | TOTAL: 67 Iteration Number : 1 pass 1 (++): 211 found - 211 modified | TOTAL: 211 pass 2 (++): 0 found - 211 modified | TOTAL: 211 pass 1 (+-): 139 found - 139 modified | TOTAL: 350 pass 2 (+-): 0 found - 139 modified | TOTAL: 350 pass 1 (--): 174 found - 174 modified | TOTAL: 524 pass 2 (--): 1 found - 175 modified | TOTAL: 525 pass 3 (--): 0 found - 175 modified | TOTAL: 525 pass 1 (-+): 137 found - 137 modified | TOTAL: 662 pass 2 (-+): 0 found - 137 modified | TOTAL: 662 Iteration Number : 2 pass 1 (xy+): 10 found - 10 modified | TOTAL: 10 pass 2 (xy+): 0 found - 10 modified | TOTAL: 10 pass 1 (xy-): 7 found - 7 modified | TOTAL: 17 pass 2 (xy-): 0 found - 7 modified | TOTAL: 17 pass 1 (yz+): 7 found - 7 modified | TOTAL: 24 pass 2 (yz+): 0 found - 7 modified | TOTAL: 24 pass 1 (yz-): 7 found - 7 modified | TOTAL: 31 pass 2 (yz-): 0 found - 7 modified | TOTAL: 31 pass 1 (xz+): 6 found - 6 modified | TOTAL: 37 pass 2 (xz+): 0 found - 6 modified | TOTAL: 37 pass 1 (xz-): 8 found - 8 modified | TOTAL: 45 pass 2 (xz-): 0 found - 8 modified | TOTAL: 45 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 4 found - 4 modified | TOTAL: 8 pass 2 (+-): 0 found - 4 modified | TOTAL: 8 pass 1 (--): 2 found - 2 modified | TOTAL: 10 pass 2 (--): 0 found - 2 modified | TOTAL: 10 pass 1 (-+): 0 found - 0 modified | TOTAL: 10 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 2 found - 2 modified | TOTAL: 2 pass 2 (yz+): 0 found - 2 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 1 found - 1 modified | TOTAL: 3 pass 2 (xz+): 0 found - 1 modified | TOTAL: 3 pass 1 (xz-): 1 found - 1 modified | TOTAL: 4 pass 2 (xz-): 0 found - 1 modified | TOTAL: 4 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 Iteration Number : 3 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 1 found - 1 modified | TOTAL: 3 pass 2 (xz-): 0 found - 1 modified | TOTAL: 3 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 5 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 993 (out of 611512: 0.162384) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2021:10:15:15:26:26 mri_pretess N 4 e 5.03 S 0.04 U 6.35 P 127% M 53400 F 3 R 26344 W 0 c 74 w 17 I 5768 O 1008 L 49.77 49.75 49.69 @#@FSLOADPOST 2021:10:15:15:26:31 mri_pretess N 4 49.79 49.75 49.69 #-------------------------------------------- #@# Fill Fri Oct 15 15:26:31 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.00357 0.02167 0.07401 -17.95227; -0.03041 1.13556 0.19166 -42.62076; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.00357 0.02167 0.07401 -17.95227; -0.03041 1.13556 0.19166 -42.62076; -0.08261 -0.18066 0.95315 9.52473; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 969 (min = 350, max = 1400), aspect = 0.41 (min = 0.10, max = 0.75) no need to search using seed (126, 123, 149), TAL = (2.0, 21.0, 5.0) talairach voxel to voxel transform 0.98971 -0.03015 -0.07079 17.15690; 0.01165 0.85297 -0.17242 38.20576; 0.08798 0.15906 1.01033 -1.26434; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 123, 149) --> (2.0, 21.0, 5.0) done. writing output to filled.mgz... filling took 1.9 minutes talairach cc position changed to (2.00, 21.00, 5.00) Erasing brainstem...done. MRImask(): AllowDiffGeom = 1 seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 21.00, 5.00) SRC: (109.79, 118.69, 178.34) search lh wm seed point around talairach space (-16.00, 21.00, 5.00), SRC: (145.42, 119.11, 181.51) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... @#@FSTIME 2021:10:15:15:26:31 mri_fill N 8 e 117.07 S 2.20 U 115.99 P 100% M 998472 F 0 R 913501 W 0 c 171 w 23 I 0 O 304 L 49.79 49.75 49.69 @#@FSLOADPOST 2021:10:15:15:28:28 mri_fill N 8 49.22 49.60 49.65 #-------------------------------------------- #@# Tessellate lh Fri Oct 15 15:28:28 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 9 found - 9 modified | TOTAL: 11 pass 2 (yz+): 0 found - 9 modified | TOTAL: 11 pass 1 (yz-): 13 found - 13 modified | TOTAL: 24 pass 2 (yz-): 0 found - 13 modified | TOTAL: 24 pass 1 (xz+): 1 found - 1 modified | TOTAL: 25 pass 2 (xz+): 0 found - 1 modified | TOTAL: 25 pass 1 (xz-): 2 found - 2 modified | TOTAL: 27 pass 2 (xz-): 0 found - 2 modified | TOTAL: 27 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 31 (out of 297269: 0.010428) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2021:10:15:15:28:28 mri_pretess N 4 e 2.45 S 0.05 U 3.80 P 156% M 36800 F 0 R 13674 W 0 c 37 w 16 I 0 O 296 L 49.22 49.60 49.65 @#@FSLOADPOST 2021:10:15:15:28:31 mri_pretess N 4 49.29 49.60 49.65 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 7.1.1 7.1.1 slice 60: 2646 vertices, 2795 faces slice 70: 9484 vertices, 9781 faces slice 80: 18807 vertices, 19180 faces slice 90: 30322 vertices, 30724 faces slice 100: 42057 vertices, 42480 faces slice 110: 53683 vertices, 54070 faces slice 120: 65065 vertices, 65452 faces slice 130: 77344 vertices, 77775 faces slice 140: 88921 vertices, 89318 faces slice 150: 100181 vertices, 100585 faces slice 160: 111244 vertices, 111639 faces slice 170: 121443 vertices, 121810 faces slice 180: 130308 vertices, 130647 faces slice 190: 138782 vertices, 139053 faces slice 200: 145871 vertices, 146117 faces slice 210: 152555 vertices, 152776 faces slice 220: 157635 vertices, 157825 faces slice 230: 160218 vertices, 160236 faces slice 240: 160218 vertices, 160236 faces slice 250: 160218 vertices, 160236 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2021:10:15:15:28:31 mri_tessellate N 3 e 1.81 S 0.03 U 2.47 P 138% M 35760 F 0 R 9240 W 0 c 14 w 7 I 0 O 7520 L 49.29 49.60 49.65 @#@FSLOADPOST 2021:10:15:15:28:32 mri_tessellate N 3 49.29 49.60 49.65 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 160218 voxel in cpt #1: X=-18 [v=160218,e=480708,f=320472] located at (-30.919024, 5.740803, 11.010292) For the whole surface: X=-18 [v=160218,e=480708,f=320472] One single component has been found nothing to do done @#@FSTIME 2021:10:15:15:28:32 mris_extract_main_component N 2 e 1.37 S 0.28 U 1.67 P 142% M 314320 F 4 R 88946 W 0 c 73 w 299 I 6168 O 11272 L 49.29 49.60 49.65 @#@FSLOADPOST 2021:10:15:15:28:34 mris_extract_main_component N 2 49.29 49.60 49.65 #-------------------------------------------- #@# Tessellate rh Fri Oct 15 15:28:34 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 1 found - 1 modified | TOTAL: 2 pass 2 (xy-): 0 found - 1 modified | TOTAL: 2 pass 1 (yz+): 8 found - 8 modified | TOTAL: 10 pass 2 (yz+): 0 found - 8 modified | TOTAL: 10 pass 1 (yz-): 7 found - 7 modified | TOTAL: 17 pass 2 (yz-): 0 found - 7 modified | TOTAL: 17 pass 1 (xz+): 2 found - 2 modified | TOTAL: 19 pass 2 (xz+): 0 found - 2 modified | TOTAL: 19 pass 1 (xz-): 1 found - 1 modified | TOTAL: 20 pass 2 (xz-): 0 found - 1 modified | TOTAL: 20 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 5 pass 2 (+++): 0 found - 4 modified | TOTAL: 5 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 28 (out of 295644: 0.009471) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2021:10:15:15:28:34 mri_pretess N 4 e 2.46 S 0.05 U 3.80 P 156% M 36804 F 0 R 13674 W 0 c 29 w 12 I 0 O 296 L 49.29 49.60 49.65 @#@FSLOADPOST 2021:10:15:15:28:36 mri_pretess N 4 49.34 49.61 49.65 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 7.1.1 7.1.1 slice 50: 42 vertices, 58 faces slice 60: 2699 vertices, 2862 faces slice 70: 9436 vertices, 9700 faces slice 80: 19636 vertices, 20039 faces slice 90: 31750 vertices, 32163 faces slice 100: 43942 vertices, 44381 faces slice 110: 56221 vertices, 56622 faces slice 120: 67846 vertices, 68286 faces slice 130: 79358 vertices, 79775 faces slice 140: 91216 vertices, 91599 faces slice 150: 102084 vertices, 102487 faces slice 160: 113245 vertices, 113657 faces slice 170: 122657 vertices, 122972 faces slice 180: 131530 vertices, 131882 faces slice 190: 139492 vertices, 139758 faces slice 200: 146600 vertices, 146857 faces slice 210: 153037 vertices, 153274 faces slice 220: 157681 vertices, 157836 faces slice 230: 159880 vertices, 159902 faces slice 240: 159880 vertices, 159902 faces slice 250: 159880 vertices, 159902 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; @#@FSTIME 2021:10:15:15:28:36 mri_tessellate N 3 e 1.80 S 0.03 U 2.46 P 138% M 35748 F 0 R 9235 W 0 c 10 w 7 I 0 O 7504 L 49.34 49.61 49.65 @#@FSLOADPOST 2021:10:15:15:28:38 mri_tessellate N 3 49.34 49.61 49.65 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 159880 voxel in cpt #1: X=-22 [v=159880,e=479706,f=319804] located at (26.823536, 4.154222, 10.966531) For the whole surface: X=-22 [v=159880,e=479706,f=319804] One single component has been found nothing to do done @#@FSTIME 2021:10:15:15:28:38 mris_extract_main_component N 2 e 1.44 S 0.28 U 1.75 P 140% M 313296 F 0 R 88664 W 0 c 13 w 317 I 0 O 11248 L 49.34 49.61 49.65 @#@FSLOADPOST 2021:10:15:15:28:40 mris_extract_main_component N 2 49.34 49.61 49.65 #-------------------------------------------- #@# Smooth1 lh Fri Oct 15 15:28:40 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Smooth1 rh Fri Oct 15 15:28:40 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix Waiting for PID 40147 of (40147 40150) to complete... Waiting for PID 40150 of (40147 40150) to complete... PIDs (40147 40150) completed and logs appended. #-------------------------------------------- #@# Inflation1 lh Fri Oct 15 15:28:46 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# Inflation1 rh Fri Oct 15 15:28:46 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Waiting for PID 40218 of (40218 40222) to complete... Waiting for PID 40222 of (40218 40222) to complete... PIDs (40218 40222) completed and logs appended. #-------------------------------------------- #@# QSphere lh Fri Oct 15 15:29:39 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# QSphere rh Fri Oct 15 15:29:39 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix Waiting for PID 40380 of (40380 40383) to complete... Waiting for PID 40383 of (40380 40383) to complete... PIDs (40380 40383) completed and logs appended. #@# Fix Topology lh Fri Oct 15 15:37:16 EDT 2021 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-005 lh #@# Fix Topology rh Fri Oct 15 15:37:16 EDT 2021 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-005 rh Waiting for PID 41068 of (41068 41071) to complete... Waiting for PID 41071 of (41068 41071) to complete... PIDs (41068 41071) completed and logs appended. mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 159263 - 477783 + 318522 = 2 --> 0 holes F =2V-4: 318522 = 318526-4 (0) 2E=3F: 955566 = 955566 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 158546 - 475632 + 317088 = 2 --> 0 holes F =2V-4: 317088 = 317092-4 (0) 2E=3F: 951264 = 951264 (0) total defect index = 0 Fri Oct 15 15:53:55 EDT 2021 setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 cd /lscratch/25105636/sub-005_ses-01/sub-005/scripts /usr/local/apps/freesurfer/7.1.1/bin/defect2seg --s sub-005 freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 defect2seg 7.1.1 Linux cn0853 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux pid 42664 mri_label2vol --defects /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig.nofix /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.defect_labels /lscratch/25105636/sub-005_ses-01/sub-005/mri/orig.mgz 1000 0 /lscratch/25105636/sub-005_ses-01/sub-005/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /lscratch/25105636/sub-005_ses-01/sub-005/mri/surface.defects.mgz mris_defects_pointset -s /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig.nofix -d /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.defect_labels -o /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.defects.pointset Reading in surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig.nofix Reading in defect segmentation /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.defect_labels #VMPC# mris_defects_pointset 436708 mris_defects_pointset done mri_label2vol --defects /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig.nofix /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.defect_labels /lscratch/25105636/sub-005_ses-01/sub-005/mri/surface.defects.mgz 2000 1 /lscratch/25105636/sub-005_ses-01/sub-005/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 Writing to /lscratch/25105636/sub-005_ses-01/sub-005/mri/surface.defects.mgz mris_defects_pointset -s /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig.nofix -d /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.defect_labels -o /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.defects.pointset Reading in surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig.nofix Reading in defect segmentation /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.defect_labels #VMPC# mris_defects_pointset 567420 mris_defects_pointset done Started at Fri Oct 15 15:53:55 EDT 2021 Ended at Fri Oct 15 15:54:02 EDT 2021 Defect2seg-Run-Time-Sec 7 Defect2seg-Run-Time-Min 0.14 Defect2seg-Run-Time-Hours 0.00 tkmeditfv sub-005 brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2021:10:15:15:53:55 defect2seg N 2 e 7.04 S 1.03 U 10.03 P 156% M 267988 F 4 R 384245 W 0 c 157 w 1447 I 6328 O 400 L 54.39 56.12 54.83 @#@FSLOADPOST 2021:10:15:15:54:02 defect2seg N 2 53.71 55.91 54.78 mris_remesh --remesh --iters 3 --input /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig.premesh --output /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.708419 remeshing to edge length 0.708419 with 3 iterations avg qual before : 0.889059 after: 0.971281 Removing intersections Remeshed surface quality stats nv0 = 159263 nv = 165936 1.0419 Area 331868 0.30063 0.03348 0.067988 0.4826 Corner 995604 60.00000 8.78781 15.616084 146.8807 Edge 497802 0.84114 0.08202 0.442175 1.3133 Hinge 497802 9.42023 10.14008 0.000018 124.2146 mris_remesh done @#@FSTIME 2021:10:15:15:54:02 mris_remesh N 7 e 53.42 S 1.59 U 56.08 P 107% M 910128 F 4 R 824226 W 0 c 164 w 3274 I 6584 O 11672 L 53.71 55.91 54.78 @#@FSLOADPOST 2021:10:15:15:54:56 mris_remesh N 7 51.36 54.89 54.50 mris_remesh --remesh --iters 3 --input /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig.premesh --output /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.708751 remeshing to edge length 0.708751 with 3 iterations avg qual before : 0.890703 after: 0.97127 Removing intersections Remeshed surface quality stats nv0 = 158546 nv = 165334 1.04281 Area 330664 0.30112 0.03347 0.079737 0.4514 Corner 991992 60.00000 8.78648 16.310681 146.9473 Edge 495996 0.84183 0.08205 0.440125 1.2356 Hinge 495996 9.47554 10.17828 0.000007 123.2883 mris_remesh done @#@FSTIME 2021:10:15:15:54:56 mris_remesh N 7 e 55.02 S 1.74 U 57.63 P 107% M 908064 F 0 R 884174 W 0 c 110 w 3235 I 0 O 11640 L 51.36 54.89 54.50 @#@FSLOADPOST 2021:10:15:15:55:51 mris_remesh N 7 50.32 53.98 54.21 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2021:10:15:15:55:51 mris_remove_intersection N 2 e 4.64 S 0.46 U 5.05 P 119% M 381256 F 4 R 185954 W 0 c 65 w 307 I 6256 O 11672 L 50.32 53.98 54.21 @#@FSLOADPOST 2021:10:15:15:55:55 mris_remove_intersection N 2 50.13 53.88 54.18 rm ../surf/lh.inflated rm: cannot remove '../surf/lh.inflated': No such file or directory /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2021:10:15:15:55:55 mris_remove_intersection N 2 e 4.61 S 0.41 U 5.08 P 119% M 380508 F 0 R 185490 W 0 c 9 w 241 I 0 O 11632 L 50.13 53.88 54.18 @#@FSLOADPOST 2021:10:15:15:56:00 mris_remove_intersection N 2 50.13 53.88 54.18 rm ../surf/rh.inflated rm: cannot remove '../surf/rh.inflated': No such file or directory #-------------------------------------------- #@# AutoDetGWStats lh Fri Oct 15 15:56:00 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 295670 voxels (1.76%) border gray 333584 voxels (1.99%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 97.6 +- 10.8 [70.0 --> 110.0] CCS GM (57.0) : 58.2 +- 12.7 [30.0 --> 110.0] white_mean = 97.5793 +/- 10.7928, gray_mean = 58.1838 +/- 12.7458 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=204 nbins=205 intensity peaks found at WM=105+-7.8, GM=49+-11.3 white_mode = 105, gray_mode = 49 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 36.3 (was 70.000000) setting MAX_BORDER_WHITE to 115.8 (was 105.000000) setting MIN_BORDER_WHITE to 49.0 (was 85.000000) setting MAX_CSF to 23.5 (was 40.000000) setting MAX_GRAY to 94.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 36.3 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 10.8 (was 40.000000) When placing the white surface white_border_hi = 115.793; white_border_low = 49; white_outside_low = 36.2542; white_inside_hi = 120; white_outside_hi = 115.793; When placing the pial surface pial_border_hi = 36.2542; pial_border_low = 10.7627; pial_outside_low = 10; pial_inside_hi = 94.2072; pial_outside_hi = 29.8813; #VMPC# mris_autodet_gwstats VmPeak 591408 mris_autodet_gwstats done @#@FSTIME 2021:10:15:15:56:00 mris_autodet_gwstats N 8 e 5.41 S 0.35 U 7.64 P 147% M 269964 F 3 R 150663 W 0 c 79 w 349 I 5512 O 8 L 50.13 53.88 54.18 @#@FSLOADPOST 2021:10:15:15:56:06 mris_autodet_gwstats N 8 50.11 53.75 54.13 #-------------------------------------------- #@# AutoDetGWStats rh Fri Oct 15 15:56:06 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 295670 voxels (1.76%) border gray 333584 voxels (1.99%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (99.0): 97.6 +- 10.8 [70.0 --> 110.0] CCS GM (57.0) : 58.2 +- 12.7 [30.0 --> 110.0] white_mean = 97.5793 +/- 10.7928, gray_mean = 58.1838 +/- 12.7458 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=204 nbins=205 intensity peaks found at WM=105+-7.8, GM=49+-10.4 white_mode = 105, gray_mode = 49 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 36.3 (was 70.000000) setting MAX_BORDER_WHITE to 115.8 (was 105.000000) setting MIN_BORDER_WHITE to 49.0 (was 85.000000) setting MAX_CSF to 23.5 (was 40.000000) setting MAX_GRAY to 94.2 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 36.3 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 10.8 (was 40.000000) When placing the white surface white_border_hi = 115.793; white_border_low = 49; white_outside_low = 36.2542; white_inside_hi = 120; white_outside_hi = 115.793; When placing the pial surface pial_border_hi = 36.2542; pial_border_low = 10.7627; pial_outside_low = 10; pial_inside_hi = 94.2072; pial_outside_hi = 29.8813; #VMPC# mris_autodet_gwstats VmPeak 637840 mris_autodet_gwstats done @#@FSTIME 2021:10:15:15:56:06 mris_autodet_gwstats N 8 e 5.40 S 0.36 U 7.60 P 147% M 268700 F 0 R 149629 W 0 c 37 w 328 I 0 O 8 L 50.11 53.75 54.13 @#@FSLOADPOST 2021:10:15:15:56:11 mris_autodet_gwstats N 8 50.02 53.67 54.10 #-------------------------------------------- #@# WhitePreAparc lh Fri Oct 15 15:56:11 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.1.1 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 331868 0.26597 0.06281 0.001993 0.6635 Corner 995604 60.00000 9.60226 7.435342 137.5751 Edge 497802 0.78767 0.11399 0.051115 1.3269 Hinge 497802 6.32806 6.48563 0.000016 137.5328 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 MRIfindBrightNonWM(): 516 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7013, nmarked2=140, nripped=7013 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 82968: xyz = (-54.0468,18.5294,21.6633) oxyz = (-54.0468,18.5294,21.6633) wxzy = (-54.0468,18.5294,21.6633) pxyz = (0,0,0) CBVO Creating mask 165936 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7013 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7013, nmarked2=140, nripped=7013 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=2 had to be increased for 150 vertices, nripped=7013 mean border=67.7, 71 (71) missing vertices, mean dist 0.4 [0.4 (%32.5)->0.7 (%67.5))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2029 min Finding expansion regions mean absolute distance = 0.63 +- 0.71 5683 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn085, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=8951503.0, rms=16.614 001: dt: 0.5000, sse=4760947.5, rms=12.013 (27.695%) 002: dt: 0.5000, sse=2985326.2, rms=9.406 (21.700%) 003: dt: 0.5000, sse=2049418.2, rms=7.681 (18.339%) 004: dt: 0.5000, sse=1606481.8, rms=6.710 (12.640%) 005: dt: 0.5000, sse=1345069.1, rms=6.059 (9.699%) 006: dt: 0.5000, sse=1255707.9, rms=5.820 (3.947%) 007: dt: 0.5000, sse=1178418.4, rms=5.602 (3.753%) rms = 5.5739/5.6016, sse=1169119.9/1178418.4, time step reduction 1 of 3 to 0.250 0 0 1 008: dt: 0.5000, sse=1169119.9, rms=5.574 (0.494%) 009: dt: 0.2500, sse=598454.6, rms=3.602 (35.371%) 010: dt: 0.2500, sse=511538.4, rms=3.201 (11.142%) rms = 3.2656/3.2010, sse=525338.3/511538.4, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 011: dt: 0.1250, sse=430895.2, rms=2.773 (13.357%) 012: dt: 0.1250, sse=323904.3, rms=2.072 (25.287%) 013: dt: 0.1250, sse=303175.2, rms=1.908 (7.941%) rms = 1.8581/1.9076, sse=297481.0/303175.2, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=297481.0, rms=1.858 (2.594%) maximum number of reductions reached, breaking from loop positioning took 2.0 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7013 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7183, nmarked2=143, nripped=7183 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=1 had to be increased for 106 vertices, nripped=7183 mean border=73.0, 102 (37) missing vertices, mean dist -0.2 [0.3 (%80.5)->0.2 (%19.5))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1349 min Finding expansion regions mean absolute distance = 0.28 +- 0.43 4373 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn085, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1813295.1, rms=7.025 015: dt: 0.5000, sse=1170898.5, rms=5.396 (23.189%) rms = 5.7383/5.3962, sse=1290081.2/1170898.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 016: dt: 0.2500, sse=674111.9, rms=3.671 (31.977%) 017: dt: 0.2500, sse=550815.7, rms=3.098 (15.590%) 018: dt: 0.2500, sse=503050.8, rms=2.845 (8.187%) rms = 2.9501/2.8447, sse=522314.2/503050.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 019: dt: 0.1250, sse=436234.5, rms=2.445 (14.042%) 020: dt: 0.1250, sse=348117.7, rms=1.788 (26.860%) 021: dt: 0.1250, sse=329110.1, rms=1.612 (9.854%) 022: dt: 0.1250, sse=322673.1, rms=1.547 (4.026%) rms = 1.5049/1.5473, sse=318678.1/322673.1, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=318678.1, rms=1.505 (2.741%) maximum number of reductions reached, breaking from loop positioning took 1.3 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7183 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7310, nmarked2=143, nripped=7310 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 117 vertices, nripped=7310 mean border=75.9, 112 (24) missing vertices, mean dist -0.1 [0.2 (%71.9)->0.2 (%28.1))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0734 min Finding expansion regions mean absolute distance = 0.19 +- 0.29 3334 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=cn085, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=791980.5, rms=4.167 rms = 5.2973/4.1673, sse=1134632.1/791980.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=489274.7, rms=2.795 (32.923%) 025: dt: 0.2500, sse=368827.4, rms=1.998 (28.531%) rms = 1.9597/1.9978, sse=363610.4/368827.4, time step reduction 2 of 3 to 0.125 0 0 1 026: dt: 0.2500, sse=363610.4, rms=1.960 (1.908%) 027: dt: 0.1250, sse=301192.6, rms=1.366 (30.317%) 028: dt: 0.1250, sse=291574.9, rms=1.247 (8.709%) rms = 1.2297/1.2466, sse=290256.4/291574.9, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=290256.4, rms=1.230 (1.359%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7310 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7343, nmarked2=144, nripped=7343 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 123 vertices, nripped=7343 mean border=76.8, 118 (16) missing vertices, mean dist -0.0 [0.2 (%56.4)->0.2 (%43.6))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0471 min Finding expansion regions mean absolute distance = 0.16 +- 0.25 2844 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=cn085, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=341131.6, rms=1.789 rms = 3.5427/1.7887, sse=643914.6/341131.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=274984.0, rms=1.052 (41.210%) 031: dt: 0.2500, sse=270153.4, rms=0.957 (8.955%) rms = 0.9809/0.9574, sse=270061.6/270153.4, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.9132/0.9574, sse=267348.5/270153.4, time step reduction 3 of 3 to 0.062 0 0 1 032: dt: 0.1250, sse=267348.5, rms=0.913 (4.619%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 5.26 minutes #VMPC# mris_place_surfaces VmPeak 2669512 mris_place_surface done @#@FSTIME 2021:10:15:15:56:11 mris_place_surface N 18 e 327.03 S 3.67 U 708.23 P 217% M 2146388 F 0 R 2101143 W 0 c 2826 w 4349 I 0 O 11672 L 50.02 53.67 54.10 @#@FSLOADPOST 2021:10:15:16:01:38 mris_place_surface N 18 50.72 51.72 53.10 #-------------------------------------------- #@# WhitePreAparc rh Fri Oct 15 16:01:38 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 7.1.1 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 4 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface with 5 iterations Area 330664 0.26604 0.06278 0.005695 0.5907 Corner 991992 60.00000 9.62941 14.320449 138.5878 Edge 495996 0.78788 0.11407 0.077872 1.3531 Hinge 495996 6.34495 6.46881 0.000004 124.7745 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 MRIfindBrightNonWM(): 516 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6996, nmarked2=193, nripped=6996 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 82667: xyz = (10.7492,16.8538,-17.5146) oxyz = (10.7492,16.8538,-17.5146) wxzy = (10.7492,16.8538,-17.5146) pxyz = (0,0,0) CBVO Creating mask 165334 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6996 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6996, nmarked2=193, nripped=6996 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=2 had to be increased for 129 vertices, nripped=6996 mean border=67.9, 11 (11) missing vertices, mean dist 0.4 [0.4 (%33.3)->0.7 (%66.7))] %84 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2015 min Finding expansion regions mean absolute distance = 0.62 +- 0.68 5194 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn085, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=8944736.0, rms=16.636 001: dt: 0.5000, sse=4779717.0, rms=12.058 (27.517%) 002: dt: 0.5000, sse=2997621.5, rms=9.443 (21.687%) 003: dt: 0.5000, sse=2046528.9, rms=7.688 (18.582%) 004: dt: 0.5000, sse=1608792.5, rms=6.721 (12.581%) 005: dt: 0.5000, sse=1346336.2, rms=6.060 (9.840%) 006: dt: 0.5000, sse=1261189.9, rms=5.840 (3.621%) 007: dt: 0.5000, sse=1182353.5, rms=5.620 (3.769%) rms = 5.6159/5.6202, sse=1187615.4/1182353.6, time step reduction 1 of 3 to 0.250 0 1 1 008: dt: 0.5000, sse=1187615.4, rms=5.616 (0.076%) 009: dt: 0.2500, sse=605720.2, rms=3.635 (35.265%) 010: dt: 0.2500, sse=516951.9, rms=3.231 (11.119%) rms = 3.3023/3.2312, sse=532806.5/516951.9, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 011: dt: 0.1250, sse=437028.2, rms=2.810 (13.038%) 012: dt: 0.1250, sse=331582.2, rms=2.127 (24.288%) 013: dt: 0.1250, sse=311969.5, rms=1.970 (7.386%) rms = 1.9267/1.9703, sse=306150.3/311969.5, time step reduction 3 of 3 to 0.062 0 0 1 014: dt: 0.1250, sse=306150.3, rms=1.927 (2.214%) maximum number of reductions reached, breaking from loop positioning took 1.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6996 removing 2 vertices from ripped group in thread:0 removing 1 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7202, nmarked2=200, nripped=7202 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=1 had to be increased for 89 vertices, nripped=7202 mean border=73.1, 42 (1) missing vertices, mean dist -0.2 [0.3 (%79.5)->0.2 (%20.5))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1397 min Finding expansion regions mean absolute distance = 0.28 +- 0.43 4385 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn085, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1827726.9, rms=7.070 015: dt: 0.5000, sse=1205380.5, rms=5.495 (22.275%) rms = 5.7716/5.4952, sse=1297061.1/1205380.5, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 016: dt: 0.2500, sse=697873.7, rms=3.774 (31.323%) 017: dt: 0.2500, sse=565195.2, rms=3.178 (15.792%) 018: dt: 0.2500, sse=513083.8, rms=2.902 (8.693%) rms = 2.9924/2.9017, sse=531693.0/513083.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 019: dt: 0.1250, sse=446722.5, rms=2.515 (13.316%) 020: dt: 0.1250, sse=359742.4, rms=1.887 (24.992%) 021: dt: 0.1250, sse=340924.8, rms=1.717 (9.001%) 022: dt: 0.1250, sse=333457.5, rms=1.648 (4.024%) 023: dt: 0.1250, sse=328517.2, rms=1.597 (3.069%) rms = 1.5575/1.5972, sse=325512.4/328517.2, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=325512.4, rms=1.558 (2.485%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7202 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7253, nmarked2=199, nripped=7253 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 122 vertices, nripped=7253 mean border=76.0, 68 (1) missing vertices, mean dist -0.1 [0.2 (%71.5)->0.2 (%28.5))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0742 min Finding expansion regions mean absolute distance = 0.19 +- 0.30 3626 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=cn085, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=763228.1, rms=4.055 rms = 5.3598/4.0545, sse=1160683.4/763228.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=473887.2, rms=2.695 (33.527%) 026: dt: 0.2500, sse=370711.9, rms=1.973 (26.806%) rms = 1.9342/1.9727, sse=366965.2/370711.9, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=366965.2, rms=1.934 (1.952%) 028: dt: 0.1250, sse=308921.2, rms=1.387 (28.291%) 029: dt: 0.1250, sse=299393.6, rms=1.276 (8.000%) rms = 1.2593/1.2760, sse=298361.4/299393.6, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=298361.3, rms=1.259 (1.311%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7253 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7303, nmarked2=201, nripped=7303 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 126 vertices, nripped=7303 mean border=76.8, 102 (1) missing vertices, mean dist -0.0 [0.2 (%56.0)->0.2 (%44.0))] %93 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0477 min Finding expansion regions mean absolute distance = 0.16 +- 0.25 2880 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=cn085, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=345443.7, rms=1.777 rms = 3.5273/1.7772, sse=648191.6/345443.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=281616.8, rms=1.057 (40.505%) 032: dt: 0.2500, sse=277919.3, rms=0.970 (8.302%) rms = 0.9824/0.9695, sse=275431.0/277919.3, time step reduction 2 of 3 to 0.125 0 0 1 RMS increased, rejecting step rms = 0.9294/0.9695, sse=275388.7/277919.3, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=275388.7, rms=0.929 (4.143%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 5.34 minutes #VMPC# mris_place_surfaces VmPeak 2681796 mris_place_surface done @#@FSTIME 2021:10:15:16:01:38 mris_place_surface N 18 e 331.94 S 3.51 U 723.36 P 218% M 2158144 F 0 R 2040134 W 0 c 2322 w 4554 I 0 O 11632 L 50.72 51.72 53.10 @#@FSLOADPOST 2021:10:15:16:07:10 mris_place_surface N 18 49.78 50.81 52.31 #-------------------------------------------- #@# CortexLabel lh Fri Oct 15 16:07:10 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 7 non-cortical segments detected only using segment with 8388 vertices erasing segment 1 (vno[0] = 78882) erasing segment 2 (vno[0] = 91923) erasing segment 3 (vno[0] = 98158) erasing segment 4 (vno[0] = 100702) erasing segment 5 (vno[0] = 105901) erasing segment 6 (vno[0] = 113668) @#@FSTIME 2021:10:15:16:07:10 mri_label2label N 5 e 28.57 S 0.51 U 29.98 P 106% M 366160 F 0 R 232574 W 0 c 32 w 320 I 0 O 13720 L 49.78 50.81 52.31 @#@FSLOADPOST 2021:10:15:16:07:39 mri_label2label N 5 48.98 50.51 52.17 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Fri Oct 15 16:07:39 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 5994 vertices erasing segment 1 (vno[0] = 54368) erasing segment 2 (vno[0] = 58274) erasing segment 3 (vno[0] = 59288) erasing segment 4 (vno[0] = 74848) erasing segment 5 (vno[0] = 94621) erasing segment 6 (vno[0] = 98158) erasing segment 7 (vno[0] = 100702) erasing segment 8 (vno[0] = 105901) erasing segment 9 (vno[0] = 113668) erasing segment 10 (vno[0] = 136832) @#@FSTIME 2021:10:15:16:07:39 mri_label2label N 5 e 28.74 S 0.50 U 30.19 P 106% M 389592 F 0 R 239857 W 0 c 28 w 312 I 0 O 13920 L 48.98 50.51 52.17 @#@FSLOADPOST 2021:10:15:16:08:08 mri_label2label N 5 48.54 50.26 52.03 #-------------------------------------------- #@# CortexLabel rh Fri Oct 15 16:08:08 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 10 non-cortical segments detected only using segment with 8335 vertices erasing segment 1 (vno[0] = 81834) erasing segment 2 (vno[0] = 93955) erasing segment 3 (vno[0] = 95893) erasing segment 4 (vno[0] = 96870) erasing segment 5 (vno[0] = 100210) erasing segment 6 (vno[0] = 103271) erasing segment 7 (vno[0] = 104017) erasing segment 8 (vno[0] = 136108) erasing segment 9 (vno[0] = 136232) @#@FSTIME 2021:10:15:16:08:08 mri_label2label N 5 e 27.40 S 0.53 U 28.82 P 107% M 382864 F 0 R 237560 W 0 c 44 w 297 I 0 O 13344 L 48.54 50.26 52.03 @#@FSLOADPOST 2021:10:15:16:08:35 mri_label2label N 5 48.36 50.08 51.92 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Fri Oct 15 16:08:35 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 14 non-cortical segments detected only using segment with 6050 vertices erasing segment 0 (vno[0] = 52742) erasing segment 2 (vno[0] = 62989) erasing segment 3 (vno[0] = 68965) erasing segment 4 (vno[0] = 93951) erasing segment 5 (vno[0] = 93955) erasing segment 6 (vno[0] = 95893) erasing segment 7 (vno[0] = 96870) erasing segment 8 (vno[0] = 100210) erasing segment 9 (vno[0] = 103271) erasing segment 10 (vno[0] = 104017) erasing segment 11 (vno[0] = 136108) erasing segment 12 (vno[0] = 136232) erasing segment 13 (vno[0] = 148024) @#@FSTIME 2021:10:15:16:08:35 mri_label2label N 5 e 26.99 S 0.53 U 28.38 P 107% M 406208 F 0 R 246081 W 0 c 49 w 311 I 0 O 13520 L 48.36 50.08 51.92 @#@FSLOADPOST 2021:10:15:16:09:02 mri_label2label N 5 48.22 49.88 51.80 #-------------------------------------------- #@# Smooth2 lh Fri Oct 15 16:09:02 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm #-------------------------------------------- #@# Smooth2 rh Fri Oct 15 16:09:02 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm Waiting for PID 44697 of (44697 44700) to complete... Waiting for PID 44700 of (44697 44700) to complete... PIDs (44697 44700) completed and logs appended. #-------------------------------------------- #@# Inflation2 lh Fri Oct 15 16:09:10 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated #-------------------------------------------- #@# Inflation2 rh Fri Oct 15 16:09:10 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Waiting for PID 44761 of (44761 44766) to complete... Waiting for PID 44766 of (44761 44766) to complete... PIDs (44761 44766) completed and logs appended. #-------------------------------------------- #@# Curv .H and .K lh Fri Oct 15 16:10:13 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/surf mris_curvature -w -seed 1234 lh.white.preaparc rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated #-------------------------------------------- #@# Curv .H and .K rh Fri Oct 15 16:10:13 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /lscratch/25105636/sub-005_ses-01/sub-005/surf reconbatchjobs /lscratch/25105636/sub-005_ses-01/sub-005/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 44966 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44969 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44972 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44975 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44978 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44981 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44984 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44987 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44990 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44993 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44996 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... Waiting for PID 44999 of (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) to complete... PIDs (44966 44969 44972 44975 44978 44981 44984 44987 44990 44993 44996 44999) completed and logs appended. #-------------------------------------------- #@# Sphere lh Fri Oct 15 16:11:53 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Sphere rh Fri Oct 15 16:11:53 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere Waiting for PID 45376 of (45376 45379) to complete... Waiting for PID 45379 of (45376 45379) to complete... PIDs (45376 45379) completed and logs appended. #-------------------------------------------- #@# Surf Reg lh Fri Oct 15 16:37:10 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_register -curv ../surf/lh.sphere /usr/local/apps/freesurfer/7.1.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Surf Reg rh Fri Oct 15 16:37:10 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_register -curv ../surf/rh.sphere /usr/local/apps/freesurfer/7.1.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg Waiting for PID 48120 of (48120 48123) to complete... Waiting for PID 48123 of (48120 48123) to complete... PIDs (48120 48123) completed and logs appended. #-------------------------------------------- #@# Jacobian white lh Fri Oct 15 17:32:20 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Oct 15 17:32:20 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white Waiting for PID 67480 of (67480 67483) to complete... Waiting for PID 67483 of (67480 67483) to complete... PIDs (67480 67483) completed and logs appended. #-------------------------------------------- #@# AvgCurv lh Fri Oct 15 17:32:23 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mrisp_paint -a 5 /usr/local/apps/freesurfer/7.1.1/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #-------------------------------------------- #@# AvgCurv rh Fri Oct 15 17:32:23 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mrisp_paint -a 5 /usr/local/apps/freesurfer/7.1.1/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv Waiting for PID 67541 of (67541 67544) to complete... Waiting for PID 67544 of (67541 67544) to complete... PIDs (67541 67544) completed and logs appended. #----------------------------------------- #@# Cortical Parc lh Fri Oct 15 17:32:25 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-005 lh ../surf/lh.sphere.reg /usr/local/apps/freesurfer/7.1.1/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot #----------------------------------------- #@# Cortical Parc rh Fri Oct 15 17:32:25 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-005 rh ../surf/rh.sphere.reg /usr/local/apps/freesurfer/7.1.1/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot Waiting for PID 67619 of (67619 67622) to complete... Waiting for PID 67622 of (67619 67622) to complete... PIDs (67619 67622) completed and logs appended. #-------------------------------------------- #@# WhiteSurfs lh Fri Oct 15 17:32:47 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot 7.1.1 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 331868 0.33720 0.11848 0.000977 2.4702 Corner 995604 60.00000 13.88325 0.468387 179.0055 Edge 497802 0.89361 0.19987 0.011351 3.4457 Hinge 497802 10.84254 11.41939 0.000000 179.0321 Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 MRIfindBrightNonWM(): 516 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 697 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 82968: xyz = (-53.6391,18.7735,21.559) oxyz = (-53.6391,18.7735,21.559) wxzy = (-53.6391,18.7735,21.559) pxyz = (0,0,0) CBVO Creating mask 165936 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=2 had to be increased for 145 vertices, nripped=9446 mean border=66.8, 79 (79) missing vertices, mean dist 0.4 [0.6 (%9.9)->0.5 (%90.1))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1858 min Finding expansion regions mean absolute distance = 0.49 +- 0.65 4160 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn085, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=4740098.0, rms=11.998 001: dt: 0.5000, sse=1789433.1, rms=7.053 (41.221%) 002: dt: 0.5000, sse=1246626.9, rms=5.690 (19.318%) 003: dt: 0.5000, sse=1137418.8, rms=5.372 (5.588%) 004: dt: 0.5000, sse=1083883.6, rms=5.209 (3.041%) rms = 5.2347/5.2089, sse=1092223.0/1083883.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 005: dt: 0.2500, sse=594311.2, rms=3.383 (35.055%) 006: dt: 0.2500, sse=481050.2, rms=2.792 (17.461%) 007: dt: 0.2500, sse=438528.3, rms=2.533 (9.285%) rms = 2.6225/2.5330, sse=453089.5/438528.4, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 008: dt: 0.1250, sse=391993.8, rms=2.218 (12.438%) 009: dt: 0.1250, sse=331936.0, rms=1.728 (22.093%) 010: dt: 0.1250, sse=319863.5, rms=1.610 (6.797%) rms = 1.5819/1.6105, sse=317239.3/319863.5, time step reduction 3 of 3 to 0.062 0 0 1 011: dt: 0.1250, sse=317239.3, rms=1.582 (1.775%) maximum number of reductions reached, breaking from loop positioning took 1.6 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=1 had to be increased for 108 vertices, nripped=9446 mean border=72.6, 108 (42) missing vertices, mean dist -0.2 [0.3 (%82.5)->0.2 (%17.5))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1332 min Finding expansion regions mean absolute distance = 0.30 +- 0.44 3872 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn085, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1871713.9, rms=7.185 012: dt: 0.5000, sse=1146359.6, rms=5.333 (25.774%) rms = 5.6489/5.3331, sse=1251557.5/1146359.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=668794.8, rms=3.633 (31.880%) 014: dt: 0.2500, sse=534921.8, rms=2.989 (17.727%) 015: dt: 0.2500, sse=483628.3, rms=2.701 (9.644%) rms = 2.8000/2.7007, sse=500496.1/483628.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 016: dt: 0.1250, sse=421365.7, rms=2.300 (14.829%) 017: dt: 0.1250, sse=338595.7, rms=1.626 (29.292%) 018: dt: 0.1250, sse=321235.4, rms=1.445 (11.127%) 019: dt: 0.1250, sse=315919.0, rms=1.381 (4.433%) rms = 1.3451/1.3814, sse=312782.0/315919.0, time step reduction 3 of 3 to 0.062 0 0 1 020: dt: 0.1250, sse=312782.0, rms=1.345 (2.629%) maximum number of reductions reached, breaking from loop positioning took 1.2 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 104 vertices, nripped=9446 mean border=75.7, 132 (39) missing vertices, mean dist -0.1 [0.2 (%73.1)->0.2 (%26.9))] %90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0721 min Finding expansion regions mean absolute distance = 0.19 +- 0.29 3215 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=cn085, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=803886.2, rms=4.223 rms = 5.2478/4.2234, sse=1116947.8/803886.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 021: dt: 0.2500, sse=493256.4, rms=2.808 (33.523%) 022: dt: 0.2500, sse=368132.7, rms=1.941 (30.859%) 023: dt: 0.2500, sse=359102.1, rms=1.880 (3.140%) rms = 1.9575/1.8802, sse=368587.8/359102.1, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 024: dt: 0.1250, sse=332151.5, rms=1.636 (13.001%) 025: dt: 0.1250, sse=296630.3, rms=1.235 (24.473%) 026: dt: 0.1250, sse=290362.0, rms=1.151 (6.833%) rms = 1.1438/1.1510, sse=289819.3/290362.0, time step reduction 3 of 3 to 0.062 0 0 1 027: dt: 0.1250, sse=289819.3, rms=1.144 (0.624%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 117 vertices, nripped=9446 mean border=76.6, 148 (34) missing vertices, mean dist -0.0 [0.2 (%56.7)->0.2 (%43.3))] %91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0461 min Finding expansion regions mean absolute distance = 0.16 +- 0.25 2863 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=cn085, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=344565.6, rms=1.781 rms = 3.5480/1.7809, sse=663117.3/344565.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 028: dt: 0.2500, sse=280014.6, rms=1.026 (42.393%) rms = 0.9362/1.0259, sse=281563.2/280014.6, time step reduction 2 of 3 to 0.125 0 1 0 029: dt: 0.2500, sse=281563.2, rms=0.936 (8.742%) 030: dt: 0.1250, sse=270441.4, rms=0.845 (9.698%) rms = 0.8336/0.8454, sse=268943.9/270441.4, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=268943.9, rms=0.834 (1.397%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 4.92 minutes #VMPC# mris_place_surfaces VmPeak 2644576 mris_place_surface done @#@FSTIME 2021:10:15:17:32:47 mris_place_surface N 25 e 307.08 S 3.79 U 675.69 P 221% M 2138600 F 1 R 2195418 W 0 c 8613 w 4015 I 352 O 11672 L 43.99 46.18 48.06 @#@FSLOADPOST 2021:10:15:17:37:54 mris_place_surface N 25 42.73 44.11 46.64 #-------------------------------------------- #@# WhiteSurfs rh Fri Oct 15 17:37:54 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot 7.1.1 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 330664 0.33789 0.11948 0.001452 1.7860 Corner 991992 60.00000 14.02956 0.364056 177.0016 Edge 495996 0.89488 0.20212 0.022356 2.9801 Hinge 495996 10.87834 11.50825 0.000033 179.9763 Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 MRIfindBrightNonWM(): 516 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 479 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 82667: xyz = (10.7492,16.8538,-17.5146) oxyz = (10.7492,16.8538,-17.5146) wxzy = (10.7492,16.8538,-17.5146) pxyz = (0,0,0) CBVO Creating mask 165334 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=2 had to be increased for 190 vertices, nripped=9167 mean border=67.0, 67 (67) missing vertices, mean dist 0.4 [0.6 (%10.5)->0.5 (%89.5))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1930 min Finding expansion regions mean absolute distance = 0.49 +- 0.64 4253 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn085, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=4621567.0, rms=11.848 001: dt: 0.5000, sse=1774001.8, rms=7.021 (40.739%) 002: dt: 0.5000, sse=1273326.1, rms=5.770 (17.824%) 003: dt: 0.5000, sse=1147245.2, rms=5.409 (6.259%) 004: dt: 0.5000, sse=1108249.9, rms=5.288 (2.223%) rms = 5.2622/5.2885, sse=1100806.9/1108249.9, time step reduction 1 of 3 to 0.250 0 0 1 005: dt: 0.5000, sse=1100807.0, rms=5.262 (0.497%) 006: dt: 0.2500, sse=515126.2, rms=2.974 (43.482%) 007: dt: 0.2500, sse=457321.0, rms=2.636 (11.380%) rms = 2.5956/2.6356, sse=449847.9/457321.0, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=449847.9, rms=2.596 (1.521%) 009: dt: 0.1250, sse=337632.9, rms=1.766 (31.961%) 010: dt: 0.1250, sse=322768.4, rms=1.623 (8.094%) rms = 1.5960/1.6231, sse=320139.5/322768.4, time step reduction 3 of 3 to 0.062 0 0 1 011: dt: 0.1250, sse=320139.6, rms=1.596 (1.668%) maximum number of reductions reached, breaking from loop positioning took 1.5 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=1 had to be increased for 149 vertices, nripped=9167 mean border=72.7, 84 (15) missing vertices, mean dist -0.2 [0.3 (%81.8)->0.2 (%18.2))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1336 min Finding expansion regions mean absolute distance = 0.30 +- 0.47 4063 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn085, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=1864366.8, rms=7.170 012: dt: 0.5000, sse=1159873.0, rms=5.372 (25.083%) rms = 5.6360/5.3720, sse=1247295.5/1159873.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 013: dt: 0.2500, sse=680103.6, rms=3.676 (31.572%) 014: dt: 0.2500, sse=546172.9, rms=3.037 (17.370%) 015: dt: 0.2500, sse=492033.2, rms=2.738 (9.868%) rms = 2.8159/2.7377, sse=505332.1/492033.3, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 016: dt: 0.1250, sse=430926.4, rms=2.352 (14.081%) 017: dt: 0.1250, sse=349533.6, rms=1.709 (27.357%) 018: dt: 0.1250, sse=330929.4, rms=1.525 (10.723%) 019: dt: 0.1250, sse=324193.9, rms=1.451 (4.909%) 020: dt: 0.1250, sse=320362.1, rms=1.400 (3.498%) rms = 1.3660/1.3998, sse=317785.5/320362.1, time step reduction 3 of 3 to 0.062 0 0 1 021: dt: 0.1250, sse=317785.5, rms=1.366 (2.419%) maximum number of reductions reached, breaking from loop positioning took 1.4 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 135 vertices, nripped=9167 mean border=75.7, 133 (8) missing vertices, mean dist -0.1 [0.2 (%72.8)->0.2 (%27.2))] %91 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0737 min Finding expansion regions mean absolute distance = 0.19 +- 0.30 3635 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=cn085, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=779790.7, rms=4.122 rms = 5.2964/4.1221, sse=1135214.6/779790.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=482356.6, rms=2.727 (33.854%) 023: dt: 0.2500, sse=368634.2, rms=1.917 (29.674%) 024: dt: 0.2500, sse=358458.7, rms=1.840 (4.017%) rms = 1.9134/1.8405, sse=367491.8/358458.7, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step 025: dt: 0.1250, sse=333781.2, rms=1.612 (12.394%) 026: dt: 0.1250, sse=300951.6, rms=1.243 (22.918%) 027: dt: 0.1250, sse=295461.1, rms=1.162 (6.523%) rms = 1.1533/1.1618, sse=295158.2/295461.1, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=295158.2, rms=1.153 (0.727%) maximum number of reductions reached, breaking from loop positioning took 1.0 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 115.7928390; border_low = 49.0000000; outside_low = 36.2542300; outside_hi = 115.7928390; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 140 vertices, nripped=9167 mean border=76.6, 174 (7) missing vertices, mean dist -0.0 [0.2 (%56.5)->0.2 (%43.5))] %92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0463 min Finding expansion regions mean absolute distance = 0.16 +- 0.25 2973 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=cn085, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=347716.6, rms=1.770 rms = 3.5188/1.7695, sse=659353.7/347716.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 029: dt: 0.2500, sse=286105.8, rms=1.038 (41.363%) 030: dt: 0.2500, sse=284086.3, rms=0.950 (8.408%) rms = 0.9456/0.9504, sse=280304.7/284086.3, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=280304.7, rms=0.946 (0.504%) 032: dt: 0.1250, sse=274143.7, rms=0.865 (8.538%) rms = 0.8327/0.8648, sse=272487.4/274143.7, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=272487.4, rms=0.833 (3.715%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 5.15 minutes #VMPC# mris_place_surfaces VmPeak 2686764 mris_place_surface done @#@FSTIME 2021:10:15:17:37:54 mris_place_surface N 25 e 320.72 S 4.69 U 695.40 P 218% M 2180388 F 0 R 2171075 W 0 c 34571 w 4016 I 0 O 11632 L 42.73 44.11 46.64 @#@FSLOADPOST 2021:10:15:17:43:15 mris_place_surface N 25 40.68 43.20 45.59 #-------------------------------------------- #@# T1PialSurf lh Fri Oct 15 17:43:15 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white 7.1.1 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 331868 0.34006 0.13201 0.000762 2.4702 Corner 995604 60.00000 15.35513 0.257365 179.4060 Edge 497802 0.89871 0.21797 0.019510 3.7907 Hinge 497802 10.99138 11.96518 0.000007 179.9534 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 MRIfindBrightNonWM(): 516 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 52.4849 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 82968: xyz = (-53.6374,18.758,21.5724) oxyz = (-53.6374,18.758,21.5724) wxzy = (-53.6374,18.758,21.5724) pxyz = (-53.6374,18.758,21.5724) CBVO Creating mask 165936 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=2 had to be increased for 386 vertices, nripped=6427 mean border=33.8, 120 (120) missing vertices, mean dist 1.5 [2.3 (%0.0)->2.8 (%100.0))] % 5 local maxima, %46 large gradients and %45 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2016 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn085, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=60527380.0, rms=43.487 001: dt: 0.5000, sse=38702508.0, rms=34.734 (20.127%) 002: dt: 0.5000, sse=24964032.0, rms=27.847 (19.830%) 003: dt: 0.5000, sse=17514574.0, rms=23.273 (16.423%) 004: dt: 0.5000, sse=13479028.0, rms=20.370 (12.475%) 005: dt: 0.5000, sse=10891992.0, rms=18.266 (10.327%) 006: dt: 0.5000, sse=8781176.0, rms=16.350 (10.494%) 007: dt: 0.5000, sse=6812250.0, rms=14.332 (12.341%) 008: dt: 0.5000, sse=5087361.5, rms=12.295 (14.213%) 009: dt: 0.5000, sse=3684839.5, rms=10.347 (15.846%) 010: dt: 0.5000, sse=2652558.8, rms=8.635 (16.542%) 011: dt: 0.5000, sse=1972852.1, rms=7.291 (15.568%) 012: dt: 0.5000, sse=1589509.5, rms=6.407 (12.115%) 013: dt: 0.5000, sse=1382776.2, rms=5.875 (8.310%) 014: dt: 0.5000, sse=1272217.0, rms=5.567 (5.236%) 015: dt: 0.5000, sse=1208153.5, rms=5.380 (3.369%) 016: dt: 0.5000, sse=1166444.5, rms=5.253 (2.362%) 017: dt: 0.5000, sse=1141649.8, rms=5.174 (1.494%) 018: dt: 0.5000, sse=1119974.1, rms=5.104 (1.358%) rms = 5.0751/5.1040, sse=1111656.8/1119974.1, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=1111656.9, rms=5.075 (0.567%) 020: dt: 0.2500, sse=905030.1, rms=4.368 (13.939%) 021: dt: 0.2500, sse=853556.9, rms=4.177 (4.371%) rms = 4.1510/4.1767, sse=847598.5/853557.0, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=847598.5, rms=4.151 (0.616%) 023: dt: 0.1250, sse=816913.8, rms=4.029 (2.932%) rms = 4.0063/4.0293, sse=811316.1/816913.8, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=811316.1, rms=4.006 (0.570%) maximum number of reductions reached, breaking from loop positioning took 2.6 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=1 had to be increased for 13637 vertices, nripped=6427 mean border=32.9, 2258 (33) missing vertices, mean dist 0.1 [0.1 (%68.5)->0.7 (%31.5))] %13 local maxima, %39 large gradients and %43 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0517 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn085, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=957400.6, rms=4.289 rms = 4.4726/4.2890, sse=1007936.7/957400.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=888867.8, rms=4.027 (6.103%) 026: dt: 0.2500, sse=861614.2, rms=3.918 (2.705%) rms = 3.8904/3.9183, sse=854425.9/861614.2, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=854425.9, rms=3.890 (0.711%) 028: dt: 0.1250, sse=832766.4, rms=3.799 (2.361%) rms = 3.7807/3.7986, sse=828532.9/832766.4, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=828532.9, rms=3.781 (0.472%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 14111 vertices, nripped=6427 mean border=32.2, 2447 (19) missing vertices, mean dist 0.1 [0.2 (%58.3)->0.5 (%41.7))] %28 local maxima, %24 large gradients and %43 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0299 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=cn085, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=890046.6, rms=4.017 rms = 4.3532/4.0174, sse=977668.7/890046.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=858540.1, rms=3.891 (3.152%) rms = 3.8709/3.8908, sse=853071.2/858540.1, time step reduction 2 of 3 to 0.125 0 0 1 031: dt: 0.2500, sse=853071.2, rms=3.871 (0.511%) 032: dt: 0.1250, sse=840429.7, rms=3.817 (1.380%) rms = 3.8040/3.8175, sse=837011.5/840429.7, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=837011.4, rms=3.804 (0.352%) maximum number of reductions reached, breaking from loop positioning took 0.5 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165936 Gdiag_no=-1 vno start=0, stop=165936 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 12153 vertices, nripped=6427 mean border=31.5, 5276 (14) missing vertices, mean dist 0.0 [0.2 (%56.9)->0.4 (%43.1))] %32 local maxima, %19 large gradients and %42 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0188 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=cn085, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=884845.1, rms=3.991 rms = 4.2466/3.9913, sse=948603.8/884845.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 034: dt: 0.2500, sse=855086.7, rms=3.872 (2.995%) 035: dt: 0.2500, sse=831852.4, rms=3.782 (2.313%) 036: dt: 0.2500, sse=818683.8, rms=3.731 (1.348%) 037: dt: 0.2500, sse=799336.5, rms=3.653 (2.085%) rms = 3.6423/3.6534, sse=796328.0/799336.5, time step reduction 2 of 3 to 0.125 0 0 1 038: dt: 0.2500, sse=796328.0, rms=3.642 (0.306%) 039: dt: 0.1250, sse=771612.1, rms=3.532 (3.028%) rms = 3.5071/3.5320, sse=765875.6/771612.1, time step reduction 3 of 3 to 0.062 0 0 1 040: dt: 0.1250, sse=765875.6, rms=3.507 (0.703%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Pinning medial wall to white surface removing intersecting faces 000: 46 intersecting 001: 9 intersecting step 1 with no progress (num=36, old_num=9) 002: 36 intersecting 003: 26 intersecting 004: 4 intersecting step 1 with no progress (num=10, old_num=4) 005: 10 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 5.31 minutes #VMPC# mris_place_surfaces VmPeak 1803284 mris_place_surface done @#@FSTIME 2021:10:15:17:43:15 mris_place_surface N 28 e 330.74 S 3.77 U 715.20 P 217% M 1280432 F 0 R 1530046 W 0 c 25376 w 3595 I 0 O 11672 L 40.68 43.20 45.59 @#@FSLOADPOST 2021:10:15:17:48:46 mris_place_surface N 28 35.35 38.28 42.73 #-------------------------------------------- #@# T1PialSurf rh Fri Oct 15 17:48:46 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white 7.1.1 7.1.1 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri setenv SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 4 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 330664 0.34092 0.13277 0.000201 2.1170 Corner 991992 60.00000 15.46579 0.075415 179.4699 Edge 495996 0.90017 0.21950 0.016158 3.4393 Hinge 495996 11.08360 12.14949 0.000042 179.9598 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=50077, wmmin=5, clip=110 MRIfindBrightNonWM(): 516 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 52.4849 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 82667: xyz = (10.7492,16.8538,-17.5146) oxyz = (10.7492,16.8538,-17.5146) wxzy = (10.7492,16.8538,-17.5146) pxyz = (10.7492,16.8538,-17.5146) CBVO Creating mask 165334 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=2 had to be increased for 305 vertices, nripped=6643 mean border=33.7, 118 (118) missing vertices, mean dist 1.5 [1.1 (%0.0)->2.9 (%100.0))] % 5 local maxima, %44 large gradients and %47 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1686 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host=cn085, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=60613200.0, rms=43.630 001: dt: 0.5000, sse=38944904.0, rms=34.933 (19.933%) 002: dt: 0.5000, sse=25256988.0, rms=28.083 (19.609%) 003: dt: 0.5000, sse=17807240.0, rms=23.530 (16.213%) 004: dt: 0.5000, sse=13731536.0, rms=20.617 (12.382%) 005: dt: 0.5000, sse=11091094.0, rms=18.484 (10.344%) 006: dt: 0.5000, sse=8919202.0, rms=16.524 (10.604%) 007: dt: 0.5000, sse=6892803.5, rms=14.457 (12.508%) 008: dt: 0.5000, sse=5136783.0, rms=12.390 (14.297%) 009: dt: 0.5000, sse=3736123.0, rms=10.452 (15.643%) 010: dt: 0.5000, sse=2721940.0, rms=8.784 (15.954%) 011: dt: 0.5000, sse=2049836.6, rms=7.476 (14.896%) 012: dt: 0.5000, sse=1632384.0, rms=6.531 (12.646%) 013: dt: 0.5000, sse=1398353.4, rms=5.934 (9.138%) 014: dt: 0.5000, sse=1266081.4, rms=5.567 (6.185%) 015: dt: 0.5000, sse=1194545.6, rms=5.356 (3.790%) 016: dt: 0.5000, sse=1146966.1, rms=5.210 (2.724%) 017: dt: 0.5000, sse=1120398.0, rms=5.125 (1.639%) 018: dt: 0.5000, sse=1101359.0, rms=5.062 (1.222%) rms = 5.0221/5.0619, sse=1089814.0/1101359.0, time step reduction 1 of 3 to 0.250 0 0 1 019: dt: 0.5000, sse=1089814.0, rms=5.022 (0.786%) 020: dt: 0.2500, sse=887634.8, rms=4.318 (14.014%) 021: dt: 0.2500, sse=836520.9, rms=4.125 (4.473%) rms = 4.1035/4.1252, sse=831664.6/836520.9, time step reduction 2 of 3 to 0.125 0 0 1 022: dt: 0.2500, sse=831664.6, rms=4.103 (0.526%) 023: dt: 0.1250, sse=801894.8, rms=3.983 (2.931%) rms = 3.9624/3.9832, sse=796916.5/801894.8, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=796916.5, rms=3.962 (0.522%) maximum number of reductions reached, breaking from loop positioning took 2.6 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=1 had to be increased for 14615 vertices, nripped=6643 mean border=32.8, 2343 (13) missing vertices, mean dist 0.1 [0.2 (%67.8)->0.7 (%32.2))] %13 local maxima, %38 large gradients and %44 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0468 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host=cn085, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=962345.9, rms=4.320 rms = 4.5381/4.3205, sse=1022654.6/962345.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=893940.7, rms=4.060 (6.029%) 026: dt: 0.2500, sse=872264.7, rms=3.973 (2.132%) rms = 3.9663/3.9735, sse=870119.4/872264.7, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=870119.4, rms=3.966 (0.180%) 028: dt: 0.1250, sse=852109.8, rms=3.891 (1.911%) rms = 3.8864/3.8905, sse=851177.2/852109.8, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=851177.2, rms=3.886 (0.106%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 14916 vertices, nripped=6643 mean border=32.1, 2669 (10) missing vertices, mean dist 0.1 [0.2 (%58.3)->0.5 (%41.7))] %27 local maxima, %23 large gradients and %44 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0270 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host=cn085, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=909623.6, rms=4.105 rms = 4.4901/4.1054, sse=1012290.0/909623.6, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=883305.8, rms=4.002 (2.528%) rms = 4.0121/4.0016, sse=885450.8/883305.8, time step reduction 2 of 3 to 0.125 0 1 1 RMS increased, rejecting step rms = 3.9880/4.0016, sse=879948.4/883305.8, time step reduction 3 of 3 to 0.062 0 0 1 031: dt: 0.1250, sse=879948.4, rms=3.988 (0.340%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 94.2071610; border_hi = 36.2542300; border_low = 10.7626910; outside_low = 10.0000000; outside_hi = 29.8813460; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=165334 Gdiag_no=-1 vno start=0, stop=165334 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 12830 vertices, nripped=6643 mean border=31.5, 5361 (10) missing vertices, mean dist 0.0 [0.2 (%53.9)->0.4 (%46.1))] %31 local maxima, %19 large gradients and %43 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0179 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host=cn085, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=935023.7, rms=4.200 rms = 4.3659/4.2002, sse=976702.0/935023.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 032: dt: 0.2500, sse=893469.9, rms=4.041 (3.794%) 033: dt: 0.2500, sse=854759.0, rms=3.894 (3.643%) 034: dt: 0.2500, sse=833293.1, rms=3.810 (2.139%) 035: dt: 0.2500, sse=811681.3, rms=3.725 (2.248%) rms = 3.6963/3.7247, sse=804608.1/811681.3, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=804608.1, rms=3.696 (0.762%) 037: dt: 0.1250, sse=777920.2, rms=3.578 (3.187%) rms = 3.5504/3.5785, sse=771423.3/777920.2, time step reduction 3 of 3 to 0.062 0 0 1 038: dt: 0.1250, sse=771423.2, rms=3.550 (0.784%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Pinning medial wall to white surface removing intersecting faces 000: 22 intersecting 001: 11 intersecting 002: 5 intersecting step 1 with no progress (num=5, old_num=5) 003: 5 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 5.02 minutes #VMPC# mris_place_surfaces VmPeak 1793016 mris_place_surface done @#@FSTIME 2021:10:15:17:48:46 mris_place_surface N 28 e 311.88 S 2.55 U 684.86 P 220% M 1269504 F 0 R 1453387 W 0 c 905 w 4280 I 0 O 11632 L 35.35 38.28 42.73 @#@FSLOADPOST 2021:10:15:17:53:58 mris_place_surface N 28 37.84 37.35 40.97 #@# white curv lh Fri Oct 15 17:53:58 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2021:10:15:17:53:58 mris_place_surface N 5 e 3.40 S 0.22 U 4.32 P 133% M 222032 F 0 R 96555 W 0 c 11 w 306 I 0 O 1304 L 37.84 37.35 40.97 @#@FSLOADPOST 2021:10:15:17:54:01 mris_place_surface N 5 37.84 37.35 40.97 #@# white area lh Fri Oct 15 17:54:01 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2021:10:15:17:54:01 mris_place_surface N 3 e 1.29 S 0.19 U 2.27 P 190% M 222052 F 0 R 66409 W 0 c 11 w 318 I 0 O 1304 L 37.84 37.35 40.97 @#@FSLOADPOST 2021:10:15:17:54:03 mris_place_surface N 3 37.77 37.35 40.95 #@# pial curv lh Fri Oct 15 17:54:03 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2021:10:15:17:54:03 mris_place_surface N 5 e 3.26 S 0.24 U 4.16 P 134% M 222116 F 0 R 96534 W 0 c 7 w 281 I 0 O 1304 L 37.77 37.35 40.95 @#@FSLOADPOST 2021:10:15:17:54:06 mris_place_surface N 5 37.77 37.35 40.95 #@# pial area lh Fri Oct 15 17:54:06 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2021:10:15:17:54:06 mris_place_surface N 3 e 1.27 S 0.19 U 2.22 P 189% M 222060 F 0 R 66415 W 0 c 7 w 277 I 0 O 1304 L 37.77 37.35 40.95 @#@FSLOADPOST 2021:10:15:17:54:07 mris_place_surface N 3 37.71 37.34 40.93 #@# thickness lh Fri Oct 15 17:54:07 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 165936 vertices processed 25000 of 165936 vertices processed 50000 of 165936 vertices processed 75000 of 165936 vertices processed 100000 of 165936 vertices processed 125000 of 165936 vertices processed 150000 of 165936 vertices processed 0 of 165936 vertices processed 25000 of 165936 vertices processed 50000 of 165936 vertices processed 75000 of 165936 vertices processed 100000 of 165936 vertices processed 125000 of 165936 vertices processed 150000 of 165936 vertices processed thickness calculation complete, 59:1366 truncations. 62703 vertices at 0 distance 141700 vertices at 1 distance 86540 vertices at 2 distance 27714 vertices at 3 distance 8447 vertices at 4 distance 2853 vertices at 5 distance 1081 vertices at 6 distance 338 vertices at 7 distance 127 vertices at 8 distance 70 vertices at 9 distance 71 vertices at 10 distance 57 vertices at 11 distance 34 vertices at 12 distance 29 vertices at 13 distance 19 vertices at 14 distance 21 vertices at 15 distance 15 vertices at 16 distance 15 vertices at 17 distance 13 vertices at 18 distance 17 vertices at 19 distance 8 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2021:10:15:17:54:07 mris_place_surface N 6 e 55.58 S 0.37 U 56.56 P 102% M 222016 F 0 R 195556 W 0 c 44 w 277 I 0 O 1304 L 37.71 37.34 40.93 @#@FSLOADPOST 2021:10:15:17:55:03 mris_place_surface N 6 37.10 37.22 40.69 #@# area and vertex vol lh Fri Oct 15 17:55:03 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /lscratch/25105636/sub-005_ses-01/sub-005/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-005 lh /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.volume masking with /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label Total face volume 322588 Total vertex volume 322354 (mask=0) #@# sub-005 lh 322354 vertexvol Done @#@FSTIME 2021:10:15:17:55:03 vertexvol N 4 e 2.91 S 0.43 U 4.11 P 156% M 373816 F 0 R 177264 W 0 c 19 w 594 I 16 O 3912 L 37.10 37.22 40.69 @#@FSLOADPOST 2021:10:15:17:55:06 vertexvol N 4 37.10 37.22 40.69 #@# white curv rh Fri Oct 15 17:55:06 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2021:10:15:17:55:06 mris_place_surface N 5 e 3.40 S 0.24 U 4.33 P 134% M 221328 F 0 R 96208 W 0 c 10 w 264 I 0 O 1296 L 37.10 37.22 40.69 @#@FSLOADPOST 2021:10:15:17:55:09 mris_place_surface N 5 37.09 37.22 40.67 #@# white area rh Fri Oct 15 17:55:09 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2021:10:15:17:55:09 mris_place_surface N 3 e 1.29 S 0.19 U 2.23 P 188% M 221360 F 0 R 66162 W 0 c 6 w 294 I 0 O 1296 L 37.09 37.22 40.67 @#@FSLOADPOST 2021:10:15:17:55:11 mris_place_surface N 3 37.09 37.22 40.67 #@# pial curv rh Fri Oct 15 17:55:11 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2021:10:15:17:55:11 mris_place_surface N 5 e 3.29 S 0.23 U 4.23 P 135% M 221576 F 0 R 96140 W 0 c 8 w 305 I 0 O 1296 L 37.09 37.22 40.67 @#@FSLOADPOST 2021:10:15:17:55:14 mris_place_surface N 5 37.25 37.25 40.66 #@# pial area rh Fri Oct 15 17:55:14 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2021:10:15:17:55:14 mris_place_surface N 3 e 1.29 S 0.20 U 2.26 P 189% M 221320 F 0 R 66170 W 0 c 3 w 308 I 0 O 1296 L 37.25 37.25 40.66 @#@FSLOADPOST 2021:10:15:17:55:15 mris_place_surface N 3 37.25 37.25 40.66 #@# thickness rh Fri Oct 15 17:55:15 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 165334 vertices processed 25000 of 165334 vertices processed 50000 of 165334 vertices processed 75000 of 165334 vertices processed 100000 of 165334 vertices processed 125000 of 165334 vertices processed 150000 of 165334 vertices processed 0 of 165334 vertices processed 25000 of 165334 vertices processed 50000 of 165334 vertices processed 75000 of 165334 vertices processed 100000 of 165334 vertices processed 125000 of 165334 vertices processed 150000 of 165334 vertices processed thickness calculation complete, 121:1241 truncations. 60289 vertices at 0 distance 139872 vertices at 1 distance 87753 vertices at 2 distance 28468 vertices at 3 distance 9032 vertices at 4 distance 3180 vertices at 5 distance 1147 vertices at 6 distance 403 vertices at 7 distance 171 vertices at 8 distance 108 vertices at 9 distance 55 vertices at 10 distance 42 vertices at 11 distance 32 vertices at 12 distance 28 vertices at 13 distance 26 vertices at 14 distance 16 vertices at 15 distance 12 vertices at 16 distance 10 vertices at 17 distance 8 vertices at 18 distance 7 vertices at 19 distance 9 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2021:10:15:17:55:15 mris_place_surface N 6 e 55.62 S 0.38 U 56.62 P 102% M 221444 F 0 R 195004 W 0 c 29 w 282 I 0 O 1296 L 37.25 37.25 40.66 @#@FSLOADPOST 2021:10:15:17:56:11 mris_place_surface N 6 37.93 37.45 40.53 #@# area and vertex vol rh Fri Oct 15 17:56:11 EDT 2021 cd /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /lscratch/25105636/sub-005_ses-01/sub-005/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume sub-005 rh /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.volume masking with /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label Total face volume 325004 Total vertex volume 324742 (mask=0) #@# sub-005 rh 324742 vertexvol Done @#@FSTIME 2021:10:15:17:56:11 vertexvol N 4 e 2.90 S 0.44 U 4.10 P 156% M 372332 F 0 R 176544 W 0 c 17 w 543 I 0 O 3888 L 37.93 37.45 40.53 @#@FSLOADPOST 2021:10:15:17:56:14 vertexvol N 4 38.17 37.51 40.53 #----------------------------------------- #@# Curvature Stats lh Fri Oct 15 17:56:14 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-005 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-005/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 302 ] Gb_filter = 0 @#@FSTIME 2021:10:15:17:56:14 mris_curvature_stats N 11 e 4.83 S 0.30 U 5.94 P 129% M 222296 F 0 R 142253 W 0 c 27 w 273 I 0 O 10480 L 38.17 37.51 40.53 @#@FSLOADPOST 2021:10:15:17:56:19 mris_curvature_stats N 11 38.08 37.50 40.51 #----------------------------------------- #@# Curvature Stats rh Fri Oct 15 17:56:19 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-005 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ sub-005/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 298 ] Gb_filter = 0 @#@FSTIME 2021:10:15:17:56:19 mris_curvature_stats N 11 e 4.84 S 0.29 U 5.96 P 129% M 221660 F 0 R 141698 W 0 c 24 w 311 I 0 O 10408 L 38.08 37.50 40.51 @#@FSLOADPOST 2021:10:15:17:56:24 mris_curvature_stats N 11 37.91 37.48 40.49 #-------------------------------------------- #@# Cortical ribbon mask Fri Oct 15 17:56:24 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel sub-005 SUBJECTS_DIR is /lscratch/25105636/sub-005_ses-01 loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to left white surface computing distance to right white surface computing distance to left pial surface computing distance to right pial surface hemi masks overlap voxels = 641 writing volume /lscratch/25105636/sub-005_ses-01/sub-005/mri/ribbon.mgz mris_volmask took 16.94 minutes writing ribbon files @#@FSTIME 2021:10:15:17:56:24 mris_volmask N 13 e 1016.49 S 4.70 U 1857.03 P 183% M 1463296 F 0 R 2731909 W 0 c 856 w 2075 I 0 O 1024 L 37.91 37.48 40.49 @#@FSLOADPOST 2021:10:15:18:13:20 mris_volmask N 13 30.72 34.02 37.28 #----------------------------------------- #@# Cortical Parc 2 lh Fri Oct 15 18:13:20 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-005 lh ../surf/lh.sphere.reg /usr/local/apps/freesurfer/7.1.1/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Cortical Parc 2 rh Fri Oct 15 18:13:20 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-005 rh ../surf/rh.sphere.reg /usr/local/apps/freesurfer/7.1.1/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot Waiting for PID 26470 of (26470 26473) to complete... Waiting for PID 26473 of (26470 26473) to complete... PIDs (26470 26473) completed and logs appended. #----------------------------------------- #@# Cortical Parc 3 lh Fri Oct 15 18:14:00 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-005 lh ../surf/lh.sphere.reg /usr/local/apps/freesurfer/7.1.1/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Cortical Parc 3 rh Fri Oct 15 18:14:00 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-005 rh ../surf/rh.sphere.reg /usr/local/apps/freesurfer/7.1.1/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot Waiting for PID 27260 of (27260 27263) to complete... Waiting for PID 27263 of (27260 27263) to complete... PIDs (27260 27263) completed and logs appended. #----------------------------------------- #@# WM/GM Contrast lh Fri Oct 15 18:14:22 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts pctsurfcon --s sub-005 --lh-only #----------------------------------------- #@# WM/GM Contrast rh Fri Oct 15 18:14:22 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts pctsurfcon --s sub-005 --rh-only Waiting for PID 27833 of (27833 27836) to complete... Waiting for PID 27836 of (27833 27836) to complete... PIDs (27833 27836) completed and logs appended. #----------------------------------------- #@# Relabel Hypointensities Fri Oct 15 18:14:29 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 678 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 550 voxels changed to hypointensity... 1509 hypointense voxels neighboring cortex changed @#@FSTIME 2021:10:15:18:14:29 mri_relabel_hypointensities N 3 e 25.23 S 1.26 U 27.50 P 113% M 507128 F 0 R 612914 W 0 c 33 w 262 I 0 O 776 L 30.33 33.21 36.76 @#@FSLOADPOST 2021:10:15:18:14:54 mri_relabel_hypointensities N 3 30.75 33.08 36.62 #----------------------------------------- #@# APas-to-ASeg Fri Oct 15 18:14:54 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /lscratch/25105636/sub-005_ses-01/sub-005/mri/ribbon.mgz --threads 4 --lh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label --lh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white --lh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial --rh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label --rh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white --rh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 outvol aseg.mgz 4 avail.processors, using 4 Loading aseg.presurf.hypos.mgz Loading /lscratch/25105636/sub-005_ses-01/sub-005/mri/ribbon.mgz Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label Done loading 0 128 64 192 1 65 2 193 3 4 5 6 66 7 8 194 9 10 67 11 12 13 14 195 68 15 16 17 18 69 19 20 196 21 22 70 23 24 25 26 197 71 27 28 29 30 72 31 32 33 198 34 35 36 37 38 39 199 40 41 42 73 43 200 44 129 45 201 46 202 47 203 48 204 49 205 50 206 51 207 52 208 53 209 54 210 74 55 211 56 212 57 213 58 214 59 215 60 216 217 61 218 219 62 220 221 75 222 223 224 63 225 226 227 228 229 230 231 232 76 233 234 235 236 237 238 239 240 130 241 242 243 244 245 246 77 247 248 249 250 251 252 253 254 255 78 79 131 80 81 82 132 83 84 133 85 134 86 87 135 88 136 89 137 90 138 91 139 92 93 140 94 141 95 96 142 97 98 143 99 100 101 144 102 103 145 104 146 105 147 106 148 107 149 108 150 109 151 110 152 111 153 112 154 113 155 114 156 157 115 158 116 159 160 117 161 162 118 163 164 119 165 166 120 167 168 121 169 122 170 171 123 172 124 173 125 174 175 176 126 177 178 127 179 180 181 182 183 184 185 186 187 188 189 190 191 nrelabeled = 174229 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1297140 mri_surf2volseg done @#@FSTIME 2021:10:15:18:14:55 mri_surf2volseg N 20 e 21.60 S 1.59 U 41.10 P 197% M 1032396 F 0 R 941029 W 0 c 291 w 1087 I 0 O 816 L 30.75 33.08 36.62 @#@FSLOADPOST 2021:10:15:18:15:16 mri_surf2volseg N 20 31.05 33.00 36.52 mri_brainvol_stats sub-005 ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1839642.0 #CBVS2 BrainSegVol 1414569.0 #CBVS2 BrainSegVolNotVent 1392016.0 #CBVS2 SupraTentVol 1266843.0 #CBVS2 SupraTentVolNotVent 1244290.0 #CBVS2 lhCtxGM 322565.2 #CBVS2 rhCtxGM 324812.2 #CBVS2 lhCerebralWM 267326.0 #CBVS2 rhCerebralWM 267758.0 #CBVS2 SubCortGMVol 65156.0 #CBVS2 CerebellumVol 147726.0 #CBVS2 CerebellumGMVol 120300.0 #CBVS2 VentChorVol 17285.0 #CBVS2 3rd4th5thCSF 5268.0 #CBVS2 AllCSF 22553.0 #CBVS2 CCVol 3086.0 @#@FSTIME 2021:10:15:18:15:16 mri_brainvol_stats N 1 e 6.18 S 0.74 U 11.17 P 192% M 263988 F 4 R 326101 W 0 c 78 w 372 I 6336 O 8 L 31.05 33.00 36.52 @#@FSLOADPOST 2021:10:15:18:15:22 mri_brainvol_stats N 1 31.20 32.96 36.47 #----------------------------------------- #@# AParc-to-ASeg aparc Fri Oct 15 18:15:22 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.annot 1000 --lh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label --lh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white --lh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial --rh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.annot 2000 --rh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label --rh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white --rh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 outvol aparc+aseg.mgz 4 avail.processors, using 4 Loading aseg.mgz Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8749 vertices from lh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8688 vertices from rh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Done loading 0 128 192 64 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 65 52 53 54 55 56 57 58 59 60 61 62 63 66 193 67 129 194 68 130 195 69 196 70 197 131 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 71 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 132 72 73 133 74 134 75 135 76 77 136 78 137 79 80 138 81 139 82 140 83 141 84 142 85 143 144 86 145 87 146 147 88 148 89 149 150 90 151 91 152 153 92 154 155 93 156 94 157 158 95 159 96 160 97 161 98 162 99 163 100 164 101 165 102 103 166 104 167 105 168 106 107 169 108 170 109 171 110 172 111 112 173 113 114 174 115 175 116 176 117 177 118 178 119 179 120 180 121 181 122 182 123 183 124 184 185 125 186 126 187 188 127 189 190 191 nrelabeled = 643987 ndotcheck = 35813 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1281580 mri_surf2volseg done @#@FSTIME 2021:10:15:18:15:22 mri_surf2volseg N 25 e 191.72 S 2.15 U 386.26 P 202% M 1016892 F 0 R 1389122 W 0 c 325 w 1098 I 0 O 944 L 31.20 32.96 36.47 @#@FSLOADPOST 2021:10:15:18:18:34 mri_surf2volseg N 25 31.79 32.54 35.66 #----------------------------------------- #@# AParc-to-ASeg aparc.a2009s Fri Oct 15 18:18:34 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_surf2volseg --o aparc.a2009s+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label --lh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white --lh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial --rh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label --rh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white --rh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 outvol aparc.a2009s+aseg.mgz 4 avail.processors, using 4 Loading aseg.mgz Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8749 vertices from lh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8688 vertices from rh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) Done loading 0 128 64 192 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 65 51 52 53 54 55 56 57 58 59 60 61 62 63 66 193 67 129 194 68 130 195 69 196 70 197 131 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 71 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 72 132 73 133 74 75 134 76 135 77 136 78 79 137 80 138 81 139 82 140 83 141 84 142 85 143 86 144 87 145 146 88 147 89 148 149 90 150 151 91 152 92 153 154 93 155 94 156 157 95 158 96 159 97 160 161 98 99 162 100 163 101 164 102 103 165 104 166 105 106 167 107 168 108 169 109 110 170 111 171 112 113 172 114 173 115 116 174 117 175 118 176 119 177 120 178 121 179 122 180 123 181 124 182 183 125 184 126 185 127 186 187 188 189 190 191 nrelabeled = 643987 ndotcheck = 35813 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1281668 mri_surf2volseg done @#@FSTIME 2021:10:15:18:18:34 mri_surf2volseg N 25 e 195.05 S 2.25 U 386.83 P 199% M 1016960 F 0 R 1477479 W 0 c 356 w 1168 I 0 O 1024 L 31.79 32.54 35.66 @#@FSLOADPOST 2021:10:15:18:21:49 mri_surf2volseg N 25 32.20 32.36 35.00 #----------------------------------------- #@# AParc-to-ASeg aparc.DKTatlas Fri Oct 15 18:21:49 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_surf2volseg --o aparc.DKTatlas+aseg.mgz --label-cortex --i aseg.mgz --threads 4 --lh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label --lh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white --lh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial --rh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label --rh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white --rh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 outvol aparc.DKTatlas+aseg.mgz 4 avail.processors, using 4 Loading aseg.mgz Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8749 vertices from lh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8688 vertices from rh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Done loading 0 128 64 192 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 65 52 53 54 55 56 57 58 59 60 61 62 63 66 193 67 129 194 68 130 195 69 196 70 197 131 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 71 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 72 132 73 133 74 75 134 76 135 77 136 78 79 137 80 138 81 139 82 140 83 141 84 142 85 143 86 144 87 145 146 88 147 148 89 149 90 150 151 91 152 92 153 154 93 155 94 156 157 95 158 96 159 97 160 161 98 99 162 100 163 101 164 102 103 165 104 166 105 106 167 107 168 108 169 109 110 170 111 171 112 113 172 114 173 115 116 174 117 175 118 176 119 177 120 178 121 179 122 180 123 181 124 182 183 125 184 126 185 127 186 187 188 189 190 191 nrelabeled = 643987 ndotcheck = 35813 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1281584 mri_surf2volseg done @#@FSTIME 2021:10:15:18:21:49 mri_surf2volseg N 25 e 194.93 S 2.22 U 386.63 P 199% M 1016884 F 0 R 1388613 W 0 c 422 w 1197 I 0 O 944 L 32.20 32.36 35.00 @#@FSLOADPOST 2021:10:15:18:25:04 mri_surf2volseg N 25 32.20 31.91 34.30 #----------------------------------------- #@# WMParc Fri Oct 15 18:25:04 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 4 --lh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.annot 3000 --lh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label --lh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white --lh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial --rh-annot /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.annot 4000 --rh-cortex-mask /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label --rh-white /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white --rh-pial /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 outvol wmparc.mgz 4 avail.processors, using 4 Loading aparc+aseg.mgz Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 8749 vertices from lh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 8688 vertices from rh hemi Loading /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Done loading 0 192 64 128 1 65 2 66 3 4 5 6 67 7 193 8 9 10 11 12 13 68 14 15 16 17 194 18 19 20 69 21 22 23 195 24 25 26 27 28 29 196 70 30 31 197 32 33 34 198 35 199 36 200 37 201 38 202 39 203 40 204 41 71 205 42 206 43 207 44 208 45 209 46 210 47 211 48 212 49 213 50 51 214 52 215 216 53 217 54 218 55 219 56 220 57 221 58 222 59 72 223 60 61 224 62 225 226 63 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 129 244 245 246 247 248 249 250 251 252 253 254 255 73 74 130 75 131 76 77 132 133 78 134 79 135 80 136 81 137 82 83 138 84 139 85 140 86 141 87 88 142 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setting seed for random number genererator to 1234 7.1.1 cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-005 --surf-wm-vol --ctab /usr/local/apps/freesurfer/7.1.1/WMParcStatsLUT.txt --etiv sysname Linux hostname cn0853 machine x86_64 user reynoldr whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1776370 mm^3 (det: 1.096678 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2021:10:15:18:26:04 mri_segstats N 24 e 226.38 S 0.93 U 467.65 P 206% M 235908 F 0 R 654104 W 0 c 437 w 1251 I 56 O 24 L 33.04 32.24 34.26 @#@FSLOADPOST 2021:10:15:18:29:50 mri_segstats N 24 33.98 33.00 34.12 #----------------------------------------- #@# Parcellation Stats lh Fri Oct 15 18:29:50 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-005 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-005 lh pial #----------------------------------------- #@# Parcellation Stats rh Fri Oct 15 18:29:50 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-005 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-005 rh pial Waiting for PID 39070 of (39070 39074 39077 39080) to complete... Waiting for PID 39074 of (39070 39074 39077 39080) to complete... Waiting for PID 39077 of (39070 39074 39077 39080) to complete... Waiting for PID 39080 of (39070 39074 39077 39080) to complete... PIDs (39070 39074 39077 39080) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Oct 15 18:30:53 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-005 lh white #----------------------------------------- #@# Parcellation Stats 2 rh Fri Oct 15 18:30:53 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-005 rh white Waiting for PID 42309 of (42309 42317) to complete... Waiting for PID 42317 of (42309 42317) to complete... PIDs (42309 42317) completed and logs appended. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Oct 15 18:31:30 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-005 lh white #----------------------------------------- #@# Parcellation Stats 3 rh Fri Oct 15 18:31:30 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-005 rh white Waiting for PID 43975 of (43975 43978) to complete... Waiting for PID 43978 of (43975 43978) to complete... PIDs (43975 43978) completed and logs appended. #-------------------------------------------- #@# ASeg Stats Fri Oct 15 18:32:03 EDT 2021 /lscratch/25105636/sub-005_ses-01/sub-005 mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/apps/freesurfer/7.1.1/ASegStatsLUT.txt --subject sub-005 setting seed for random number genererator to 1234 7.1.1 cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/apps/freesurfer/7.1.1/ASegStatsLUT.txt --subject sub-005 sysname Linux hostname cn0853 machine x86_64 user reynoldr whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1776370 mm^3 (det: 1.096678 ) Computing euler number orig.nofix lheno = -18, rheno = -22 orig.nofix lhholes = 10, rhholes = 12 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2021:10:15:18:32:03 mri_segstats N 32 e 85.43 S 1.22 U 309.32 P 363% M 271844 F 0 R 668948 W 0 c 465 w 340 I 0 O 24 L 35.03 34.00 34.35 @#@FSLOADPOST 2021:10:15:18:33:28 mri_segstats N 32 34.14 34.07 34.35 /lscratch/25105636/sub-005_ses-01/sub-005/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /lscratch/25105636/sub-005_ses-01; ln -s /usr/local/apps/freesurfer/7.1.1/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Fri Oct 15 18:33:28 EDT 2021 mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface Waiting for PID 48112 of (48112 48115 48118 48121 48125) to complete... Waiting for PID 48115 of (48112 48115 48118 48121 48125) to complete... Waiting for PID 48118 of (48112 48115 48118 48121 48125) to complete... Waiting for PID 48121 of (48112 48115 48118 48121 48125) to complete... Waiting for PID 48125 of (48112 48115 48118 48121 48125) to complete... PIDs (48112 48115 48118 48121 48125) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-005 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface Waiting for PID 50245 of (50245 50248 50251 50254) to complete... Waiting for PID 50248 of (50245 50248 50251 50254) to complete... Waiting for PID 50251 of (50245 50248 50251 50254) to complete... Waiting for PID 50254 of (50245 50248 50251 50254) to complete... PIDs (50245 50248 50251 50254) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-005 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-005 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-005 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-005 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-005 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface Waiting for PID 51533 of (51533 51536 51539 51542 51545) to complete... Waiting for PID 51536 of (51533 51536 51539 51542 51545) to complete... Waiting for PID 51539 of (51533 51536 51539 51542 51545) to complete... Waiting for PID 51542 of (51533 51536 51539 51542 51545) to complete... Waiting for PID 51545 of (51533 51536 51539 51542 51545) to complete... PIDs (51533 51536 51539 51542 51545) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject sub-005 --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface Waiting for PID 52310 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52313 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52316 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52319 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52322 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52330 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52333 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... Waiting for PID 52336 of (52310 52313 52316 52319 52322 52330 52333 52336) to complete... PIDs (52310 52313 52316 52319 52322 52330 52333 52336) completed and logs appended. mris_label2annot --s sub-005 --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt Number of ctab entries 9 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/label cmdline mris_label2annot --s sub-005 --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname cn0853 machine x86_64 user reynoldr subject sub-005 hemi lh SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 ColorTable /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 146507 unhit vertices Writing annot to /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.mpm.vpnl.annot @#@FSTIME 2021:10:15:18:35:18 mris_label2annot N 26 e 1.19 S 0.18 U 1.83 P 169% M 186892 F 0 R 57652 W 0 c 8 w 270 I 8 O 2600 L 37.76 35.34 34.78 @#@FSLOADPOST 2021:10:15:18:35:20 mris_label2annot N 26 37.76 35.34 34.78 mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 53658 of (53658 53661 53664 53667 53670) to complete... Waiting for PID 53661 of (53658 53661 53664 53667 53670) to complete... Waiting for PID 53664 of (53658 53661 53664 53667 53670) to complete... Waiting for PID 53667 of (53658 53661 53664 53667 53670) to complete... Waiting for PID 53670 of (53658 53661 53664 53667 53670) to complete... PIDs (53658 53661 53664 53667 53670) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 53746 of (53746 53749 53752 53755) to complete... Waiting for PID 53749 of (53746 53749 53752 53755) to complete... Waiting for PID 53752 of (53746 53749 53752 53755) to complete... Waiting for PID 53755 of (53746 53749 53752 53755) to complete... PIDs (53746 53749 53752 53755) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-005 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface Waiting for PID 53841 of (53841 53844 53847 53850 53853) to complete... Waiting for PID 53844 of (53841 53844 53847 53850 53853) to complete... Waiting for PID 53847 of (53841 53844 53847 53850 53853) to complete... Waiting for PID 53850 of (53841 53844 53847 53850 53853) to complete... Waiting for PID 53853 of (53841 53844 53847 53850 53853) to complete... PIDs (53841 53844 53847 53850 53853) completed and logs appended. mris_label2annot --s sub-005 --hemi lh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/label cmdline mris_label2annot --s sub-005 --hemi lh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname cn0853 machine x86_64 user reynoldr subject sub-005 hemi lh SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 ColorTable /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 112164 unhit vertices Writing annot to /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.BA_exvivo.annot @#@FSTIME 2021:10:15:18:36:23 mris_label2annot N 38 e 1.26 S 0.18 U 1.91 P 166% M 187824 F 0 R 57785 W 0 c 5 w 260 I 8 O 2608 L 35.50 35.21 34.78 @#@FSLOADPOST 2021:10:15:18:36:24 mris_label2annot N 38 35.50 35.21 34.78 mris_label2annot --s sub-005 --hemi lh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/label cmdline mris_label2annot --s sub-005 --hemi lh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname cn0853 machine x86_64 user reynoldr subject sub-005 hemi lh SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 ColorTable /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 134308 unhit vertices Writing annot to /lscratch/25105636/sub-005_ses-01/sub-005/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2021:10:15:18:36:24 mris_label2annot N 38 e 1.20 S 0.20 U 1.82 P 168% M 187380 F 0 R 57816 W 0 c 9 w 293 I 0 O 2600 L 35.50 35.21 34.78 @#@FSLOADPOST 2021:10:15:18:36:26 mris_label2annot N 38 35.50 35.21 34.78 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-005 lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /lscratch/25105636/sub-005_ses-01/sub-005/mri/wm.mgz... reading input surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white... reading input pial surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial... reading input white surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 322588 Total vertex volume 322354 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1776370 mm^3 (det: 1.096678 ) 1509 973 3243 2.489 0.493 0.129 0.032 24 1.8 BA1_exvivo 4231 2799 7155 2.339 0.479 0.104 0.018 37 3.4 BA2_exvivo 1220 786 1207 1.955 0.407 0.115 0.024 8 1.3 BA3a_exvivo 2895 1888 4266 2.038 0.533 0.102 0.021 24 2.3 BA3b_exvivo 2198 1375 4875 2.986 0.560 0.106 0.025 17 2.2 BA4a_exvivo 1734 1085 3109 2.902 0.468 0.097 0.025 10 1.8 BA4p_exvivo 13413 9136 31899 2.873 0.610 0.113 0.026 114 14.0 BA6_exvivo 3157 2153 6647 2.753 0.425 0.111 0.020 31 2.6 BA44_exvivo 4807 3322 10237 2.642 0.542 0.122 0.025 55 4.9 BA45_exvivo 4285 3142 6863 2.028 0.579 0.137 0.032 53 5.7 V1_exvivo 9973 6971 17942 2.254 0.632 0.142 0.033 139 13.3 V2_exvivo 2938 1958 5708 2.632 0.564 0.119 0.022 30 2.7 MT_exvivo 723 547 2128 2.901 0.743 0.138 0.034 8 0.9 perirhinal_exvivo 689 464 1647 2.695 1.033 0.103 0.024 7 0.8 entorhinal_exvivo @#@FSTIME 2021:10:15:18:36:26 mris_anatomical_stats N 12 e 7.89 S 0.73 U 12.11 P 162% M 570352 F 0 R 339449 W 0 c 32 w 902 I 0 O 24 L 35.50 35.21 34.78 @#@FSLOADPOST 2021:10:15:18:36:33 mris_anatomical_stats N 12 34.66 35.04 34.72 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-005 lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /lscratch/25105636/sub-005_ses-01/sub-005/mri/wm.mgz... reading input surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white... reading input pial surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.pial... reading input white surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 322588 Total vertex volume 322354 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1776370 mm^3 (det: 1.096678 ) 1026 624 2205 2.514 0.507 0.122 0.031 14 1.2 BA1_exvivo 1800 1165 3061 2.357 0.528 0.089 0.015 11 1.1 BA2_exvivo 1060 685 973 1.924 0.400 0.118 0.025 7 1.2 BA3a_exvivo 1755 1146 2084 1.778 0.361 0.089 0.017 11 1.1 BA3b_exvivo 2165 1350 4650 3.054 0.507 0.095 0.023 12 1.9 BA4a_exvivo 1364 843 2231 2.801 0.442 0.100 0.026 9 1.5 BA4p_exvivo 7332 4958 17766 2.903 0.602 0.111 0.026 62 7.4 BA6_exvivo 2079 1430 4567 2.745 0.443 0.113 0.021 24 1.8 BA44_exvivo 2065 1406 4901 2.766 0.592 0.114 0.024 23 1.9 BA45_exvivo 4548 3365 7446 2.021 0.589 0.134 0.031 56 5.8 V1_exvivo 4917 3495 7899 2.072 0.579 0.158 0.040 77 8.0 V2_exvivo 785 530 1503 2.561 0.678 0.132 0.024 10 1.0 MT_exvivo 325 248 1126 3.135 0.723 0.145 0.035 4 0.4 perirhinal_exvivo 407 284 1032 3.047 0.616 0.087 0.016 1 0.3 entorhinal_exvivo @#@FSTIME 2021:10:15:18:36:33 mris_anatomical_stats N 12 e 7.98 S 0.71 U 12.28 P 162% M 570452 F 0 R 339120 W 0 c 40 w 760 I 0 O 24 L 34.66 35.04 34.72 @#@FSLOADPOST 2021:10:15:18:36:41 mris_anatomical_stats N 12 34.53 35.01 34.72 #-------------------------------------------- #@# BA_exvivo Labels rh Fri Oct 15 18:36:41 EDT 2021 mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface Waiting for PID 54127 of (54127 54130 54133 54136 54139) to complete... Waiting for PID 54130 of (54127 54130 54133 54136 54139) to complete... Waiting for PID 54133 of (54127 54130 54133 54136 54139) to complete... Waiting for PID 54136 of (54127 54130 54133 54136 54139) to complete... Waiting for PID 54139 of (54127 54130 54133 54136 54139) to complete... PIDs (54127 54130 54133 54136 54139) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-005 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface Waiting for PID 54319 of (54319 54322 54325 54328) to complete... Waiting for PID 54322 of (54319 54322 54325 54328) to complete... Waiting for PID 54325 of (54319 54322 54325 54328) to complete... Waiting for PID 54328 of (54319 54322 54325 54328) to complete... PIDs (54319 54322 54325 54328) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-005 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-005 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-005 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-005 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-005 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface Waiting for PID 54398 of (54398 54401 54404 54407 54410) to complete... Waiting for PID 54401 of (54398 54401 54404 54407 54410) to complete... Waiting for PID 54404 of (54398 54401 54404 54407 54410) to complete... Waiting for PID 54407 of (54398 54401 54404 54407 54410) to complete... Waiting for PID 54410 of (54398 54401 54404 54407 54410) to complete... PIDs (54398 54401 54404 54407 54410) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject sub-005 --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface Waiting for PID 54496 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54499 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54502 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54505 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54508 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54511 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54514 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... Waiting for PID 54517 of (54496 54499 54502 54505 54508 54511 54514 54517) to complete... PIDs (54496 54499 54502 54505 54508 54511 54514 54517) completed and logs appended. mris_label2annot --s sub-005 --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt Number of ctab entries 9 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/label cmdline mris_label2annot --s sub-005 --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname cn0853 machine x86_64 user reynoldr subject sub-005 hemi rh SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 ColorTable /usr/local/apps/freesurfer/7.1.1/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 147127 unhit vertices Writing annot to /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.mpm.vpnl.annot @#@FSTIME 2021:10:15:18:38:31 mris_label2annot N 26 e 1.18 S 0.17 U 1.85 P 170% M 186172 F 0 R 57436 W 0 c 9 w 297 I 0 O 2584 L 36.35 35.37 34.87 @#@FSLOADPOST 2021:10:15:18:38:32 mris_label2annot N 26 35.84 35.28 34.84 mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 54796 of (54796 54799 54802 54805 54808) to complete... Waiting for PID 54799 of (54796 54799 54802 54805 54808) to complete... Waiting for PID 54802 of (54796 54799 54802 54805 54808) to complete... Waiting for PID 54805 of (54796 54799 54802 54805 54808) to complete... Waiting for PID 54808 of (54796 54799 54802 54805 54808) to complete... PIDs (54796 54799 54802 54805 54808) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 55039 of (55039 55042 55045 55048) to complete... Waiting for PID 55042 of (55039 55042 55045 55048) to complete... Waiting for PID 55045 of (55039 55042 55045 55048) to complete... Waiting for PID 55048 of (55039 55042 55045 55048) to complete... PIDs (55039 55042 55045 55048) completed and logs appended. mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /lscratch/25105636/sub-005_ses-01/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-005 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface Waiting for PID 55137 of (55137 55140 55144 55148 55151) to complete... Waiting for PID 55140 of (55137 55140 55144 55148 55151) to complete... Waiting for PID 55144 of (55137 55140 55144 55148 55151) to complete... Waiting for PID 55148 of (55137 55140 55144 55148 55151) to complete... Waiting for PID 55151 of (55137 55140 55144 55148 55151) to complete... PIDs (55137 55140 55144 55148 55151) completed and logs appended. mris_label2annot --s sub-005 --hemi rh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/label cmdline mris_label2annot --s sub-005 --hemi rh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname cn0853 machine x86_64 user reynoldr subject sub-005 hemi rh SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 ColorTable /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 113239 unhit vertices Writing annot to /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.BA_exvivo.annot @#@FSTIME 2021:10:15:18:39:35 mris_label2annot N 38 e 1.25 S 0.19 U 1.87 P 165% M 187060 F 0 R 57533 W 0 c 7 w 259 I 0 O 2592 L 35.69 35.36 34.90 @#@FSLOADPOST 2021:10:15:18:39:36 mris_label2annot N 38 35.69 35.36 34.90 mris_label2annot --s sub-005 --hemi rh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt Number of ctab entries 15 7.1.1 cwd /lscratch/25105636/sub-005_ses-01/sub-005/label cmdline mris_label2annot --s sub-005 --hemi rh --ctab /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname cn0853 machine x86_64 user reynoldr subject sub-005 hemi rh SUBJECTS_DIR /lscratch/25105636/sub-005_ses-01 ColorTable /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 135909 unhit vertices Writing annot to /lscratch/25105636/sub-005_ses-01/sub-005/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2021:10:15:18:39:36 mris_label2annot N 38 e 1.18 S 0.18 U 1.83 P 169% M 186724 F 0 R 57504 W 0 c 6 w 276 I 0 O 2592 L 35.69 35.36 34.90 @#@FSLOADPOST 2021:10:15:18:39:37 mris_label2annot N 38 35.48 35.32 34.89 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-005 rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /lscratch/25105636/sub-005_ses-01/sub-005/mri/wm.mgz... reading input surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white... reading input pial surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial... reading input white surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 325004 Total vertex volume 324742 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1776370 mm^3 (det: 1.096678 ) 1261 793 2930 2.610 0.561 0.120 0.028 16 1.4 BA1_exvivo 3903 2492 6404 2.364 0.454 0.096 0.017 31 2.6 BA2_exvivo 1295 852 1313 1.943 0.487 0.106 0.023 7 1.3 BA3a_exvivo 2533 1642 3806 2.023 0.573 0.105 0.022 20 2.2 BA3b_exvivo 2294 1398 4715 2.870 0.567 0.101 0.027 17 2.3 BA4a_exvivo 1713 1084 2976 2.845 0.538 0.101 0.027 11 2.2 BA4p_exvivo 11038 7360 25743 2.944 0.558 0.108 0.023 90 10.0 BA6_exvivo 4506 3081 8948 2.669 0.483 0.113 0.023 42 4.2 BA44_exvivo 6254 4434 13662 2.582 0.584 0.131 0.027 81 6.8 BA45_exvivo 4529 3375 6782 1.978 0.531 0.151 0.039 65 6.9 V1_exvivo 9148 6359 15865 2.237 0.545 0.144 0.034 131 12.4 V2_exvivo 2701 1790 4853 2.670 0.477 0.109 0.019 23 2.2 MT_exvivo 355 267 1075 3.110 0.867 0.122 0.029 3 0.4 perirhinal_exvivo 565 408 1542 2.841 1.312 0.134 0.049 12 1.3 entorhinal_exvivo @#@FSTIME 2021:10:15:18:39:37 mris_anatomical_stats N 12 e 8.22 S 0.71 U 12.51 P 160% M 568432 F 0 R 366047 W 0 c 29 w 730 I 0 O 24 L 35.48 35.32 34.89 @#@FSLOADPOST 2021:10:15:18:39:46 mris_anatomical_stats N 12 35.12 35.25 34.87 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-005 rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /lscratch/25105636/sub-005_ses-01/sub-005/mri/wm.mgz... reading input surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white... reading input pial surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.pial... reading input white surface /lscratch/25105636/sub-005_ses-01/sub-005/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 325004 Total vertex volume 324742 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/apps/freesurfer/7.1.1/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1776370 mm^3 (det: 1.096678 ) 884 570 1807 2.394 0.553 0.124 0.029 13 1.0 BA1_exvivo 2330 1474 4229 2.474 0.453 0.090 0.015 17 1.3 BA2_exvivo 1161 760 1117 1.953 0.495 0.110 0.023 7 1.1 BA3a_exvivo 2011 1317 2518 1.858 0.419 0.096 0.018 12 1.5 BA3b_exvivo 1350 827 2960 2.840 0.579 0.119 0.041 15 2.1 BA4a_exvivo 1434 904 2476 2.932 0.574 0.096 0.023 7 1.5 BA4p_exvivo 7015 4651 16261 2.917 0.548 0.106 0.021 56 6.0 BA6_exvivo 1418 998 3258 2.691 0.416 0.118 0.026 17 1.4 BA44_exvivo 1766 1229 4349 2.709 0.631 0.130 0.027 25 1.9 BA45_exvivo 4339 3218 6321 1.960 0.524 0.149 0.038 63 6.7 V1_exvivo 4759 3442 7910 2.088 0.528 0.156 0.039 75 7.2 V2_exvivo 378 267 1065 2.958 0.511 0.105 0.018 4 0.3 MT_exvivo 33 24 113 3.627 0.590 0.103 0.033 0 0.0 perirhinal_exvivo 547 394 1749 3.348 0.893 0.112 0.038 7 1.0 entorhinal_exvivo @#@FSTIME 2021:10:15:18:39:46 mris_anatomical_stats N 12 e 8.18 S 0.69 U 12.44 P 160% M 568832 F 0 R 366180 W 0 c 25 w 755 I 0 O 24 L 35.12 35.25 34.87 @#@FSLOADPOST 2021:10:15:18:39:54 mris_anatomical_stats N 12 34.79 35.18 34.85 Started at Fri Oct 15 11:51:37 EDT 2021 Ended at Fri Oct 15 18:39:54 EDT 2021 #@#%# recon-all-run-time-hours 6.805 recon-all -s sub-005 finished without error at Fri Oct 15 18:39:54 EDT 2021 done 62551.306u 439.846s 6:48:17.52 257.1% 0+0k 821768+1024176io 37pf+0w if ( 0 ) then mv /lscratch/25105636/sub-005_ses-01/sub-005/label /lscratch/25105636/sub-005_ses-01/sub-005/mri /lscratch/25105636/sub-005_ses-01/sub-005/scripts /lscratch/25105636/sub-005_ses-01/sub-005/stats /lscratch/25105636/sub-005_ses-01/sub-005/surf /lscratch/25105636/sub-005_ses-01/sub-005/tmp /lscratch/25105636/sub-005_ses-01/sub-005/touch /lscratch/25105636/sub-005_ses-01/sub-005/trash /lscratch/25105636/sub-005_ses-01/. rmdir /lscratch/25105636/sub-005_ses-01/sub-005 @SUMA_Make_Spec_FS -fs_setup -NIFTI -sid sub-005 -fspath /lscratch/25105636/sub-005_ses-01 ++ Running @SUMA_Make_Spec_FS version: 2.2.4 ++ sourcing $FREESURFER_HOME/SetUpFreeSurfer.csh ++ creating directory './SUMA' for results... -- found 6 LH surfaces -- found 6 RH surfaces echo: No match. No COR files, converting mri/orig.mgz ... mri_convert -ot cor mri/orig.mgz mri/orig reading from mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to mri/orig... mri_convert -ot nii /lscratch/25105636/sub-005_ses-01/mri/orig.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/orig.nii reading from /lscratch/25105636/sub-005_ses-01/mri/orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/orig.nii... ++ created AFNI file './SUMA/sub-005_SurfVol.nii' Made roi label table for AFNI - fs_table.niml.lt mri_convert -ot nii mri/T1.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/T1.nii reading from mri/T1.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/T1.nii... mri_convert -ot nii mri/aparc+aseg.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/aparc+aseg.nii reading from mri/aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/aparc+aseg.nii... ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file /lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aparc+aseg.nii + setting labeltable + loading and re-writing dataset aparc+aseg.nii (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets mri_convert -ot nii mri/aparc.a2009s+aseg.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/aparc.a2009s+aseg.nii reading from mri/aparc.a2009s+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/aparc.a2009s+aseg.nii... ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file /lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aparc.a2009s+aseg.nii + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg.nii (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aparc.a2009s+aseg. mri_convert -ot nii mri/aseg.auto.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/aseg.auto.nii reading from mri/aseg.auto.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/aseg.auto.nii... mri_convert -ot nii mri/aseg.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/aseg.nii reading from mri/aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/aseg.nii... ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ** AFNI converts NIFTI_datatype=8 (INT32) in file /lscratch/25105636/sub-005_ses-01/SUMA/aseg.nii to FLOAT32 Warnings of this type will be muted for this session. Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. ++ Processing AFNI dataset aseg.nii + setting labeltable + loading and re-writing dataset aseg.nii (/lscratch/25105636/sub-005_ses-01/SUMA/aseg.nii in NIFTI storage) ++ 3drefit processed 1 datasets Notice: SessionAtlases.niml already exists, appending to it aseg. mri_convert -ot nii mri/brain.finalsurfs.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/brain.finalsurfs.nii reading from mri/brain.finalsurfs.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/brain.finalsurfs.nii... mri_convert -ot nii mri/brain.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/brain.nii reading from mri/brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/brain.nii... mri_convert -ot nii mri/brainmask.auto.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/brainmask.auto.nii reading from mri/brainmask.auto.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/brainmask.auto.nii... mri_convert -ot nii mri/brainmask.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/brainmask.nii reading from mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/brainmask.nii... mri_convert -ot nii mri/norm.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/norm.nii reading from mri/norm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/norm.nii... mri_convert -ot nii mri/nu.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/nu.nii reading from mri/nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/nu.nii... mri_convert -ot nii mri/lh.ribbon.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/lh.ribbon.nii reading from mri/lh.ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/lh.ribbon.nii... mri_convert -ot nii mri/rh.ribbon.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/rh.ribbon.nii reading from mri/rh.ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/rh.ribbon.nii... mri_convert -ot nii mri/wm.asegedit.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/wm.asegedit.nii reading from mri/wm.asegedit.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/wm.asegedit.nii... mri_convert -ot nii mri/wm.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/wm.nii reading from mri/wm.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/wm.nii... mri_convert -ot nii mri/wm.seg.mgz /lscratch/25105636/sub-005_ses-01/./SUMA/wm.seg.nii reading from mri/wm.seg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /lscratch/25105636/sub-005_ses-01/./SUMA/wm.seg.nii... -- running 'mris_convert lh.smoothwm lh.smoothwm.asc' Saving lh.smoothwm.asc as a surface Reading lh.smoothwm.asc ... Comment: #!ascii version of lh.smoothwm Performing affine transform... Writing surface... -- running 'mris_convert lh.pial lh.pial.asc' Saving lh.pial.asc as a surface Reading lh.pial.asc ... Comment: #!ascii version of lh.pial Performing affine transform... Writing surface... -- running 'mris_convert lh.inflated lh.inflated.asc' Saving lh.inflated.asc as a surface Reading lh.inflated.asc ... Comment: #!ascii version of lh.inflated Performing affine transform... Writing surface... -- running 'mris_convert lh.sphere lh.sphere.asc' Saving lh.sphere.asc as a surface Reading lh.sphere.asc ... Comment: #!ascii version of lh.sphere Performing affine transform... Writing surface... -- running 'mris_convert lh.white lh.white.asc' Saving lh.white.asc as a surface Reading lh.white.asc ... Comment: #!ascii version of lh.white Performing affine transform... Writing surface... -- running 'mris_convert lh.sphere.reg lh.sphere.reg.asc' Saving lh.sphere.reg.asc as a surface Reading lh.sphere.reg.asc ... Comment: #!ascii version of lh.sphere.reg Performing affine transform... Writing surface... -- running 'mris_convert rh.smoothwm rh.smoothwm.asc' Saving rh.smoothwm.asc as a surface Reading rh.smoothwm.asc ... Comment: #!ascii version of rh.smoothwm Performing affine transform... Writing surface... -- running 'mris_convert rh.pial rh.pial.asc' Saving rh.pial.asc as a surface Reading rh.pial.asc ... Comment: #!ascii version of rh.pial Performing affine transform... Writing surface... -- running 'mris_convert rh.inflated rh.inflated.asc' Saving rh.inflated.asc as a surface Reading rh.inflated.asc ... Comment: #!ascii version of rh.inflated Performing affine transform... Writing surface... -- running 'mris_convert rh.sphere rh.sphere.asc' Saving rh.sphere.asc as a surface Reading rh.sphere.asc ... Comment: #!ascii version of rh.sphere Performing affine transform... Writing surface... -- running 'mris_convert rh.white rh.white.asc' Saving rh.white.asc as a surface Reading rh.white.asc ... Comment: #!ascii version of rh.white Performing affine transform... Writing surface... -- running 'mris_convert rh.sphere.reg rh.sphere.reg.asc' Saving rh.sphere.reg.asc as a surface Reading rh.sphere.reg.asc ... Comment: #!ascii version of rh.sphere.reg Performing affine transform... Writing surface... ++ Notice FSread_annot (SUMA_FSread_annot.c:298 @18:40:32): Guessed FS annot version of 2009 ++ Notice FSread_annot (SUMA_FSread_annot.c:310 @18:40:32): Guessed left hemisphere ++ Notice FSread_annot (SUMA_FSread_annot.c:333 @18:40:32): Using /usr/local/apps/freesurfer/7.1.1/FreeSurferColorLUT.txt ++ Notice FSread_annot (SUMA_FSread_annot.c:344 @18:40:32): Setting -FScmaprange to [13100 13199] ++ Notice FSread_annot (SUMA_FSread_annot.c:298 @18:40:32): Guessed FS annot version of 2009 ++ Notice FSread_annot (SUMA_FSread_annot.c:312 @18:40:32): Guessed right hemisphere ++ Notice FSread_annot (SUMA_FSread_annot.c:333 @18:40:32): Using /usr/local/apps/freesurfer/7.1.1/FreeSurferColorLUT.txt ++ Notice FSread_annot (SUMA_FSread_annot.c:349 @18:40:32): Setting -FScmaprange to [14100 14199] ++ Converting surf dsets: lh.thickness ++ Converting surf dsets: lh.curv ++ Converting surf dsets: lh.sulc ++ Converting surf dsets: rh.thickness ++ Converting surf dsets: rh.curv ++ Converting surf dsets: rh.sulc ++ created spec file'./SUMA/sub-005_lh.spec' ++ created spec file'./SUMA/sub-005_rh.spec' ++ created spec file'./SUMA/sub-005_both.spec' ------------------------------------------------------------------ Running MapIcosahedron for both hemispheres at ld values of 141 60 ++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @18:40:51): Adding -NN_dset_map ./lh.aparc.a2009s.annot.niml.dset ** ** To view in SUMA, run: suma -spec std.141.sub-005_lh.spec ** ** ++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @18:41:40): Adding -NN_dset_map ./rh.aparc.a2009s.annot.niml.dset ** ** To view in SUMA, run: suma -spec std.141.sub-005_rh.spec ** ** ++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @18:42:28): Adding -NN_dset_map ./lh.aparc.a2009s.annot.niml.dset ** ** To view in SUMA, run: suma -spec std.60.sub-005_lh.spec ** ** ++ Notice MapIcosahedron (SUMA_MapIcosahedron.c:810 @18:42:41): Adding -NN_dset_map ./rh.aparc.a2009s.annot.niml.dset ** ** To view in SUMA, run: suma -spec std.60.sub-005_rh.spec ** ** ------------------------------------------------------------------ Please verify that the datasets are aligned properly in both afni and suma. You may do this by running the following commands: cd ./SUMA afni -niml & suma -spec sub-005_both.spec -sv sub-005_SurfVol.nii ++ Going to make renumbered ROIs now. --> done for colorbar and making tissue maps. See '@SUMA_renumber_FS -help' for description. ++ Running @SUMA_renumber_FS version: 1.6 ++ found ./aparc+aseg.nii ++ found ./aparc.a2009s+aseg.nii ++ Renumbering FS whole brain (./aparc+aseg.nii). ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_all.nii.gz ++ ... getting gm... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_gm.nii.gz ++ ... getting wmat... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_wmat.nii.gz ++ ... getting csf... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_csf.nii.gz ++ ... getting vent... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_vent.nii.gz ++ ... getting othr... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_othr.nii.gz ++ ... getting unkn... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_unkn.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./fs_ap_latvent.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./fs_ap_wm.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc+aseg_REN_gmrois.nii.gz ++ Running checks now. ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./__zarglefizz_070.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./__zarglefizz_071.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./__zarglefizz_072.nii.gz ++ Attaching labeltable to: aparc+aseg_REN_all.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_all.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_all.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_all.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_gm.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_gm.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_gm.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_gm.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_gmrois.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_gmrois.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_gmrois.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_gmrois.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_wmat.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_wmat.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_wmat.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_wmat.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_csf.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_csf.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_csf.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_csf.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_vent.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_vent.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_vent.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_vent.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_othr.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_othr.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_othr.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_othr.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc+aseg_REN_unkn.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc+aseg_REN_unkn.nii.gz + setting labeltable + loading and re-writing dataset aparc+aseg_REN_unkn.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc+aseg_REN_unkn.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ OK through '2000' dsets. ++ Renumbering FS whole brain (./aparc.a2009s+aseg.nii). ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_all.nii.gz ++ ... getting gm... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_gm.nii.gz ++ ... getting wmat... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_wmat.nii.gz ++ ... getting csf... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_csf.nii.gz ++ ... getting vent... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_vent.nii.gz ++ ... getting othr... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_othr.nii.gz ++ ... getting unkn... ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_unkn.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./aparc.a2009s+aseg_REN_gmrois.nii.gz ++ Running checks now. ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./__zarglefizz_070.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./__zarglefizz_071.nii.gz ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./__zarglefizz_072.nii.gz ++ Attaching labeltable to: aparc.a2009s+aseg_REN_all.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_all.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_all.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_all.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_gm.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_gm.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_gm.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_gm.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_gmrois.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_gmrois.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_gmrois.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_gmrois.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_wmat.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_wmat.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_wmat.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_wmat.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_csf.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_csf.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_csf.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_csf.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_vent.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_vent.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_vent.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_vent.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_othr.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_othr.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_othr.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_othr.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ Attaching labeltable to: aparc.a2009s+aseg_REN_unkn.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset aparc.a2009s+aseg_REN_unkn.nii.gz + setting labeltable + loading and re-writing dataset aparc.a2009s+aseg_REN_unkn.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/aparc.a2009s+aseg_REN_unkn.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ OK through '2009' dsets. ++ Going to make a nice WB mask. ... and some useful QC images. ... and some useful ROI info tables. ++ Prepare for running adjunct_suma_fs_mask_and_qc (ver = 0.33) ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./dset_tiss.nii.gz ++ 3drefit: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset dset_tiss.nii.gz + loading and re-writing dataset dset_tiss.nii.gz (/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/dset_tiss.nii.gz in NIFTI storage) ++ 3drefit processed 1 datasets ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ./dset_mask.nii.gz ++ no -frac option: defaulting to -union ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 2 (for dilations) ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 1808324 survived, 14968892 were zero ++ writing result mask1.nii.gz... ++ Output dataset ./mask1.nii.gz ++ no -frac option: defaulting to -union ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 1808324 survived, 14968892 were zero ++ filled 50 holes (1458 voxels) ++ writing result mask2.nii.gz... ++ Output dataset ./mask2.nii.gz ++ no -frac option: defaulting to -union ++ processing 1 input dataset(s), NN=2... ++ padding all datasets by 0 (for dilations) ++ frac 0 over 1 volumes gives min count 0 ++ voxel limits: 0 clipped, 1577538 survived, 15199678 were zero ++ writing result mask3.nii.gz... ++ Output dataset ./mask3.nii.gz ++ 3dcopy: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ olay_alpha has known value: Yes ++ My command: @chauffeur_afni -ulay ../sub-005_SurfVol.nii -olay dset_mask.nii.gz -box_focus_slices ../brainmask.nii -ulay_range 0% 98% -func_range 3 -cbar_ncolors 2 -cbar_topval -cbar 2=red 1=red .00066=none -pbar_posonly -thr_olay 1.0001 -olay_alpha Yes -olay_boxed Yes -opacity 4 -blowup 2 -prefix qc_00_fs_brainmask_sub-005 -montx 6 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean ++ Using AFNI ver : AFNI_21.3.01 ++ chauffeur ver : 6.29 ------------------ start of optionizing ------------------ ++ Found input file: ../sub-005_SurfVol.nii ++ Found input file: dset_mask.nii.gz ++ Found focus refbox file: ../brainmask.nii ++ Using blowup factor: 2 ++ Using opacity: 4 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_NGxDltu7K2X ++ Converted 0 to labels ++ Final subbrick indices: -1 -1 -1 ++ Copy ulay to visualize (volumetric) within user's range: ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 146.000000] ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_NGxDltu7K2X/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_NGxDltu7K2X/tmp_olay.nii ++ User-entered function range value value (3) ++ Dimensions (xyzt): 256 256 256 1 ++ (initial) Slice spacing ordered (x,y,z) is: 42 42 42 ++ 3dAutobox: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Auto bbox: x=58..204 y=58..195 z=45..237 ++ 3dAutobox: output dataset = ./__tmp_chauf_NGxDltu7K2X/ulay_box_0.nii ++ 3dmaskdump: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_NGxDltu7K2X/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_xW_uBjGnBTrWxIMGDR7Ohg argv[10]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ Output dataset /tmp/3dcalc_AFN_xW_uBjGnBTrWxIMGDR7Ohg+orig.BRIK ++ 3915198 voxels in the entire dataset (no mask) ++ 1 voxels in the boxes and/or balls ++ Using only the boxes+balls mask ++ How many coors? 3 ++ Will have the ref box central coors : SET_DICOM_XYZ -9.008209 -13.974 23.942 ++ Will have the ref box central gapord: 24 32 23 ------------------- end of optionizing ------------------- -- trying to start Xvfb :381 [1] 10026 +/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/__tmp_chauf_NGxDltu7K2X++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_00_fs_brainmask_sub-005.axi.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_00_fs_brainmask_sub-005.sag.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_00_fs_brainmask_sub-005.cor.png' AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=6x1:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=6x1:23:0:black crop=0:0,0:0 -com SET_PBAR_ALL +2 2=red 1=red .00066=none -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 146.000000 -com SET_FUNC_RANGE 3 -com SET_THRESHNEW 1.0001 * -com SET_FUNC_ALPHA Yes -com SET_FUNC_BOXED Yes -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -9.008209 -13.974 23.942 -com SAVE_PNG axialimage ./qc_00_fs_brainmask_sub-005.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_00_fs_brainmask_sub-005.sag blowup=2 -com SAVE_PNG coronalimage ./qc_00_fs_brainmask_sub-005.cor blowup=2 -com QUITT ./__tmp_chauf_NGxDltu7K2X +* Removing temporary image directory './__tmp_chauf_NGxDltu7K2X'. [1] + Done Xvfb :381 -screen 0 1024x768x24 ++ DONE (good exit) see: ./qc_00_fs_brainmask_sub-005* +++ Transforming all input to rgb for a good reason +++ Writing image to ../qc_00_fs_brainmask_sub-005.jpg +++ Arranging 3 images (each 3072x512) into a 1x3 matrix. You can view image ../qc_00_fs_brainmask_sub-005.jpg with: aiv ../qc_00_fs_brainmask_sub-005.jpg ++ My command: @chauffeur_afni -ulay ../sub-005_SurfVol.nii -olay ../fs_parc_wb_mask.nii.gz -box_focus_slices ../brainmask.nii -ulay_range 0% 98% -func_range 1 -cbar Reds_and_Blues_Inv -pbar_posonly -opacity 4 -blowup 2 -prefix qc_01_fs_parc_wb_mask_sub-005 -montx 6 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean ++ Using AFNI ver : AFNI_21.3.01 ++ chauffeur ver : 6.29 ------------------ start of optionizing ------------------ ++ Found input file: ../sub-005_SurfVol.nii ++ Found input file: ../fs_parc_wb_mask.nii.gz ++ Found focus refbox file: ../brainmask.nii ++ Using blowup factor: 2 ++ Using opacity: 4 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_IF6wriYoVcw ++ Converted 0 to labels ++ Final subbrick indices: -1 -1 -1 ++ Copy ulay to visualize (volumetric) within user's range: ++ Ulay to be visualized within user range: [0%, 98%] -> [0.000000, 146.000000] ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_IF6wriYoVcw/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_IF6wriYoVcw/tmp_olay.nii ++ User-entered function range value value (1) ++ Dimensions (xyzt): 256 256 256 1 ++ (initial) Slice spacing ordered (x,y,z) is: 42 42 42 ++ 3dAutobox: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Auto bbox: x=58..204 y=58..195 z=45..237 ++ 3dAutobox: output dataset = ./__tmp_chauf_IF6wriYoVcw/ulay_box_0.nii ++ 3dmaskdump: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_IF6wriYoVcw/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_z7Juv85Gld0FBc4tpNqX7w argv[10]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ Output dataset /tmp/3dcalc_AFN_z7Juv85Gld0FBc4tpNqX7w+orig.BRIK ++ 3915198 voxels in the entire dataset (no mask) ++ 1 voxels in the boxes and/or balls ++ Using only the boxes+balls mask ++ How many coors? 3 ++ Will have the ref box central coors : SET_DICOM_XYZ -9.008209 -13.974 23.942 ++ Will have the ref box central gapord: 24 32 23 ------------------- end of optionizing ------------------- -- trying to start Xvfb :285 [1] 10306 +/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/__tmp_chauf_IF6wriYoVcw++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_01_fs_parc_wb_mask_sub-005.axi.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_01_fs_parc_wb_mask_sub-005.sag.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_01_fs_parc_wb_mask_sub-005.cor.png' AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=6x1:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=6x1:23:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 146.000000 -com SET_FUNC_RANGE 1 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -9.008209 -13.974 23.942 -com SAVE_PNG axialimage ./qc_01_fs_parc_wb_mask_sub-005.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_01_fs_parc_wb_mask_sub-005.sag blowup=2 -com SAVE_PNG coronalimage ./qc_01_fs_parc_wb_mask_sub-005.cor blowup=2 -com QUITT ./__tmp_chauf_IF6wriYoVcw +* Removing temporary image directory './__tmp_chauf_IF6wriYoVcw'. [1] + Done Xvfb :285 -screen 0 1024x768x24 ++ DONE (good exit) see: ./qc_01_fs_parc_wb_mask_sub-005* +++ Transforming all input to rgb for a good reason +++ Writing image to ../qc_01_fs_parc_wb_mask_sub-005.jpg +++ Arranging 3 images (each 3072x512) into a 1x3 matrix. You can view image ../qc_01_fs_parc_wb_mask_sub-005.jpg with: aiv ../qc_01_fs_parc_wb_mask_sub-005.jpg ++ My command: @chauffeur_afni -ulay ../sub-005_SurfVol.nii -olay dset_tiss.nii.gz -box_focus_slices ../brainmask.nii -ulay_range 0% 110% -func_range 256 -cbar ROI_glasbey_256 FLIP -pbar_posonly -opacity 6 -blowup 2 -prefix qc_02_fs_tiss_sub-005 -montx 6 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean ++ Using AFNI ver : AFNI_21.3.01 ++ chauffeur ver : 6.29 ------------------ start of optionizing ------------------ ++ Found input file: ../sub-005_SurfVol.nii ++ Found input file: dset_tiss.nii.gz ++ Found focus refbox file: ../brainmask.nii ++ Using blowup factor: 2 ++ Using opacity: 6 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_Eb5pD58wrWp ++ Converted 0 to labels ++ Final subbrick indices: -1 -1 -1 ++ Copy ulay to visualize (volumetric) within user's range: ++ Ulay range calc for >100%ile ulay max: calculating 98%ile value, and then multiplying it by a scale factor = 1.12244, in order to produce the 98%ile value ++ Ulay to be visualized within user range: [0%, 110%] -> [0.000000, 163.876240] ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_Eb5pD58wrWp/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_Eb5pD58wrWp/tmp_olay.nii ++ User-entered function range value value (256) ++ Dimensions (xyzt): 256 256 256 1 ++ (initial) Slice spacing ordered (x,y,z) is: 42 42 42 ++ 3dAutobox: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Auto bbox: x=58..204 y=58..195 z=45..237 ++ 3dAutobox: output dataset = ./__tmp_chauf_Eb5pD58wrWp/ulay_box_0.nii ++ 3dmaskdump: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_Eb5pD58wrWp/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_37J7hZtPmbBqtanEb5KhdA argv[10]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ Output dataset /tmp/3dcalc_AFN_37J7hZtPmbBqtanEb5KhdA+orig.BRIK ++ 3915198 voxels in the entire dataset (no mask) ++ 1 voxels in the boxes and/or balls ++ Using only the boxes+balls mask ++ How many coors? 3 ++ Will have the ref box central coors : SET_DICOM_XYZ -9.008209 -13.974 23.942 ++ Will have the ref box central gapord: 24 32 23 ------------------- end of optionizing ------------------- -- trying to start Xvfb :545 [1] 10589 +/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/__tmp_chauf_Eb5pD58wrWp++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_02_fs_tiss_sub-005.axi.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_02_fs_tiss_sub-005.sag.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_02_fs_tiss_sub-005.cor.png' AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=6 mont=6x1:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=6x1:23:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 ROI_glasbey_256 FLIP -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 163.876240 -com SET_FUNC_RANGE 256 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -9.008209 -13.974 23.942 -com SAVE_PNG axialimage ./qc_02_fs_tiss_sub-005.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_02_fs_tiss_sub-005.sag blowup=2 -com SAVE_PNG coronalimage ./qc_02_fs_tiss_sub-005.cor blowup=2 -com QUITT ./__tmp_chauf_Eb5pD58wrWp +* Removing temporary image directory './__tmp_chauf_Eb5pD58wrWp'. [1] + Done Xvfb :545 -screen 0 1024x768x24 ++ DONE (good exit) see: ./qc_02_fs_tiss_sub-005* +++ Transforming all input to rgb for a good reason +++ Writing image to ../qc_02_fs_tiss_sub-005.jpg +++ Arranging 3 images (each 3072x512) into a 1x3 matrix. You can view image ../qc_02_fs_tiss_sub-005.jpg with: aiv ../qc_02_fs_tiss_sub-005.jpg ++ My command: @chauffeur_afni -ulay ../sub-005_SurfVol.nii -olay dset_tiss.nii.gz<2> -box_focus_slices ../brainmask.nii -ulay_range 0% 110% -func_range 256 -cbar ROI_glasbey_256 FLIP -pbar_posonly -opacity 6 -blowup 2 -prefix qc_03_fs_gm_sub-005 -montx 6 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean ++ Using AFNI ver : AFNI_21.3.01 ++ chauffeur ver : 6.29 ------------------ start of optionizing ------------------ ++ Found input file: ../sub-005_SurfVol.nii ++ Found input file: dset_tiss.nii.gz<2> ++ Found focus refbox file: ../brainmask.nii ++ Using blowup factor: 2 ++ Using opacity: 6 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_HzZxgt1701h ++ Converted 0 to labels ++ Final subbrick indices: -1 -1 -1 ++ Copy ulay to visualize (volumetric) within user's range: ++ Ulay range calc for >100%ile ulay max: calculating 98%ile value, and then multiplying it by a scale factor = 1.12244, in order to produce the 98%ile value ++ Ulay to be visualized within user range: [0%, 110%] -> [0.000000, 163.876240] ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_HzZxgt1701h/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_HzZxgt1701h/tmp_olay.nii ++ User-entered function range value value (256) ++ Dimensions (xyzt): 256 256 256 1 ++ (initial) Slice spacing ordered (x,y,z) is: 42 42 42 ++ 3dAutobox: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Auto bbox: x=58..204 y=58..195 z=45..237 ++ 3dAutobox: output dataset = ./__tmp_chauf_HzZxgt1701h/ulay_box_0.nii ++ 3dmaskdump: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_HzZxgt1701h/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_WzYsC-CGRUN8c96XoEIqIQ argv[10]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ Output dataset /tmp/3dcalc_AFN_WzYsC-CGRUN8c96XoEIqIQ+orig.BRIK ++ 3915198 voxels in the entire dataset (no mask) ++ 1 voxels in the boxes and/or balls ++ Using only the boxes+balls mask ++ How many coors? 3 ++ Will have the ref box central coors : SET_DICOM_XYZ -9.008209 -13.974 23.942 ++ Will have the ref box central gapord: 24 32 23 ------------------- end of optionizing ------------------- -- trying to start Xvfb :141 [1] 10872 +/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/__tmp_chauf_HzZxgt1701h++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_03_fs_gm_sub-005.axi.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_03_fs_gm_sub-005.sag.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_03_fs_gm_sub-005.cor.png' AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=6 mont=6x1:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=6x1:23:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 ROI_glasbey_256 FLIP -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 163.876240 -com SET_FUNC_RANGE 256 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -9.008209 -13.974 23.942 -com SAVE_PNG axialimage ./qc_03_fs_gm_sub-005.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_03_fs_gm_sub-005.sag blowup=2 -com SAVE_PNG coronalimage ./qc_03_fs_gm_sub-005.cor blowup=2 -com QUITT ./__tmp_chauf_HzZxgt1701h +* Removing temporary image directory './__tmp_chauf_HzZxgt1701h'. [1] + Done Xvfb :141 -screen 0 1024x768x24 ++ DONE (good exit) see: ./qc_03_fs_gm_sub-005* +++ Transforming all input to rgb for a good reason +++ Writing image to ../qc_03_fs_gm_sub-005.jpg +++ Arranging 3 images (each 3072x512) into a 1x3 matrix. You can view image ../qc_03_fs_gm_sub-005.jpg with: aiv ../qc_03_fs_gm_sub-005.jpg ++ My command: @chauffeur_afni -ulay ../sub-005_SurfVol.nii -olay dset_tiss.nii.gz<1> -box_focus_slices ../brainmask.nii -ulay_range 0% 110% -func_range 256 -cbar ROI_glasbey_256 FLIP -pbar_posonly -opacity 6 -blowup 2 -prefix qc_04_fs_wm_sub-005 -montx 6 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean ++ Using AFNI ver : AFNI_21.3.01 ++ chauffeur ver : 6.29 ------------------ start of optionizing ------------------ ++ Found input file: ../sub-005_SurfVol.nii ++ Found input file: dset_tiss.nii.gz<1> ++ Found focus refbox file: ../brainmask.nii ++ Using blowup factor: 2 ++ Using opacity: 6 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_3EAknXJYZ89 ++ Converted 0 to labels ++ Final subbrick indices: -1 -1 -1 ++ Copy ulay to visualize (volumetric) within user's range: ++ Ulay range calc for >100%ile ulay max: calculating 98%ile value, and then multiplying it by a scale factor = 1.12244, in order to produce the 98%ile value ++ Ulay to be visualized within user range: [0%, 110%] -> [0.000000, 163.876240] ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_3EAknXJYZ89/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_3EAknXJYZ89/tmp_olay.nii ++ User-entered function range value value (256) ++ Dimensions (xyzt): 256 256 256 1 ++ (initial) Slice spacing ordered (x,y,z) is: 42 42 42 ++ 3dAutobox: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Auto bbox: x=58..204 y=58..195 z=45..237 ++ 3dAutobox: output dataset = ./__tmp_chauf_3EAknXJYZ89/ulay_box_0.nii ++ 3dmaskdump: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_3EAknXJYZ89/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_DxqYP_ZEs5zOL3lM7OHBLg argv[10]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ Output dataset /tmp/3dcalc_AFN_DxqYP_ZEs5zOL3lM7OHBLg+orig.BRIK ++ 3915198 voxels in the entire dataset (no mask) ++ 1 voxels in the boxes and/or balls ++ Using only the boxes+balls mask ++ How many coors? 3 ++ Will have the ref box central coors : SET_DICOM_XYZ -9.008209 -13.974 23.942 ++ Will have the ref box central gapord: 24 32 23 ------------------- end of optionizing ------------------- -- trying to start Xvfb :143 [1] 11156 +/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/__tmp_chauf_3EAknXJYZ89++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_04_fs_wm_sub-005.axi.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_04_fs_wm_sub-005.sag.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_04_fs_wm_sub-005.cor.png' AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=6 mont=6x1:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=6 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=6 mont=6x1:23:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 ROI_glasbey_256 FLIP -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 163.876240 -com SET_FUNC_RANGE 256 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -9.008209 -13.974 23.942 -com SAVE_PNG axialimage ./qc_04_fs_wm_sub-005.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_04_fs_wm_sub-005.sag blowup=2 -com SAVE_PNG coronalimage ./qc_04_fs_wm_sub-005.cor blowup=2 -com QUITT ./__tmp_chauf_3EAknXJYZ89 +* Removing temporary image directory './__tmp_chauf_3EAknXJYZ89'. [1] + Done Xvfb :143 -screen 0 1024x768x24 ++ DONE (good exit) see: ./qc_04_fs_wm_sub-005* +++ Transforming all input to rgb for a good reason +++ Writing image to ../qc_04_fs_wm_sub-005.jpg +++ Arranging 3 images (each 3072x512) into a 1x3 matrix. You can view image ../qc_04_fs_wm_sub-005.jpg with: aiv ../qc_04_fs_wm_sub-005.jpg ++ My command: @chauffeur_afni -ulay ../sub-005_SurfVol.nii -olay ../aparc+aseg_REN_all.nii.gz -box_focus_slices ../brainmask.nii -ulay_range 0% 110% -func_range 256 -cbar ROI_i256 -pbar_posonly -opacity 4 -blowup 2 -prefix qc_05_fs_aa_REN_all_sub-005 -montx 6 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 4 -do_clean ++ Using AFNI ver : AFNI_21.3.01 ++ chauffeur ver : 6.29 ------------------ start of optionizing ------------------ ++ Found input file: ../sub-005_SurfVol.nii ++ Found input file: ../aparc+aseg_REN_all.nii.gz ++ Found focus refbox file: ../brainmask.nii ++ Using blowup factor: 2 ++ Using opacity: 4 ++ Making temporary work directory to copy vis files: ./__tmp_chauf_xHIfiNByKef ++ Converted 0 to labels ++ Final subbrick indices: -1 -1 -1 ++ Copy ulay to visualize (volumetric) within user's range: ++ Ulay range calc for >100%ile ulay max: calculating 98%ile value, and then multiplying it by a scale factor = 1.12244, in order to produce the 98%ile value ++ Ulay to be visualized within user range: [0%, 110%] -> [0.000000, 163.876240] ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_xHIfiNByKef/tmp_ulay.nii ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Output dataset ././__tmp_chauf_xHIfiNByKef/tmp_olay.nii ++ User-entered function range value value (256) ++ Dimensions (xyzt): 256 256 256 1 ++ (initial) Slice spacing ordered (x,y,z) is: 42 42 42 ++ 3dAutobox: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Auto bbox: x=58..204 y=58..195 z=45..237 ++ 3dAutobox: output dataset = ./__tmp_chauf_xHIfiNByKef/ulay_box_0.nii ++ 3dmaskdump: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=./__tmp_chauf_xHIfiNByKef/ulay_box_0.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/tmp argv[8]=-prefix argv[9]=3dcalc_AFN_N9Jk6FraA2j6MwgWEP4G2A argv[10]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ Output dataset /tmp/3dcalc_AFN_N9Jk6FraA2j6MwgWEP4G2A+orig.BRIK ++ 3915198 voxels in the entire dataset (no mask) ++ 1 voxels in the boxes and/or balls ++ Using only the boxes+balls mask ++ How many coors? 3 ++ Will have the ref box central coors : SET_DICOM_XYZ -9.008209 -13.974 23.942 ++ Will have the ref box central gapord: 24 32 23 ------------------- end of optionizing ------------------- -- trying to start Xvfb :841 [1] 11645 +/lscratch/25105636/sub-005_ses-01/SUMA/__workdir_fs_qc_3t8MW75hmEk/__tmp_chauf_xHIfiNByKef++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_05_fs_aa_REN_all_sub-005.axi.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_05_fs_aa_REN_all_sub-005.sag.png' ++ Writing one 3072x512 image to filter '/usr/bin/pnmtopng -compression 9 > ./qc_05_fs_aa_REN_all_sub-005.cor.png' AFNI QUITTs! +++ Command Echo: afni -q -no1D -noplugins -no_detach -com SWITCH_UNDERLAY tmp_ulay.nii -com SWITCH_OVERLAY tmp_olay.nii -com SEE_OVERLAY + -com OPEN_WINDOW sagittalimage opacity=4 mont=6x1:24:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=6x1:32:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=6x1:23:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 1 ROI_i256 -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 163.876240 -com SET_FUNC_RANGE 256 -com SET_THRESHNEW 0 * -com SET_FUNC_ALPHA No -com SET_FUNC_BOXED No -com SET_FUNC_RESAM NN.NN -com SET_XHAIRS OFF -com SET_XHAIR_GAP -1 -com SET_DICOM_XYZ -9.008209 -13.974 23.942 -com SAVE_PNG axialimage ./qc_05_fs_aa_REN_all_sub-005.axi blowup=2 -com SAVE_PNG sagittalimage ./qc_05_fs_aa_REN_all_sub-005.sag blowup=2 -com SAVE_PNG coronalimage ./qc_05_fs_aa_REN_all_sub-005.cor blowup=2 -com QUITT ./__tmp_chauf_xHIfiNByKef +* Removing temporary image directory './__tmp_chauf_xHIfiNByKef'. [1] + Done Xvfb :841 -screen 0 1024x768x24 ++ DONE (good exit) see: ./qc_05_fs_aa_REN_all_sub-005* +++ Transforming all input to rgb for a good reason +++ Writing image to ../qc_05_fs_aa_REN_all_sub-005.jpg +++ Arranging 3 images (each 3072x512) into a 1x3 matrix. You can view image ../qc_05_fs_aa_REN_all_sub-005.jpg with: aiv ../qc_05_fs_aa_REN_all_sub-005.jpg ++ Cleanup ++ Prepare for running adjunct_suma_fs_roi_info (ver = 0.3) ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=brainmask.nii argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_xUYvhhcUa_WTwHrR87FKUg argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Scaling output to type byte brick(s) ++ Sub-brick 0: no scale factor ++ Computing output statistics ++ ------------- Process afni_fs_aparc+aseg_2000.txt --------------- # Nvox FR_BR_MASK FR_PARC_MASK FR_ALL_ROI # SEG__TYPE FILE_NAME ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_all.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_fCMJamAB56eEaRSVYyocGA argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 1839642 1.000000 1.166148 1.280548 # br_mask brainmask.nii 1577538 0.857524 1.000000 1.098101 # parc_mask fs_parc_wb_mask.nii.gz 1436605 0.780916 0.910663 1.000000 # all aparc+aseg_REN_all.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_gm.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_rv7s0boHs0l5iAr_uwz2fQ argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 851306 0.462756 0.539642 0.592582 # gm aparc+aseg_REN_gm.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_gmrois.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_gQURjkD3JTf7JmDuQvQosA argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 851306 0.462756 0.539642 0.592582 # gmrois aparc+aseg_REN_gmrois.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_wmat.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_sG-FbBVepMVwtKcZk2ujuQ argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 562510 0.305771 0.356575 0.391555 # wmat aparc+aseg_REN_wmat.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_vent.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_8qYz1EXiQJpZO0nfGZPVnw argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 21287 0.011571 0.013494 0.014817 # vent aparc+aseg_REN_vent.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_csf.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_19hWFN9R3dRTsvKyoIS9Aw argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 1266 0.000688 0.000803 0.000881 # csf aparc+aseg_REN_csf.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_othr.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_09dh7Iqesbg1zU-Hs8RXzA argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 236 0.000128 0.000150 0.000164 # othr aparc+aseg_REN_othr.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc+aseg_REN_unkn.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_T4UUWzkjGghZXKE2_6H8Ng argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 0 0.000000 0.000000 0.000000 # unkn aparc+aseg_REN_unkn.nii.gz ++ Start counting the ROIs. # Nvox FR_BR_MASK FR_PARC_MASK FR_ALL_ROI # VAL TISS__TYPE STRING_LABEL 0 0.000000 0.000000 0.000000 # 0 tiss__unkn Unknown 264141 0.143583 0.167439 0.183865 # 1 tiss__wmat Left-Cerebral-White-Matter 0 0.000000 0.000000 0.000000 # 2 tiss__gm Left-Cerebral-Cortex 8400 0.004566 0.005325 0.005847 # 3 tiss__vent Left-Lateral-Ventricle 503 0.000273 0.000319 0.000350 # 4 tiss__vent Left-Inf-Lat-Vent 13869 0.007539 0.008791 0.009654 # 5 tiss__wmat Left-Cerebellum-White-Matter 60332 0.032795 0.038244 0.041996 # 6 tiss__gm Left-Cerebellum-Cortex 8614 0.004682 0.005460 0.005996 # 7 tiss__gm Left-Thalamus-Proper 4172 0.002268 0.002645 0.002904 # 8 tiss__gm Left-Caudate 6874 0.003737 0.004357 0.004785 # 9 tiss__gm Left-Putamen 1975 0.001074 0.001252 0.001375 # 10 tiss__gm Left-Pallidum 8400 0.004566 0.005325 0.005847 # 11 tiss__vent 3rd-Ventricle 503 0.000273 0.000319 0.000350 # 12 tiss__vent 4th-Ventricle 21863 0.011884 0.013859 0.015218 # 13 tiss__gm Brain-Stem 4464 0.002426 0.002830 0.003107 # 14 tiss__gm Left-Hippocampus 1612 0.000876 0.001022 0.001122 # 15 tiss__gm Left-Amygdala 1266 0.000688 0.000803 0.000881 # 16 tiss__csf CSF 875 0.000476 0.000555 0.000609 # 17 tiss__gm Left-Accumbens-area 4043 0.002198 0.002563 0.002814 # 18 tiss__gm Left-VentralDC 34 0.000018 0.000021 0.000024 # 19 tiss__othr Left-vessel 443 0.000241 0.000281 0.000308 # 20 tiss__vent Left-choroid-plexus 264867 0.143977 0.167899 0.184370 # 21 tiss__wmat Right-Cerebral-White-Matter 0 0.000000 0.000000 0.000000 # 22 tiss__gm Right-Cerebral-Cortex 6790 0.003691 0.004304 0.004726 # 23 tiss__vent Right-Lateral-Ventricle 726 0.000395 0.000460 0.000505 # 24 tiss__vent Right-Inf-Lat-Vent 13557 0.007369 0.008594 0.009437 # 25 tiss__wmat Right-Cerebellum-White-Matter 59968 0.032598 0.038014 0.041743 # 26 tiss__gm Right-Cerebellum-Cortex 8584 0.004666 0.005441 0.005975 # 27 tiss__gm Right-Thalamus-Proper 4505 0.002449 0.002856 0.003136 # 28 tiss__gm Right-Caudate 6573 0.003573 0.004167 0.004575 # 29 tiss__gm Right-Putamen 1894 0.001029 0.001201 0.001318 # 30 tiss__gm Right-Pallidum 4318 0.002347 0.002737 0.003006 # 31 tiss__gm Right-Hippocampus 1924 0.001046 0.001220 0.001339 # 32 tiss__gm Right-Amygdala 735 0.000400 0.000466 0.000512 # 33 tiss__gm Right-Accumbens-area 3994 0.002171 0.002532 0.002780 # 34 tiss__gm Right-VentralDC 29 0.000016 0.000018 0.000020 # 35 tiss__othr Right-vessel 423 0.000230 0.000268 0.000294 # 36 tiss__vent Right-choroid-plexus 13869 0.007539 0.008791 0.009654 # 37 tiss__vent 5th-Ventricle 2990 0.001625 0.001895 0.002081 # 38 tiss__wmat WM-hypointensities 0 0.000000 0.000000 0.000000 # 39 tiss__othr non-WM-hypointensities 173 0.000094 0.000110 0.000120 # 40 tiss__othr Optic-Chiasm 976 0.000530 0.000619 0.000679 # 41 tiss__wmat CC_Posterior 494 0.000268 0.000313 0.000344 # 42 tiss__wmat CC_Mid_Posterior 392 0.000213 0.000248 0.000273 # 43 tiss__wmat CC_Central 509 0.000277 0.000323 0.000354 # 44 tiss__wmat CC_Mid_Anterior 715 0.000389 0.000453 0.000498 # 45 tiss__wmat CC_Anterior 0 0.000000 0.000000 0.000000 # 46 tiss__unkn ctx-lh-unknown 3184 0.001731 0.002018 0.002216 # 47 tiss__gm ctx-lh-bankssts 2495 0.001356 0.001582 0.001737 # 48 tiss__gm ctx-lh-caudalanteriorcingulate 10066 0.005472 0.006381 0.007007 # 49 tiss__gm ctx-lh-caudalmiddlefrontal 4439 0.002413 0.002814 0.003090 # 50 tiss__gm ctx-lh-cuneus 1292 0.000702 0.000819 0.000899 # 51 tiss__gm ctx-lh-entorhinal 12109 0.006582 0.007676 0.008429 # 52 tiss__gm ctx-lh-fusiform 16029 0.008713 0.010161 0.011158 # 53 tiss__gm ctx-lh-inferiorparietal 14176 0.007706 0.008986 0.009868 # 54 tiss__gm ctx-lh-inferiortemporal 3274 0.001780 0.002075 0.002279 # 55 tiss__gm ctx-lh-isthmuscingulate 20130 0.010942 0.012760 0.014012 # 56 tiss__gm ctx-lh-lateraloccipital 10345 0.005623 0.006558 0.007201 # 57 tiss__gm ctx-lh-lateralorbitofrontal 9045 0.004917 0.005734 0.006296 # 58 tiss__gm ctx-lh-lingual 6747 0.003667 0.004277 0.004696 # 59 tiss__gm ctx-lh-medialorbitofrontal 13906 0.007559 0.008815 0.009680 # 60 tiss__gm ctx-lh-middletemporal 2539 0.001380 0.001609 0.001767 # 61 tiss__gm ctx-lh-parahippocampal 5613 0.003051 0.003558 0.003907 # 62 tiss__gm ctx-lh-paracentral 7453 0.004051 0.004724 0.005188 # 63 tiss__gm ctx-lh-parsopercularis 2974 0.001617 0.001885 0.002070 # 64 tiss__gm ctx-lh-parsorbitalis 6272 0.003409 0.003976 0.004366 # 65 tiss__gm ctx-lh-parstriangularis 3213 0.001746 0.002037 0.002236 # 66 tiss__gm ctx-lh-pericalcarine 12799 0.006957 0.008113 0.008909 # 67 tiss__gm ctx-lh-postcentral 3921 0.002131 0.002486 0.002729 # 68 tiss__gm ctx-lh-posteriorcingulate 19826 0.010777 0.012568 0.013801 # 69 tiss__gm ctx-lh-precentral 12707 0.006907 0.008055 0.008845 # 70 tiss__gm ctx-lh-precuneus 3694 0.002008 0.002342 0.002571 # 71 tiss__gm ctx-lh-rostralanteriorcingulate 21862 0.011884 0.013858 0.015218 # 72 tiss__gm ctx-lh-rostralmiddlefrontal 34585 0.018800 0.021923 0.024074 # 73 tiss__gm ctx-lh-superiorfrontal 16554 0.008998 0.010493 0.011523 # 74 tiss__gm ctx-lh-superiorparietal 15842 0.008611 0.010042 0.011027 # 75 tiss__gm ctx-lh-superiortemporal 10892 0.005921 0.006904 0.007582 # 76 tiss__gm ctx-lh-supramarginal 1137 0.000618 0.000721 0.000791 # 77 tiss__gm ctx-lh-frontalpole 2783 0.001513 0.001764 0.001937 # 78 tiss__gm ctx-lh-temporalpole 1432 0.000778 0.000908 0.000997 # 79 tiss__gm ctx-lh-transversetemporal 8100 0.004403 0.005135 0.005638 # 80 tiss__gm ctx-lh-insula 0 0.000000 0.000000 0.000000 # 81 tiss__unkn ctx-rh-unknown 3073 0.001670 0.001948 0.002139 # 82 tiss__gm ctx-rh-bankssts 2634 0.001432 0.001670 0.001833 # 83 tiss__gm ctx-rh-caudalanteriorcingulate 11141 0.006056 0.007062 0.007755 # 84 tiss__gm ctx-rh-caudalmiddlefrontal 3933 0.002138 0.002493 0.002738 # 85 tiss__gm ctx-rh-cuneus 1371 0.000745 0.000869 0.000954 # 86 tiss__gm ctx-rh-entorhinal 11965 0.006504 0.007585 0.008329 # 87 tiss__gm ctx-rh-fusiform 19973 0.010857 0.012661 0.013903 # 88 tiss__gm ctx-rh-inferiorparietal 12919 0.007023 0.008189 0.008993 # 89 tiss__gm ctx-rh-inferiortemporal 2884 0.001568 0.001828 0.002007 # 90 tiss__gm ctx-rh-isthmuscingulate 18464 0.010037 0.011704 0.012852 # 91 tiss__gm ctx-rh-lateraloccipital 11183 0.006079 0.007089 0.007784 # 92 tiss__gm ctx-rh-lateralorbitofrontal 8588 0.004668 0.005444 0.005978 # 93 tiss__gm ctx-rh-lingual 7483 0.004068 0.004743 0.005209 # 94 tiss__gm ctx-rh-medialorbitofrontal 16374 0.008901 0.010379 0.011398 # 95 tiss__gm ctx-rh-middletemporal 1859 0.001011 0.001178 0.001294 # 96 tiss__gm ctx-rh-parahippocampal 5282 0.002871 0.003348 0.003677 # 97 tiss__gm ctx-rh-paracentral 6157 0.003347 0.003903 0.004286 # 98 tiss__gm ctx-rh-parsopercularis 4314 0.002345 0.002735 0.003003 # 99 tiss__gm ctx-rh-parsorbitalis 8026 0.004363 0.005088 0.005587 # 100 tiss__gm ctx-rh-parstriangularis 3159 0.001717 0.002002 0.002199 # 101 tiss__gm ctx-rh-pericalcarine 13223 0.007188 0.008382 0.009204 # 102 tiss__gm ctx-rh-postcentral 4240 0.002305 0.002688 0.002951 # 103 tiss__gm ctx-rh-posteriorcingulate 19583 0.010645 0.012414 0.013631 # 104 tiss__gm ctx-rh-precentral 11762 0.006394 0.007456 0.008187 # 105 tiss__gm ctx-rh-precuneus 2976 0.001618 0.001886 0.002071 # 106 tiss__gm ctx-rh-rostralanteriorcingulate 21638 0.011762 0.013716 0.015062 # 107 tiss__gm ctx-rh-rostralmiddlefrontal 31392 0.017064 0.019899 0.021851 # 108 tiss__gm ctx-rh-superiorfrontal 15801 0.008589 0.010016 0.010999 # 109 tiss__gm ctx-rh-superiorparietal 16164 0.008786 0.010246 0.011251 # 110 tiss__gm ctx-rh-superiortemporal 11625 0.006319 0.007369 0.008092 # 111 tiss__gm ctx-rh-supramarginal 1440 0.000783 0.000913 0.001002 # 112 tiss__gm ctx-rh-frontalpole 2384 0.001296 0.001511 0.001659 # 113 tiss__gm ctx-rh-temporalpole 1189 0.000646 0.000754 0.000828 # 114 tiss__gm ctx-rh-transversetemporal 8353 0.004540 0.005295 0.005814 # 115 tiss__gm ctx-rh-insula 0 0.000000 0.000000 0.000000 # 220 tiss__unkn Left-undetermined 0 0.000000 0.000000 0.000000 # 221 tiss__unkn Right-undetermined ++ Done making: stats_fs_rois_2000_sub-005.1D ++ ------------- Process afni_fs_aparc+aseg_2009.txt --------------- # Nvox FR_BR_MASK FR_PARC_MASK FR_ALL_ROI # SEG__TYPE FILE_NAME ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_all.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN__oA7b7z4ZgdrInjDTG9RTw argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 1839642 1.000000 1.166148 1.280548 # br_mask brainmask.nii 1577538 0.857524 1.000000 1.098101 # parc_mask fs_parc_wb_mask.nii.gz 1436605 0.780916 0.910663 1.000000 # all aparc.a2009s+aseg_REN_all.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_gm.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_46osoQjvbya4K73TK9fWfw argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 851306 0.462756 0.539642 0.592582 # gm aparc.a2009s+aseg_REN_gm.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_gmrois.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_67aQxWC1RAVVNlbRjHs6VQ argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 851306 0.462756 0.539642 0.592582 # gmrois aparc.a2009s+aseg_REN_gmrois.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_wmat.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_aK4rILqTbQ6ox3rFhr1CDw argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 562510 0.305771 0.356575 0.391555 # wmat aparc.a2009s+aseg_REN_wmat.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_vent.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_7c9N4J584J3OYedJwXQzyg argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 21287 0.011571 0.013494 0.014817 # vent aparc.a2009s+aseg_REN_vent.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_csf.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_p638t-HLTVSarKaEjZr2hw argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 1266 0.000688 0.000803 0.000881 # csf aparc.a2009s+aseg_REN_csf.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_othr.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_pOK1vUKDCTz2kwUTXZHPqg argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 236 0.000128 0.000150 0.000164 # othr aparc.a2009s+aseg_REN_othr.nii.gz ++ Executing 3dcalc() argv[0]=3dcalc argv[1]=-a argv[2]=aparc.a2009s+aseg_REN_unkn.nii.gz argv[3]=-expr argv[4]=step(a) argv[5]=-session argv[6]=/tmp argv[7]=-prefix argv[8]=3dcalc_AFN_SSf-bCXPxpf2qdBDj9bYJA argv[9]=-verbose ++ 3dcalc: AFNI version=AFNI_21.3.01 (Oct 12 2021) [64-bit] ++ Authored by: A cast of thousands ++ Computing sub-brick 0 ++ Computing output statistics 0 0.000000 0.000000 0.000000 # unkn aparc.a2009s+aseg_REN_unkn.nii.gz ++ Start counting the ROIs. # Nvox FR_BR_MASK FR_PARC_MASK FR_ALL_ROI # VAL TISS__TYPE STRING_LABEL 0 0.000000 0.000000 0.000000 # 0 tiss__unkn Unknown 264141 0.143583 0.167439 0.183865 # 1 tiss__wmat Left-Cerebral-White-Matter 0 0.000000 0.000000 0.000000 # 2 tiss__gm Left-Cerebral-Cortex 8400 0.004566 0.005325 0.005847 # 3 tiss__vent Left-Lateral-Ventricle 503 0.000273 0.000319 0.000350 # 4 tiss__vent Left-Inf-Lat-Vent 13869 0.007539 0.008791 0.009654 # 5 tiss__wmat Left-Cerebellum-White-Matter 60332 0.032795 0.038244 0.041996 # 6 tiss__gm Left-Cerebellum-Cortex 8614 0.004682 0.005460 0.005996 # 7 tiss__gm Left-Thalamus-Proper 4172 0.002268 0.002645 0.002904 # 8 tiss__gm Left-Caudate 6874 0.003737 0.004357 0.004785 # 9 tiss__gm Left-Putamen 1975 0.001074 0.001252 0.001375 # 10 tiss__gm Left-Pallidum 8400 0.004566 0.005325 0.005847 # 11 tiss__vent 3rd-Ventricle 503 0.000273 0.000319 0.000350 # 12 tiss__vent 4th-Ventricle 21863 0.011884 0.013859 0.015218 # 13 tiss__gm Brain-Stem 4464 0.002426 0.002830 0.003107 # 14 tiss__gm Left-Hippocampus 1612 0.000876 0.001022 0.001122 # 15 tiss__gm Left-Amygdala 1266 0.000688 0.000803 0.000881 # 16 tiss__csf CSF 875 0.000476 0.000555 0.000609 # 17 tiss__gm Left-Accumbens-area 4043 0.002198 0.002563 0.002814 # 18 tiss__gm Left-VentralDC 34 0.000018 0.000021 0.000024 # 19 tiss__othr Left-vessel 443 0.000241 0.000281 0.000308 # 20 tiss__vent Left-choroid-plexus 264867 0.143977 0.167899 0.184370 # 21 tiss__wmat Right-Cerebral-White-Matter 0 0.000000 0.000000 0.000000 # 22 tiss__gm Right-Cerebral-Cortex 6790 0.003691 0.004304 0.004726 # 23 tiss__vent Right-Lateral-Ventricle 726 0.000395 0.000460 0.000505 # 24 tiss__vent Right-Inf-Lat-Vent 13557 0.007369 0.008594 0.009437 # 25 tiss__wmat Right-Cerebellum-White-Matter 59968 0.032598 0.038014 0.041743 # 26 tiss__gm Right-Cerebellum-Cortex 8584 0.004666 0.005441 0.005975 # 27 tiss__gm Right-Thalamus-Proper 4505 0.002449 0.002856 0.003136 # 28 tiss__gm Right-Caudate 6573 0.003573 0.004167 0.004575 # 29 tiss__gm Right-Putamen 1894 0.001029 0.001201 0.001318 # 30 tiss__gm Right-Pallidum 4318 0.002347 0.002737 0.003006 # 31 tiss__gm Right-Hippocampus 1924 0.001046 0.001220 0.001339 # 32 tiss__gm Right-Amygdala 735 0.000400 0.000466 0.000512 # 33 tiss__gm Right-Accumbens-area 3994 0.002171 0.002532 0.002780 # 34 tiss__gm Right-VentralDC 29 0.000016 0.000018 0.000020 # 35 tiss__othr Right-vessel 423 0.000230 0.000268 0.000294 # 36 tiss__vent Right-choroid-plexus 13869 0.007539 0.008791 0.009654 # 37 tiss__vent 5th-Ventricle 2990 0.001625 0.001895 0.002081 # 38 tiss__wmat WM-hypointensities 0 0.000000 0.000000 0.000000 # 39 tiss__othr non-WM-hypointensities 173 0.000094 0.000110 0.000120 # 40 tiss__othr Optic-Chiasm 976 0.000530 0.000619 0.000679 # 41 tiss__wmat CC_Posterior 494 0.000268 0.000313 0.000344 # 42 tiss__wmat CC_Mid_Posterior 392 0.000213 0.000248 0.000273 # 43 tiss__wmat CC_Central 509 0.000277 0.000323 0.000354 # 44 tiss__wmat CC_Mid_Anterior 715 0.000389 0.000453 0.000498 # 45 tiss__wmat CC_Anterior 0 0.000000 0.000000 0.000000 # 46 tiss__unkn ctx-lh-unknown 0 0.000000 0.000000 0.000000 # 47 tiss__unkn ctx-rh-unknown 0 0.000000 0.000000 0.000000 # 48 tiss__unkn ctx_lh_Unknown 2789 0.001516 0.001768 0.001941 # 49 tiss__gm ctx_lh_G_and_S_frontomargin 4821 0.002621 0.003056 0.003356 # 50 tiss__gm ctx_lh_G_and_S_occipital_inf 4381 0.002381 0.002777 0.003049 # 51 tiss__gm ctx_lh_G_and_S_paracentral 4057 0.002205 0.002572 0.002824 # 52 tiss__gm ctx_lh_G_and_S_subcentral 2454 0.001334 0.001556 0.001708 # 53 tiss__gm ctx_lh_G_and_S_transv_frontopol 5894 0.003204 0.003736 0.004103 # 54 tiss__gm ctx_lh_G_and_S_cingul-Ant 3475 0.001889 0.002203 0.002419 # 55 tiss__gm ctx_lh_G_and_S_cingul-Mid-Ant 3229 0.001755 0.002047 0.002248 # 56 tiss__gm ctx_lh_G_and_S_cingul-Mid-Post 1947 0.001058 0.001234 0.001355 # 57 tiss__gm ctx_lh_G_cingul-Post-dorsal 1160 0.000631 0.000735 0.000807 # 58 tiss__gm ctx_lh_G_cingul-Post-ventral 4795 0.002606 0.003039 0.003338 # 59 tiss__gm ctx_lh_G_cuneus 4986 0.002710 0.003161 0.003471 # 60 tiss__gm ctx_lh_G_front_inf-Opercular 1759 0.000956 0.001115 0.001224 # 61 tiss__gm ctx_lh_G_front_inf-Orbital 4966 0.002699 0.003148 0.003457 # 62 tiss__gm ctx_lh_G_front_inf-Triangul 15729 0.008550 0.009971 0.010949 # 63 tiss__gm ctx_lh_G_front_middle 27716 0.015066 0.017569 0.019293 # 64 tiss__gm ctx_lh_G_front_sup 1828 0.000994 0.001159 0.001272 # 65 tiss__gm ctx_lh_G_Ins_lg_and_S_cent_ins 3190 0.001734 0.002022 0.002220 # 66 tiss__gm ctx_lh_G_insular_short 7802 0.004241 0.004946 0.005431 # 67 tiss__gm ctx_lh_G_occipital_middle 3884 0.002111 0.002462 0.002703 # 68 tiss__gm ctx_lh_G_occipital_sup 5844 0.003177 0.003704 0.004068 # 69 tiss__gm ctx_lh_G_oc-temp_lat-fusifor 6682 0.003632 0.004236 0.004651 # 70 tiss__gm ctx_lh_G_oc-temp_med-Lingual 4091 0.002224 0.002593 0.002848 # 71 tiss__gm ctx_lh_G_oc-temp_med-Parahip 7499 0.004076 0.004754 0.005220 # 72 tiss__gm ctx_lh_G_orbital 7067 0.003841 0.004480 0.004919 # 73 tiss__gm ctx_lh_G_pariet_inf-Angular 6529 0.003549 0.004139 0.004545 # 74 tiss__gm ctx_lh_G_pariet_inf-Supramar 7017 0.003814 0.004448 0.004884 # 75 tiss__gm ctx_lh_G_parietal_sup 5825 0.003166 0.003692 0.004055 # 76 tiss__gm ctx_lh_G_postcentral 9640 0.005240 0.006111 0.006710 # 77 tiss__gm ctx_lh_G_precentral 7585 0.004123 0.004808 0.005280 # 78 tiss__gm ctx_lh_G_precuneus 2572 0.001398 0.001630 0.001790 # 79 tiss__gm ctx_lh_G_rectus 2116 0.001150 0.001341 0.001473 # 80 tiss__gm ctx_lh_G_subcallosal 1237 0.000672 0.000784 0.000861 # 81 tiss__gm ctx_lh_G_temp_sup-G_T_transv 7669 0.004169 0.004861 0.005338 # 82 tiss__gm ctx_lh_G_temp_sup-Lateral 2239 0.001217 0.001419 0.001558 # 83 tiss__gm ctx_lh_G_temp_sup-Plan_polar 2210 0.001201 0.001401 0.001538 # 84 tiss__gm ctx_lh_G_temp_sup-Plan_tempo 9403 0.005111 0.005960 0.006545 # 85 tiss__gm ctx_lh_G_temporal_inf 9167 0.004983 0.005811 0.006381 # 86 tiss__gm ctx_lh_G_temporal_middle 581 0.000316 0.000368 0.000404 # 87 tiss__gm ctx_lh_Lat_Fis-ant-Horizont 810 0.000440 0.000513 0.000564 # 88 tiss__gm ctx_lh_Lat_Fis-ant-Vertical 1288 0.000700 0.000816 0.000896 # 89 tiss__gm ctx_lh_Lat_Fis-post 5402 0.002936 0.003424 0.003760 # 90 tiss__gm ctx_lh_Pole_occipital 5976 0.003248 0.003788 0.004160 # 91 tiss__gm ctx_lh_Pole_temporal 3692 0.002007 0.002340 0.002570 # 92 tiss__gm ctx_lh_S_calcarine 4727 0.002570 0.002996 0.003290 # 93 tiss__gm ctx_lh_S_central 2415 0.001313 0.001531 0.001681 # 94 tiss__gm ctx_lh_S_cingul-Marginalis 1139 0.000619 0.000722 0.000793 # 95 tiss__gm ctx_lh_S_circular_insula_ant 2351 0.001278 0.001490 0.001636 # 96 tiss__gm ctx_lh_S_circular_insula_inf 2653 0.001442 0.001682 0.001847 # 97 tiss__gm ctx_lh_S_circular_insula_sup 2016 0.001096 0.001278 0.001403 # 98 tiss__gm ctx_lh_S_collat_transv_ant 938 0.000510 0.000594 0.000653 # 99 tiss__gm ctx_lh_S_collat_transv_post 6048 0.003287 0.003834 0.004210 # 100 tiss__gm ctx_lh_S_front_inf 2305 0.001253 0.001461 0.001604 # 101 tiss__gm ctx_lh_S_front_middle 6670 0.003626 0.004228 0.004643 # 102 tiss__gm ctx_lh_S_front_sup 303 0.000165 0.000192 0.000211 # 103 tiss__gm ctx_lh_S_interm_prim-Jensen 4381 0.002381 0.002777 0.003049 # 104 tiss__gm ctx_lh_S_intrapariet_and_P_trans 1716 0.000933 0.001088 0.001194 # 105 tiss__gm ctx_lh_S_oc_middle_and_Lunatus 2443 0.001328 0.001549 0.001701 # 106 tiss__gm ctx_lh_S_oc_sup_and_transversal 1634 0.000888 0.001036 0.001137 # 107 tiss__gm ctx_lh_S_occipital_ant 1585 0.000861 0.001005 0.001103 # 108 tiss__gm ctx_lh_S_oc-temp_lat 3674 0.001997 0.002329 0.002557 # 109 tiss__gm ctx_lh_S_oc-temp_med_and_Lingual 982 0.000534 0.000622 0.000683 # 110 tiss__gm ctx_lh_S_orbital_lateral 1205 0.000655 0.000764 0.000839 # 111 tiss__gm ctx_lh_S_orbital_med-olfact 3384 0.001839 0.002145 0.002356 # 112 tiss__gm ctx_lh_S_orbital-H_Shaped 4300 0.002337 0.002726 0.002993 # 113 tiss__gm ctx_lh_S_parieto_occipital 1587 0.000863 0.001006 0.001105 # 114 tiss__gm ctx_lh_S_pericallosal 4536 0.002466 0.002875 0.003157 # 115 tiss__gm ctx_lh_S_postcentral 3410 0.001854 0.002161 0.002374 # 116 tiss__gm ctx_lh_S_precentral-inf-part 3348 0.001820 0.002122 0.002330 # 117 tiss__gm ctx_lh_S_precentral-sup-part 771 0.000419 0.000489 0.000537 # 118 tiss__gm ctx_lh_S_suborbital 1558 0.000847 0.000988 0.001085 # 119 tiss__gm ctx_lh_S_subparietal 3024 0.001644 0.001917 0.002105 # 120 tiss__gm ctx_lh_S_temporal_inf 12712 0.006910 0.008058 0.008849 # 121 tiss__gm ctx_lh_S_temporal_sup 617 0.000335 0.000391 0.000429 # 122 tiss__gm ctx_lh_S_temporal_transverse 0 0.000000 0.000000 0.000000 # 123 tiss__unkn ctx_rh_Unknown 2518 0.001369 0.001596 0.001753 # 124 tiss__gm ctx_rh_G_and_S_frontomargin 4845 0.002634 0.003071 0.003372 # 125 tiss__gm ctx_rh_G_and_S_occipital_inf 3771 0.002050 0.002390 0.002625 # 126 tiss__gm ctx_rh_G_and_S_paracentral 3621 0.001968 0.002295 0.002520 # 127 tiss__gm ctx_rh_G_and_S_subcentral 3348 0.001820 0.002122 0.002330 # 128 tiss__gm ctx_rh_G_and_S_transv_frontopol 8488 0.004614 0.005380 0.005908 # 129 tiss__gm ctx_rh_G_and_S_cingul-Ant 3920 0.002131 0.002485 0.002729 # 130 tiss__gm ctx_rh_G_and_S_cingul-Mid-Ant 3570 0.001940 0.002263 0.002485 # 131 tiss__gm ctx_rh_G_and_S_cingul-Mid-Post 1530 0.000832 0.000970 0.001065 # 132 tiss__gm ctx_rh_G_cingul-Post-dorsal 1016 0.000552 0.000644 0.000707 # 133 tiss__gm ctx_rh_G_cingul-Post-ventral 3764 0.002046 0.002386 0.002620 # 134 tiss__gm ctx_rh_G_cuneus 5281 0.002871 0.003348 0.003676 # 135 tiss__gm ctx_rh_G_front_inf-Opercular 1985 0.001079 0.001258 0.001382 # 136 tiss__gm ctx_rh_G_front_inf-Orbital 4355 0.002367 0.002761 0.003031 # 137 tiss__gm ctx_rh_G_front_inf-Triangul 13733 0.007465 0.008705 0.009559 # 138 tiss__gm ctx_rh_G_front_middle 22597 0.012283 0.014324 0.015729 # 139 tiss__gm ctx_rh_G_front_sup 1970 0.001071 0.001249 0.001371 # 140 tiss__gm ctx_rh_G_Ins_lg_and_S_cent_ins 2826 0.001536 0.001791 0.001967 # 141 tiss__gm ctx_rh_G_insular_short 7214 0.003921 0.004573 0.005021 # 142 tiss__gm ctx_rh_G_occipital_middle 4087 0.002222 0.002591 0.002845 # 143 tiss__gm ctx_rh_G_occipital_sup 6785 0.003688 0.004301 0.004723 # 144 tiss__gm ctx_rh_G_oc-temp_lat-fusifor 5917 0.003216 0.003751 0.004119 # 145 tiss__gm ctx_rh_G_oc-temp_med-Lingual 2905 0.001579 0.001841 0.002022 # 146 tiss__gm ctx_rh_G_oc-temp_med-Parahip 10196 0.005542 0.006463 0.007097 # 147 tiss__gm ctx_rh_G_orbital 10520 0.005718 0.006669 0.007323 # 148 tiss__gm ctx_rh_G_pariet_inf-Angular 6249 0.003397 0.003961 0.004350 # 149 tiss__gm ctx_rh_G_pariet_inf-Supramar 6134 0.003334 0.003888 0.004270 # 150 tiss__gm ctx_rh_G_parietal_sup 5657 0.003075 0.003586 0.003938 # 151 tiss__gm ctx_rh_G_postcentral 9948 0.005408 0.006306 0.006925 # 152 tiss__gm ctx_rh_G_precentral 6534 0.003552 0.004142 0.004548 # 153 tiss__gm ctx_rh_G_precuneus 2330 0.001266 0.001477 0.001622 # 154 tiss__gm ctx_rh_G_rectus 1511 0.000821 0.000958 0.001052 # 155 tiss__gm ctx_rh_G_subcallosal 1102 0.000599 0.000698 0.000767 # 156 tiss__gm ctx_rh_G_temp_sup-G_T_transv 7756 0.004216 0.004917 0.005399 # 157 tiss__gm ctx_rh_G_temp_sup-Lateral 2722 0.001480 0.001725 0.001895 # 158 tiss__gm ctx_rh_G_temp_sup-Plan_polar 2069 0.001125 0.001312 0.001440 # 159 tiss__gm ctx_rh_G_temp_sup-Plan_tempo 8664 0.004710 0.005492 0.006031 # 160 tiss__gm ctx_rh_G_temporal_inf 11668 0.006343 0.007396 0.008122 # 161 tiss__gm ctx_rh_G_temporal_middle 724 0.000394 0.000459 0.000504 # 162 tiss__gm ctx_rh_Lat_Fis-ant-Horizont 766 0.000416 0.000486 0.000533 # 163 tiss__gm ctx_rh_Lat_Fis-ant-Vertical 2103 0.001143 0.001333 0.001464 # 164 tiss__gm ctx_rh_Lat_Fis-post 7459 0.004054 0.004728 0.005192 # 165 tiss__gm ctx_rh_Pole_occipital 5778 0.003141 0.003663 0.004022 # 166 tiss__gm ctx_rh_Pole_temporal 3521 0.001914 0.002232 0.002451 # 167 tiss__gm ctx_rh_S_calcarine 5153 0.002801 0.003266 0.003587 # 168 tiss__gm ctx_rh_S_central 2273 0.001235 0.001441 0.001582 # 169 tiss__gm ctx_rh_S_cingul-Marginalis 1614 0.000877 0.001023 0.001123 # 170 tiss__gm ctx_rh_S_circular_insula_ant 2265 0.001231 0.001436 0.001577 # 171 tiss__gm ctx_rh_S_circular_insula_inf 2188 0.001189 0.001387 0.001523 # 172 tiss__gm ctx_rh_S_circular_insula_sup 2097 0.001140 0.001329 0.001460 # 173 tiss__gm ctx_rh_S_collat_transv_ant 631 0.000343 0.000400 0.000439 # 174 tiss__gm ctx_rh_S_collat_transv_post 4714 0.002562 0.002988 0.003281 # 175 tiss__gm ctx_rh_S_front_inf 5632 0.003061 0.003570 0.003920 # 176 tiss__gm ctx_rh_S_front_middle 6754 0.003671 0.004281 0.004701 # 177 tiss__gm ctx_rh_S_front_sup 600 0.000326 0.000380 0.000418 # 178 tiss__gm ctx_rh_S_interm_prim-Jensen 4382 0.002382 0.002778 0.003050 # 179 tiss__gm ctx_rh_S_intrapariet_and_P_trans 1491 0.000810 0.000945 0.001038 # 180 tiss__gm ctx_rh_S_oc_middle_and_Lunatus 2141 0.001164 0.001357 0.001490 # 181 tiss__gm ctx_rh_S_oc_sup_and_transversal 1745 0.000949 0.001106 0.001215 # 182 tiss__gm ctx_rh_S_occipital_ant 1982 0.001077 0.001256 0.001380 # 183 tiss__gm ctx_rh_S_oc-temp_lat 3276 0.001781 0.002077 0.002280 # 184 tiss__gm ctx_rh_S_oc-temp_med_and_Lingual 820 0.000446 0.000520 0.000571 # 185 tiss__gm ctx_rh_S_orbital_lateral 1594 0.000866 0.001010 0.001109 # 186 tiss__gm ctx_rh_S_orbital_med-olfact 3391 0.001843 0.002150 0.002360 # 187 tiss__gm ctx_rh_S_orbital-H_Shaped 3719 0.002021 0.002357 0.002589 # 188 tiss__gm ctx_rh_S_parieto_occipital 1936 0.001052 0.001227 0.001348 # 189 tiss__gm ctx_rh_S_pericallosal 4146 0.002254 0.002628 0.002886 # 190 tiss__gm ctx_rh_S_postcentral 2995 0.001628 0.001898 0.002085 # 191 tiss__gm ctx_rh_S_precentral-inf-part 3547 0.001928 0.002248 0.002469 # 192 tiss__gm ctx_rh_S_precentral-sup-part 466 0.000253 0.000295 0.000324 # 193 tiss__gm ctx_rh_S_suborbital 2110 0.001147 0.001338 0.001469 # 194 tiss__gm ctx_rh_S_subparietal 2049 0.001114 0.001299 0.001426 # 195 tiss__gm ctx_rh_S_temporal_inf 12913 0.007019 0.008185 0.008989 # 196 tiss__gm ctx_rh_S_temporal_sup 471 0.000256 0.000298 0.000328 # 197 tiss__gm ctx_rh_S_temporal_transverse 0 0.000000 0.000000 0.000000 # 220 tiss__unkn Left-undetermined 0 0.000000 0.000000 0.000000 # 221 tiss__unkn Right-undetermined ++ Done making: stats_fs_rois_2009_sub-005.1D ++ Compressing all remaining .nii files, except for SurfVol. @SUMA_Make_Spec_FS ... finished if ( 0 ) then echo ++ FINISHED FS ++ FINISHED FS COPY_AND_EXIT: if ( 1 && -d /lscratch/25105636/sub-005_ses-01 ) then echo ++ Used /lscratch ++ Used /lscratch echo ++ Copy from: /lscratch/25105636/sub-005_ses-01 ++ Copy from: /lscratch/25105636/sub-005_ses-01 echo to: /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01 to: /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01 mkdir -p /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01 cp -pr /lscratch/25105636/sub-005_ses-01/fsaverage /lscratch/25105636/sub-005_ses-01/label /lscratch/25105636/sub-005_ses-01/mri /lscratch/25105636/sub-005_ses-01/scripts /lscratch/25105636/sub-005_ses-01/stats /lscratch/25105636/sub-005_ses-01/SUMA /lscratch/25105636/sub-005_ses-01/surf /lscratch/25105636/sub-005_ses-01/tmp /lscratch/25105636/sub-005_ses-01/touch /lscratch/25105636/sub-005_ses-01/trash /data/APMULTI/APMULTI_TEST/apmulti_root.005/apmulti_demo/data_12_fs/sub-005/ses-01/. endif exit 0