afni.nimh.nih.gov
| May 22, 2015 06:00PM | |
Registered: 9 years ago Posts: 5 |
Hello All,
I am new to AFNI (which means my question is very naive :D) and have just gone through the bootcamp slides but havent got few answers:
I am using uber_subject.py to create a script for generating statistical map from design matrix. I have few regreassors like sndpwr(in dB's) heart and lung which have negative values in it. I am passing it as stim files in uber_subject.py GUI. But when i create a proc.py script i am getting warning saying few values in stim files are negative. I am looking to regression analysis on the data and get contrast for eg: sndpwr-1*Z-1*Y
My question is can i pass sndpwr, heart etc with negative stim values as regressors in the stim section of uber_subject.py gui?
With the negative tsim values i am not able to get output files stat.subject$$ ..
Any suggestion is greatly appreciated!
Thanks!
Sushil
Here is the cmd output:
+ Fixed clip level = 1637.579956
+ Used gradual clip level = 1316.520996 .. 1836.563843
+ Number voxels above clip level = 1437108
+ Clustering voxels ...
+ Largest cluster has 1426398 voxels
+ Clustering voxels ...
+ Largest cluster has 1424012 voxels
+ Filled 1220 voxels in small holes; now have 1425232 voxels
+ Filled 56354 voxels in large holes; now have 1481586 voxels
+ Clustering voxels ...
+ Largest cluster has 1481565 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 11731811 voxels
+ Mask now has 1481565 voxels
++ 1481565 voxels in the mask [out of 13213376: 11.21%]
++ first 17 x-planes are zero [from R]
++ last 11 x-planes are zero [from L]
++ first 56 y-planes are zero [from A]
++ last 38 y-planes are zero [from P]
++ first 118 z-planes are zero [from I]
++ last 28 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ Output dataset ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig.BRIK
++ CPU time = 3.820000 sec
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig
#++ Applying threshold of 4875.000000 on /Users/sdb99/Subject18/subject_results/group.sub18fri/subj.sub18fri/sub18fri.results/__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns_wt -a ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig -expr 'min(1,(a/4875.000000))'
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_pb01.sub18fri.r01.tshift_ts_rs_ns_wt+orig.BRIK
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_mprage-s18-obl_ns_ob_al_junk_wtal -weight ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns_wt+orig -source ./__tt_mprage-s18-obl_ns_ob+orig -prefix ./__tt_mprage-s18-obl_ns_ob_temp_al_junk -base ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig -nocmass -1Dmatrix_save ./mprage-s18-obl_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_mprage-s18-obl_ns_ob+orig.HEAD
++ Base dataset: ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1752214 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1481178 voxels [11.2%] in weight mask
++ Output dataset ./__tt_mprage-s18-obl_ns_ob_al_junk_wtal+orig.BRIK
++ Number of points for matching = 1481178
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -56.2..56.2 -87.6..87.6 -87.6..87.6
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 4
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU to here=8.3 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 1481178 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1389241 total points stored in 2602 'RHDD(6.54321)' bloks
+ - Initial cost = 0.029359
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
*****************************************************************************************************************************************************************
+ - Finalish cost = -0.022072 ; 424 funcs
*******
+ - Final cost = -0.022073 ; 132 funcs
+ Final fine fit Parameters:
x-shift=-4.0994 y-shift=-2.3632 z-shift= 0.6421
z-angle=-0.3081 x-angle= 3.3832 y-angle=-2.8356
x-scale= 0.9853 y-scale= 1.0035 z-scale= 0.9888
y/x-shear= 0.0971 z/x-shear= 0.0040 z/y-shear= 0.0551
+ - Fine net CPU time = 65.9 s
++ Computing output image
++ image warp: parameters = -4.0994 -2.3632 0.6421 -0.3081 3.3832 -2.8356 0.9853 1.0035 0.9888 0.0971 0.0040 0.0551
++ Output dataset ./__tt_mprage-s18-obl_ns_ob_temp_al_junk+orig.BRIK
++ Wrote -1Dmatrix_save ./mprage-s18-obl_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 76.8 sec Elapsed = 42.0
++ ###########################################################
++ ### Please check results visually for alignment quality ###
++ ###########################################################
#Script is running (command trimmed):
cat_matvec -ONELINE ./mprage-s18-obl_al_junk_e2a_only_mat.aff12.1D ./__tt_mprage-s18-obl_ns_obla2e_mat.1D -I > ./mprage-s18-obl_al_junk_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig -1Dmatrix_apply ./mprage-s18-obl_al_junk_mat.aff12.1D -prefix ./mprage-s18-obl_al_junk -input ./__tt_mprage-s18-obl_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_mprage-s18-obl_ns+orig.HEAD
++ Base dataset: ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig.HEAD
++ Loading datasets
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=4.3 s]
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - no weight image
+ - using 11 points from base image [use_all=0]
+ * Exit alignment setup routine
++ using -1Dmatrix_apply
++ Computing output image
++ image warp: parameters = 0.9841 -0.0082 0.0487 -9.1408 0.1024 1.0005 0.0314 -18.0979 -0.0416 0.0300 0.9909 5.0908
++ Output dataset ./mprage-s18-obl_al_junk+orig.BRIK
++ 3dAllineate: total CPU time = 7.9 sec Elapsed = 7.3
++ ###########################################################
#++ Creating final output: skullstripped anat data
#Script is running (command trimmed):
3dcopy ./__tt_mprage-s18-obl_ns+orig mprage-s18-obl_ns
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
#++ Creating final output: anat data aligned to epi
# copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "align_epi_anat.py -anat2epi -anat mprage-s18-obl+orig \
-save_skullstrip -suffix _al_junk -epi pb01.sub18fri.r01.tshift+orig \
-epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off" \
./mprage-s18-obl_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_pb01.sub18fri.r01.tshift*
#Script is running:
\rm -f ./__tt_mprage-s18-obl*
# Finished alignment successfully
@auto_tlrc -base TT_N27+tlrc -input mprage-s18-obl_ns+orig -no_ss
*********** Warning *************
Dataset centers are 58.261184 mm
apart. If registration fails, or if
parts of the original anatomy gets
cropped, try adding option
-init_xform AUTO_CENTER
to your @auto_tlrc command.
*********************************
Padding ...
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ output dataset: ./__ats_tmp__ref_TT_N27_40pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK
Clipping -0.000100 3693.000100 ...
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_mprage-s18-obl_ns+tlrc.BRIK
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_mprage-s18-obl_ns+tlrc.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
RMS[0] = 83.2858 50.3984 ITER = 10/137
83.2858
Warping has converged.
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad40_mprage-s18-obl_ns+orig.HEAD -> __ats_tmp___pad40_mprage-s18-obl_ns.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad40_mprage-s18-obl_ns+orig.BRIK -> __ats_tmp___pad40_mprage-s18-obl_ns.skl+orig.BRIK
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp___pad40_mprage-s18-obl_ns+orig.BRIK
Unpadding ...
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ output dataset: ./__ats_tmp___upad40_mprage-s18-obl_ns+orig.BRIK
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_mprage-s18-obl_ns+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_mprage-s18-obl_ns+orig.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset mprage-s18-obl_ns+orig __ats_tmp___upad40_mprage-s18-obl_ns+tlrc
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_mprage-s18-obl_ns+tlrc
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Warning: ignoring +tlrc on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___upad40_mprage-s18-obl_ns+tlrc.HEAD -> mprage-s18-obl_ns+tlrc.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___upad40_mprage-s18-obl_ns+tlrc.BRIK -> mprage-s18-obl_ns+tlrc.BRIK
Cleanup ...
cat_matvec mprage-s18-obl_ns+tlrc::WARP_DATA -I
if ( ! -f mprage-s18-obl_ns+tlrc.HEAD ) then
foreach run ( 01 )
3dvolreg -verbose -zpad 1 -base pb01.sub18fri.r01.tshift+orig[2] -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub18fri.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb01.sub18fri.r01.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.sub18fri.r01.tshift+orig.BRIK is 1.882632 degrees from plumb.
++ Reading in base dataset ./pb01.sub18fri.r01.tshift+orig.BRIK
++ Oblique dataset:./pb01.sub18fri.r01.tshift+orig.BRIK is 1.882632 degrees from plumb.
++ Reading input dataset ./pb01.sub18fri.r01.tshift+orig.BRIK
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
+ Automask has 55631 voxels
+ 7777 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 362 sub-bricks: 0..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..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..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..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359..360..361..
++ CPU time for realignment=19 s [=0.0526 s/sub-brick]
++ Min : roll=-0.062 pitch=-0.040 yaw=-0.086 dS=-0.217 dL=-0.028 dP=-0.192
++ Mean: roll=-0.022 pitch=+0.089 yaw=-0.019 dS=-0.050 dL=+0.011 dP=-0.104
++ Max : roll=+0.010 pitch=+0.260 yaw=+0.059 dS=+0.097 dL=+0.054 dP=+0.014
++ Max displacements (mm) for each sub-brick:
0.05 0.08 0.00 0.05 0.12 0.20 0.21 0.19 0.22 0.17 0.17 0.18 0.17 0.19 0.13 0.12 0.15 0.13 0.11 0.09 0.06 0.07 0.08 0.12 0.15 0.14 0.11 0.10 0.09 0.11 0.11 0.11 0.07 0.10 0.11 0.08 0.08 0.07 0.07 0.09 0.09 0.07 0.07 0.10 0.12 0.12 0.12 0.11 0.12 0.16 0.13 0.08 0.11 0.13 0.18 0.14 0.13 0.13 0.14 0.16 0.11 0.21 0.24 0.28 0.25 0.26 0.31 0.37 0.41 0.35 0.39 0.42 0.43 0.40 0.34 0.39 0.39 0.39 0.40 0.34 0.33 0.35 0.36 0.34 0.34 0.41 0.34 0.37 0.36 0.43 0.38 0.37 0.38 0.39 0.35 0.35 0.38 0.33 0.27 0.30 0.29 0.26 0.27 0.26 0.25 0.27 0.27 0.27 0.28 0.33 0.31 0.28 0.31 0.29 0.28 0.27 0.25 0.22 0.25 0.21 0.27 0.27 0.31 0.27 0.31 0.30 0.30 0.29 0.27 0.29 0.33 0.29 0.28 0.28 0.30 0.32 0.36 0.36 0.37 0.36 0.32 0.33 0.40 0.33 0.31 0.33 0.35 0.34 0.34 0.33 0.28 0.28 0.34 0.27 0.31 0.29 0.32 0.31 0.31 0.25 0.23 0.17 0.25 0.21 0.21 0.20 0.26 0.24 0.24 0.24 0.22 0.27 0.23 0.19 0.20 0.20 0.23 0.18 0.17 0.21 0.23 0.25 0.26 0.23 0.22 0.21 0.22 0.23 0.22 0.24 0.21 0.21 0.25 0.23 0.22 0.22 0.22 0.24 0.22 0.22 0.21 0.19 0.19 0.21 0.20 0.19 0.18 0.18 0.19 0.19 0.17 0.19 0.22 0.18 0.19 0.19 0.18 0.16 0.22 0.22 0.25 0.17 0.18 0.17 0.21 0.18 0.22 0.19 0.24 0.20 0.20 0.25 0.17 0.19 0.24 0.26 0.24 0.27 0.24 0.35 0.37 0.40 0.40 0.33 0.36 0.34 0.35 0.23 0.30 0.29 0.24 0.29 0.24 0.26 0.24 0.26 0.28 0.25 0.28 0.26 0.31 0.27 0.31 0.32 0.34 0.33 0.34 0.33 0.37 0.37 0.34 0.32 0.36 0.39 0.38 0.39 0.38 0.42 0.41 0.38 0.33 0.36 0.37 0.35 0.32 0.30 0.36 0.32 0.35 0.36 0.33 0.27 0.31 0.35 0.34 0.34 0.28 0.22 0.22 0.24 0.21 0.23 0.20 0.28 0.33 0.32 0.26 0.23 0.26 0.23 0.24 0.32 0.36 0.36 0.34 0.30 0.27 0.30 0.24 0.21 0.27 0.24 0.25 0.23 0.30 0.26 0.28 0.22 0.28 0.26 0.31 0.24 0.28 0.22 0.31 0.25 0.33 0.36 0.27 0.28 0.21 0.31 0.31 0.32 0.34 0.29 0.30 0.31 0.41 0.29 0.33 0.25 0.37 0.35 0.40 0.24 0.24 0.33 0.29 0.31 0.28 0.21
++ Max displacement in automask = 0.43 (mm) at sub-brick 72
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.sub18fri.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE mprage-s18-obl_ns+tlrc::WARP_DATA -I mprage-s18-obl_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dAllineate -base mprage-s18-obl_ns+tlrc -input pb01.sub18fri.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r01
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb01.sub18fri.r01.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.sub18fri.r01.tshift+orig.BRIK is 1.882632 degrees from plumb.
++ Source dataset: ./pb01.sub18fri.r01.tshift+orig.HEAD
++ Base dataset: ./mprage-s18-obl_ns+tlrc.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 3.0000 mm
++ OpenMP thread count = 4
++ ========== Applying transformation to 362 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=1.3 s]
++ ========== sub-brick #1 ========== [total CPU to here=1.4 s]
++ ========== sub-brick #2 ========== [total CPU to here=1.4 s]
++ ========== sub-brick #3 ========== [total CPU to here=1.5 s]
++ ========== sub-brick #4 ========== [total CPU to here=1.6 s]
++ ========== sub-brick #5 ========== [total CPU to here=1.7 s]
++ ========== sub-brick #6 ========== [total CPU to here=1.8 s]
++ ========== sub-brick #7 ========== [total CPU to here=1.8 s]
++ ========== sub-brick #8 ========== [total CPU to here=1.9 s]
++ ========== sub-brick #9 ========== [total CPU to here=1.9 s]
++ ========== sub-brick #10 ========== [total CPU to here=2.0 s]
++ ========== sub-brick #11 ========== [total CPU to here=2.1 s]
++ ========== sub-brick #12 ========== [total CPU to here=2.1 s]
++ ========== sub-brick #13 ========== [total CPU to here=2.2 s]
++ ========== sub-brick #14 ========== [total CPU to here=2.3 s]
++ ========== sub-brick #15 ========== [total CPU to here=2.4 s]
++ ========== sub-brick #16 ========== [total CPU to here=2.4 s]
++ ========== sub-brick #17 ========== [total CPU to here=2.5 s]
++ ========== sub-brick #18 ========== [total CPU to here=2.6 s]
..
..
++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 26.1 sec Elapsed = 20.5
++ ###########################################################
3dAllineate -base mprage-s18-obl_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./rm.epi.all1+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 1.882632 degrees from plumb.
++ Output dataset ./rm.epi.1.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 18.1 sec Elapsed = 18.6
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.epi.min.r01+tlrc.BRIK
end
cat dfile.r01.1D
3dcopy rm.epi.min.r01+tlrc mask_epi_extents
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
foreach run ( 01 )
3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub18fri.r01.volreg
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.sub18fri.r01.volreg+tlrc.BRIK
end
3dcopy mprage-s18-obl_ns+tlrc anat_final.sub18fri
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
3dAllineate -source mprage-s18-obl+orig -master anat_final.sub18fri+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers
++ Source dataset: ./mprage-s18-obl+orig.HEAD
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=5.0 s]
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./anat_w_skull_warped+tlrc.BRIK
++ 3dAllineate: total CPU time = 22.6 sec Elapsed = 11.1
++ ###########################################################
foreach run ( 01 )
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.sub18fri.r01.blur pb02.sub18fri.r01.volreg+tlrc
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
Program 3dmerge
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (119.3 MB)
-- Wrote edited dataset: ./pb03.sub18fri.r01.blur+tlrc.BRIK
Editing sub-brick 0
Editing sub-brick 1
Editing sub-brick 2
Editing sub-brick 3
Editing sub-brick 4
....
.....
....
end
foreach run ( 01 )
3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub18fri.r01.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.sub18fri.r01.blur+tlrc
++ Forming automask
+ Fixed clip level = 1593.594360
+ Used gradual clip level = 1364.120850 .. 1839.525879
+ Number voxels above clip level = 50128
+ Clustering voxels ...
+ Largest cluster has 49833 voxels
+ Clustering voxels ...
+ Largest cluster has 49272 voxels
+ Filled 235 voxels in small holes; now have 49507 voxels
+ Filled 4 voxels in large holes; now have 49511 voxels
+ Clustering voxels ...
+ Largest cluster has 49508 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 123292 voxels
+ Mask now has 49508 voxels
++ Dilating automask
+ Clustering voxels ...
+ Largest cluster has 115236 voxels
++ 57564 voxels in the mask [out of 172800: 33.31%]
++ first 1 x-planes are zero [from R]
++ last 4 x-planes are zero [from L]
++ first 2 y-planes are zero [from A]
++ last 5 y-planes are zero [from P]
++ first 4 z-planes are zero [from I]
++ last 0 z-planes are zero [from S]
++ Output dataset ./rm.mask_r01+tlrc.BRIK
++ CPU time = 0.650000 sec
end
3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub18fri
++ processing 1 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 57564 survived, 115236 were zero
++ writing result full_mask.sub18fri...
++ Output dataset ./full_mask.sub18fri+tlrc.BRIK
3dresample -master full_mask.sub18fri+tlrc -input mprage-s18-obl_ns+tlrc -prefix rm.resam.anat
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub18fri
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 53959 survived, 118841 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_anat.sub18fri...
++ Output dataset ./mask_anat.sub18fri+tlrc.BRIK
3dABoverlap -no_automask full_mask.sub18fri+tlrc mask_anat.sub18fri+tlrc
tee out.mask_ae_overlap.txt
++ 3dOverlap: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
#A=./full_mask.sub18fri+tlrc.BRIK B=./mask_anat.sub18fri+tlrc.BRIK
#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A)
57564 53959 63938 47585 9979 6374 17.3355 11.8127 0.8654 0.9116 0.9924
3ddot -demean full_mask.sub18fri+tlrc mask_anat.sub18fri+tlrc
tee out.mask_ae_corr.txt
0.784506
3dresample -master full_mask.sub18fri+tlrc -prefix ./rm.resam.group -input /Users/sdb99/abin/TT_N27+tlrc
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 55366 survived, 117434 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_group...
++ Output dataset ./mask_group+tlrc.BRIK
foreach run ( 01 )
3dTstat -prefix rm.mean_r01 pb03.sub18fri.r01.blur+tlrc
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r01+tlrc.BRIK
3dcalc -a pb03.sub18fri.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub18fri.r01.scale
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.sub18fri.r01.scale+tlrc.BRIK
end
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub18fri
total number of censored TRs = 0
3dDeconvolve -input pb04.sub18fri.r01.scale+tlrc.HEAD -censor motion_sub18fri_censor.1D -polort 5 -num_stimts 16 -stim_times 1 stimuli/s18-dis-der-sndpwr.txt GAM -stim_label 1 dis-der-sndpwr -stim_times 2 stimuli/s18-heart.txt GAM -stim_label 2 heart -stim_times 3 stimuli/s18-lungs.txt GAM -stim_label 3 lungs -stim_times 4 stimuli/s18-sndpwr.txt GAM -stim_label 4 sndpwr -stim_file 5 motion_demean.1D[0] -stim_base 5 -stim_label 5 roll_01 -stim_file 6 motion_demean.1D[1] -stim_base 6 -stim_label 6 pitch_01 -stim_file 7 motion_demean.1D[2] -stim_base 7 -stim_label 7 yaw_01 -stim_file 8 motion_demean.1D[3] -stim_base 8 -stim_label 8 dS_01 -stim_file 9 motion_demean.1D[4] -stim_base 9 -stim_label 9 dL_01 -stim_file 10 motion_demean.1D[5] -stim_base 10 -stim_label 10 dP_01 -stim_file 11 motion_deriv.1D[0] -stim_base 11 -stim_label 11 roll_02 -stim_file 12 motion_deriv.1D[1] -stim_base 12 -stim_label 12 pitch_02 -stim_file 13 motion_deriv.1D[2] -stim_base 13 -stim_label 13 yaw_02 -stim_file 14 motion_deriv.1D[3] -stim_base 14 -stim_label 14 dS_02 -stim_file 15 motion_deriv.1D[4] -stim_base 15 -stim_label 15 dL_02 -stim_file 16 motion_deriv.1D[5] -stim_base 16 -stim_label 16 dP_02 -gltsym SYM: sndpwr-1*heart-1*dis-der-sndpwr -1*lungs -glt_label 1 sndpwr_contrast -gltsym SYM: dis-der-sndpwr -lungs -glt_label 2 dis-der-sndpwr-lungs -gltsym SYM: heart -lungs -glt_label 3 heart-lungs -gltsym SYM: 0.333*dis-der-sndpwr +0.333*heart +0.333*lungs -glt_label 4 mean.DHL -gltsym SYM: dis-der-sndpwr -0.5*heart -0.5*lungs -glt_label 5 D-HL -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -errts errts.sub18fri -bucket stats.sub18fri
*+ WARNING: '-stim_times 3' didn't read any good times from file 'stimuli/s18-lungs.txt'
++ 3dDeconvolve: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset pb04.sub18fri.r01.scale+tlrc.HEAD
++ STAT automask has 150911 voxels (out of 172800 = 87.3%)
++ Skipping check for initial transients
++ Input polort=5; Longest run=724.0 s; Recommended minimum polort=5 ++ OK ++
++ -stim_times using TR=2 s for stimulus timing conversion
++ -stim_times using TR=2 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using GLOBAL times
*+ WARNING: '-stim_times 1' (GLOBAL) has 360 times outside range 0 .. 722 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
-0.00033521 -0.00080065 -0.00031457 -0.00075729 -0.001189 -0.0011157 -0.0011393 -0.0009936 -0.00039896 -0.0012745 -0.001677 -0.00078611 -0.00090805 -0.0015619 -0.0021151 -0.0013384 -0.0012254 -0.0014131 -0.0013692 -0.0022498 -0.0013194 -0.0012966 -0.0012612 -0.0014383 -0.0017519 -0.0020166 -0.0018996 -0.0016561 -0.0016934 -0.0023928 -0.0017936 -0.001478 -0.0017891 -0.001319 -0.00093228 -0.0018412 -0.0016798 -0.0012272 -0.0017156 -0.0010843 -0.001368 -0.0014586 -0.0013864 -0.0017816 -0.00097647 -0.00074393 -0.0011494 -0.001874 -0.0013458 -0.0012806 -0.00098596 -0.0010554 -0.0012612 -0.0016581 -0.0016946 -0.00086249 -0.00090011 -0.0012635 -0.0013297 -0.0015283 -0.0018435 -0.00094732 -0.0010019 -0.0016497 -0.0010593 -0.00041586 -0.0016805 -0.0011409 -0.0011641 -0.0012335 -0.0014618 -0.00072225 -0.0010285 -0.001572 -0.001169 -0.00047179 -0.00075702 -0.0013343 -0.0011784 -0.00054674 -0.0006481 -0.0009147 -0.0014466 -0.00055693 -0.00063124 -0.0018422 -0.0014234 -0.00090477 -0.0017458 -0.0011796 -0.00028771 -0.0020169 -0.0022075 -0.0015181 -0.0015074 -0.0017257 -0.0021419 -0.0019365 -0.0009708 -0.0011883 -0.0012868 -0.0011995 -0.0015956 -0.00058397 -0.00050529 -0.0013771 -0.001331 -0.00091854 -0.0011353 -0.0017077 -0.0012412 -0.0010625 -0.0012855 -0.00087241 -0.0012668 -0.00176 -0.0014228 -0.00077562 -0.0016853 -0.00089719 -0.00053753 -0.0013926 -0.00078348 -0.0017391 -0.0017018 -0.00098777 -0.0017562 -0.001285 -0.0011263 -0.00077809 -0.0012755 -0.0021087 -0.001539 -0.00018512 -0.0013921 -0.00095747 -0.0009337 -0.0023318 -0.0012434 -0.00068321 -0.001643 -0.0016882 -0.001388 -0.0011987 -0.0018013 -0.0013577 -0.0010807 -0.0011451 -0.00071461 -0.0010498 -0.00089263 -0.00082241 -0.00079144 -0.00040043 -0.0010156 -0.0014817 -0.00065941 -0.0010021 -0.0011768 -0.0014355 -0.001407 -0.0012132 -0.0010416 -0.0012322 -0.0011426 -0.0015412 -0.0012513 -0.00042612 -0.00087084 -0.0008127 -0.0012559 -0.0010876 -0.0012375 -0.0014603 -0.0010197 -0.0011795 -0.0021858 -0.0013803 -0.0011851 -0.0017416 -0.0012107 -0.0016088 -0.0013057 -0.0013119 -0.001527 -0.0017342 -0.0014097 -0.00088016 -0.0015783 -0.0018108 -0.0013308 -0.0019654 -0.0018034 -0.0010704 -0.001406 -0.0011312 -0.0015329 -0.0012809 -0.0017147 -0.001838 -0.00073073 -0.001048 -0.0016941 -0.001416 -0.0009804 -0.0015934 -0.00075055 -0.0011214 -0.0012941 -0.00099531 -0.0017494 -0.0013531 -0.0010363 -0.001196 -0.0016989 -0.0015519 -0.00070721 -0.0016278 -0.0021144 -0.00086777 -0.0010911 -0.001824 -0.0016726 -0.0011928 -0.0018075 -0.0012007 -0.00083597 -0.0017495 -0.0015741 -0.0014518 -0.0015369 -0.0018104 -0.0018114 -0.00077776 -0.0020599 -0.0017328 -0.0011388 -0.0014981 -0.001736 -0.00094106 -0.0011598 -0.0014084 -0.0013401 -0.0009457 -0.0011199 -0.00079298 -0.00021199 -0.0013639 -0.0021085 -0.0010829 -0.00064974 -0.0019349 -0.0019064 -0.001331 -0.0015279 -0.001426 -0.0016878 -0.0009596 -0.0011862 -0.00089052 -0.0011737 -0.0014053 -0.00094183 -0.00086661 -0.00077598 -0.0012326 -0.0012317 -0.00082557 -0.00074735 -0.0014462 -0.00086694 -0.00079106 -0.00078837 -0.00081753 -0.00091292 -0.0011294 -0.0006283 -0.00081676 -0.00082247 -0.00077335 -0.0016144 -0.00048817 -0.00074297 -0.0015748 -0.0012727 -0.0014331 -0.001844 -0.0013343 -0.0016193 -0.0019768 -0.0014983 -0.0011643 -0.00098428 -0.0011579 -0.0018035 -0.0013473 -0.00074985 -0.0013867 -0.0018602 -0.0010332 -0.00082867 -0.0020013 -0.001693 -0.00047956 -0.0011509 -0.0018467 -0.0013535 -0.0011524 -0.0011984 -0.0015431 -0.0019434 -0.0011064 -0.00053092 -0.0009897 -0.0010925 -0.00097376 -0.00078873 -0.00033222 -0.0019131 -0.00082683 -0.00027045 -0.0017654 -0.0011477 -0.0011111 -0.00085222 -0.0018299 -0.0016863 -0.00060763 -0.0010158 -0.0011903 -0.00090387 -0.001572 -0.0012238 -0.00024587 -0.0010557 -0.0013312 -0.0020034 -0.00092383 -0.00060547 -0.0010234 -0.0015 -0.0017718 -0.00075465 -0.00085238 -0.00081407 -0.0011766 -0.0015139 -0.00093331 -0.00062086 -0.0010944 -0.0013375 -0.0011193 -0.0014382 -0.0016644 -0.00069853 -0.00089108 -0.0013167 -0.00078364 -0.00082634 -0.0010653
*+ WARNING: '-stim_times 1' file 'stimuli/s18-dis-der-sndpwr.txt' has 0 duplicate and 1 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
++ ** GUESSED ** -stim_times 2 using GLOBAL times
*+ WARNING: '-stim_times 2' (GLOBAL) has 116 times outside range 0 .. 722 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
-0.279 -3.229 -3.5957 -3.3176 -0.034927 -2.2409 -6.678 -3.4342 -1.9999 -8.3584 -0.62135 -2.0644 -1.7942 -0.59761 -3.614 -5.5434 -11.403 -4.7095 -0.58027 -5.7555 -0.1233 -6.8775 -0.9493 -0.046737 -11.127 -9.3933 -9.6199 -0.62529 -1.192 -1.246 -1.7678 -1.3375 -0.23264 -0.40082 -0.68628 -0.43081 -0.80747 -4.6299 -4.6098 -7.6304 -4.744 -6.2811 -4.2214 -0.36617 -0.095402 -0.94951 -2.5717 -0.42375 -3.8442 -5.7512 -0.69589 -6.9687 -1.8901 -4.6272 -9.9362 -0.091347 -1.571 -3.2272 -0.84451 -4.8573 -1.0034 -3.4041 -2.6522 -2.5115 -6.6941 -6.546 -0.86224 -0.71194 -9.218 -12.415 -2.4015 -4.246 -0.13364 -8.8978 -1.2167 -2.8001 -2.4707 -0.43889 -6.1311 -8.0479 -3.5204 -8.7851 -1.8118 -1.3603 -1.1307 -5.394 -5.2664 -3.1067 -3.2471 -28.448 -10.959 -0.45195 -12.707 -5.4603 -1.4005 -5.7206 -10.505 -1.7241 -11.749 -0.89892 -0.7275 -2.4604 -5.1116 -3.0717 -2.9136 -1.3719 -2.8084 -11.051 -2.4584 -0.26153 -18.588 -9.7706 -2.3536 -0.55641 -24.231 -14.8
*+ WARNING: '-stim_times 2' file 'stimuli/s18-heart.txt' has 0 duplicate and 5651 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
++ ** GUESSED ** -stim_times 3 using GLOBAL times
*+ WARNING: '-stim_times 3' (GLOBAL) has 362 times outside range 0 .. 722 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
-1159.6 -2818.3 -2466 -2655.2 -2392.8 -2495.8 -2363.6 -2590.5 -2424.1 -2159.6 -2563.3 -2372.1 -2489.6 -2555.9 -2606.6 -2656.7 -2662.3 -2473.2 -2536.1 -2620.6 -2505.6 -2196.9 -2191.2 -2603.4 -2331.7 -2623.2 -2607.3 -2711.5 -2610.3 -2682.5 -2635.7 -2763.4 -2421 -2865.1 -1647.8 -2300 -2776 -2549.5 -2784.9 -2435.2 -2661.1 -2587.8 -2442.6 -2624 -2123.7 -1921.5 -2819 -2489.1 -2646.1 -2608.2 -2466.8 -2387.5 -3197.3 -1529.3 -2540.3 -2128.8 -2587.9 -2055 -2426.7 -2573 -2479.5 -2664.8 -1218.8 -3025 -2315.2 -2657.2 -2364.1 -2602.2 -2213 -2524.7 -2539.3 -2189.9 -2399.1 -2694.5 -2350.8 -2736.4 -2254 -2471.2 -2403.2 -2413.9 -2551.5 -2413.8 -2743.6 -2720.2 -2410.5 -2508.5 -2291.8 -2423.3 -2148.6 -2614.2 -2278.7 -2798.2 -2514.2 -2568.6 -2659.8 -2338.5 -2382.9 -2604.7 -2548.8 -2847.5 -2105.1 -2245.1 -2660.1 -2580.1 -2766.3 -2616.9 -2632.1 -2563.6 -2461.5 -2574.4 -2387.8 -2698.5 -2268.6 -2437.6 -2557.9 -2540.6 -2489.2 -2541.7 -2426.9 -2488.2 -2522.3 -2276.4 -2766.1 -2283.6 -2666.9 -2067.9 -2824 -2395.9 -2507.6 -2771.9 -2161.6 -2311.4 -2599.5 -2598.9 -2395.4 -2376.7 -2433.6 -2280.6 -2624.1 -2476 -2497 -2871.1 -2068 -2711.3 -2705.9 -2345.8 -2626.5 -2416 -2463.2 -2627.1 -2457.5 -2739.5 -1770.6 -2122.2 -3046.5 -1910.4 -2952.4 -2292.7 -2774.1 -2485.5 -2574.2 -2391.8 -2411.5 -1814 -2841.9 -2294.1 -2710.4 -2385.4 -2670.5 -2428.6 -2530.2 -2446.4 -2233.7 -2571.2 -2740.9 -2289.1 -2572.7 -2434.8 -2637.1 -2551.6 -2487.4 -2620.9 -2300.3 -2611.9 -2475.7 -2560 -2574.4 -2454.3 -2532.3 -2626.6 -2491.1 -2601.2 -2617.7 -2439.7 -2537.1 -2480.8 -2427.2 -2580.4 -2483.3 -2439.5 -2490.3 -2580.6 -2512.2 -2530.3 -2544.6 -2574.4 -2406.8 -2639.3 -2412.9 -1803.4 -2694.7 -2502.5 -2560 -2636.4 -2812 -2303.1 -2648.4 -2528.3 -2568.6 -2580.4 -2587.2 -2308.4 -2956 -2107.4 -2750.2 -2370.2 -2696.5 -1253.8 -2566.2 -2608.2 -2461.8 -2508.7 -2441.7 -2880.9 -1625.5 -2420 -2703.9 -2494.4 -2418.6 -2530.8 -2071 -2376 -2618 -2562.7 -2591.1 -2381.4 -2793.7 -2320.6 -2741.4 -1601.7 -2338.3 -2908.4 -1058.7 -3010.9 -2325.2 -2773.6 -2487.1 -2472.8 -2592.3 -2301.7 -2919.4 -2237.2 -2815.6 -2450.4 -2573.4 -2334.2 -2694.7 -2394.9 -2733.3 -2211.9 -2738.6 -2529.9 -2351.5 -2588.4 -2379 -2604.2 -2412.9 -2450.4 -2446 -2395.1 -2510.3 -2572 -2467.1 -2524.4 -2535.3 -2570.6 -2353.4 -2506.8 -2685.8 -2229.1 -2744.4 -2636.6 -2571.1 -2202.9 -2561.5 -2462.8 -2536 -2500.3 -2547 -2469.4 -2442.2 -2779.9 -2314 -2782.5 -1771.3 -2335 -2733.7 -2410.7 -2795.7 -2231.5 -2799.3 -2286 -2016.5 -2766.2 -2418.4 -2604.9 -2428.9 -2730.4 -2579.7 -2778.5 -2489.6 -2033.9 -2715.2 -2257.4 -2831.8 -1809.2 -2825.5 -2313.7 -2541.7 -2292.5 -2737.3 -2101.9 -2600.6 -2195 -2601.4 -1918.7 -2933.7 -597.79 -2275.8 -3064.2 -2190.5 -2994.3 -1811 -2924.1 -2405.2 -2643 -2748.8 -2289.2 -2788.2 -2037.8 -2933.1 -1597.1 -2761.6 -1786.7 -2860 -2305 -2994.6 -484.42 -1582.7 -3130.2 -2198.7 -3280.2
*+ WARNING: !! '-stim_times 3' file 'stimuli/s18-lungs.txt' has no good stimulus time values
++ ** GUESSED ** -stim_times 4 using GLOBAL times
*+ WARNING: '-stim_times 4' file 'stimuli/s18-sndpwr.txt' has 2 duplicate and 65339 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
*+ WARNING: -gltsym: Can't interpret '*' scale factor in 'sndpwr-1*heart-1*dis-der-sndpwr' -- replaced by 1
*+ WARNING: -gltsym: '*' scale factor in 'sndpwr-1*heart-1*dis-der-sndpwr' not at start of string?
** ERROR: -gltsym: can't match symbolic name 'heart-1*dis-der-sndpwr'
------------------------------------------------------------
GLT matrix from 'SYM: sndpwr-1*heart-1*dis-der-sndpwr -1*lungs':
0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
** ERROR: -gltsym errors immediately above from file 'SYM: sndpwr-1*heart-1*dis-der-sndpwr -1*lungs'
------------------------------------------------------------
GLT matrix from 'SYM: dis-der-sndpwr -lungs':
0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: heart -lungs':
0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: 0.333*dis-der-sndpwr +0.333*heart +0.333*lungs':
0 0 0 0 0 0 0.333 0.333 0.333 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: dis-der-sndpwr -0.5*heart -0.5*lungs':
0 0 0 0 0 0 1 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0
** FATAL ERROR: Can't continue after the above -gltsym problems!
** Program compile date = May 8 2015
I am new to AFNI (which means my question is very naive :D) and have just gone through the bootcamp slides but havent got few answers:
I am using uber_subject.py to create a script for generating statistical map from design matrix. I have few regreassors like sndpwr(in dB's) heart and lung which have negative values in it. I am passing it as stim files in uber_subject.py GUI. But when i create a proc.py script i am getting warning saying few values in stim files are negative. I am looking to regression analysis on the data and get contrast for eg: sndpwr-1*Z-1*Y
My question is can i pass sndpwr, heart etc with negative stim values as regressors in the stim section of uber_subject.py gui?
With the negative tsim values i am not able to get output files stat.subject$$ ..
Any suggestion is greatly appreciated!
Thanks!
Sushil
Here is the cmd output:
+ Fixed clip level = 1637.579956
+ Used gradual clip level = 1316.520996 .. 1836.563843
+ Number voxels above clip level = 1437108
+ Clustering voxels ...
+ Largest cluster has 1426398 voxels
+ Clustering voxels ...
+ Largest cluster has 1424012 voxels
+ Filled 1220 voxels in small holes; now have 1425232 voxels
+ Filled 56354 voxels in large holes; now have 1481586 voxels
+ Clustering voxels ...
+ Largest cluster has 1481565 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 11731811 voxels
+ Mask now has 1481565 voxels
++ 1481565 voxels in the mask [out of 13213376: 11.21%]
++ first 17 x-planes are zero [from R]
++ last 11 x-planes are zero [from L]
++ first 56 y-planes are zero [from A]
++ last 38 y-planes are zero [from P]
++ first 118 z-planes are zero [from I]
++ last 28 z-planes are zero [from S]
++ applying mask to original data
++ Writing masked data
++ Output dataset ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig.BRIK
++ CPU time = 3.820000 sec
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig
#++ Applying threshold of 4875.000000 on /Users/sdb99/Subject18/subject_results/group.sub18fri/subj.sub18fri/sub18fri.results/__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns_wt -a ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig -expr 'min(1,(a/4875.000000))'
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tt_pb01.sub18fri.r01.tshift_ts_rs_ns_wt+orig.BRIK
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix ./__tt_mprage-s18-obl_ns_ob_al_junk_wtal -weight ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns_wt+orig -source ./__tt_mprage-s18-obl_ns_ob+orig -prefix ./__tt_mprage-s18-obl_ns_ob_temp_al_junk -base ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig -nocmass -1Dmatrix_save ./mprage-s18-obl_al_junk_e2a_only_mat.aff12.1D -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_mprage-s18-obl_ns_ob+orig.HEAD
++ Base dataset: ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig.HEAD
++ Loading datasets
++ 1752214 voxels in -source_automask+4
++ Zero-pad: not needed
++ 1481178 voxels [11.2%] in weight mask
++ Output dataset ./__tt_mprage-s18-obl_ns_ob_al_junk_wtal+orig.BRIK
++ Number of points for matching = 1481178
++ Local correlation: blok type = 'RHDD(6.54321)'
++ shift param auto-range: -56.2..56.2 -87.6..87.6 -87.6..87.6
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ OpenMP thread count = 4
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ ========== sub-brick #0 ========== [total CPU to here=8.3 s]
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - copying weight image
+ - using 1481178 points from base image [use_all=0]
+ * Exit alignment setup routine
+ 1389241 total points stored in 2602 'RHDD(6.54321)' bloks
+ - Initial cost = 0.029359
+ - Initial fine Parameters = 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
*****************************************************************************************************************************************************************
+ - Finalish cost = -0.022072 ; 424 funcs
*******
+ - Final cost = -0.022073 ; 132 funcs
+ Final fine fit Parameters:
x-shift=-4.0994 y-shift=-2.3632 z-shift= 0.6421
z-angle=-0.3081 x-angle= 3.3832 y-angle=-2.8356
x-scale= 0.9853 y-scale= 1.0035 z-scale= 0.9888
y/x-shear= 0.0971 z/x-shear= 0.0040 z/y-shear= 0.0551
+ - Fine net CPU time = 65.9 s
++ Computing output image
++ image warp: parameters = -4.0994 -2.3632 0.6421 -0.3081 3.3832 -2.8356 0.9853 1.0035 0.9888 0.0971 0.0040 0.0551
++ Output dataset ./__tt_mprage-s18-obl_ns_ob_temp_al_junk+orig.BRIK
++ Wrote -1Dmatrix_save ./mprage-s18-obl_al_junk_e2a_only_mat.aff12.1D
++ 3dAllineate: total CPU time = 76.8 sec Elapsed = 42.0
++ ###########################################################
++ ### Please check results visually for alignment quality ###
++ ###########################################################
#Script is running (command trimmed):
cat_matvec -ONELINE ./mprage-s18-obl_al_junk_e2a_only_mat.aff12.1D ./__tt_mprage-s18-obl_ns_obla2e_mat.1D -I > ./mprage-s18-obl_al_junk_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig -1Dmatrix_apply ./mprage-s18-obl_al_junk_mat.aff12.1D -prefix ./mprage-s18-obl_al_junk -input ./__tt_mprage-s18-obl_ns+orig -master SOURCE -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -onepass
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: ./__tt_mprage-s18-obl_ns+orig.HEAD
++ Base dataset: ./__tt_pb01.sub18fri.r01.tshift_ts_rs_ns+orig.HEAD
++ Loading datasets
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -10.000000 .. 10.000000
+ Range param#2 [y-shift] = -10.000000 .. 10.000000
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=4.3 s]
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - no weight image
+ - using 11 points from base image [use_all=0]
+ * Exit alignment setup routine
++ using -1Dmatrix_apply
++ Computing output image
++ image warp: parameters = 0.9841 -0.0082 0.0487 -9.1408 0.1024 1.0005 0.0314 -18.0979 -0.0416 0.0300 0.9909 5.0908
++ Output dataset ./mprage-s18-obl_al_junk+orig.BRIK
++ 3dAllineate: total CPU time = 7.9 sec Elapsed = 7.3
++ ###########################################################
#++ Creating final output: skullstripped anat data
#Script is running (command trimmed):
3dcopy ./__tt_mprage-s18-obl_ns+orig mprage-s18-obl_ns
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
#++ Creating final output: anat data aligned to epi
# copy is not necessary
#++ Saving history
#Script is running (command trimmed):
3dNotes -h "align_epi_anat.py -anat2epi -anat mprage-s18-obl+orig \
-save_skullstrip -suffix _al_junk -epi pb01.sub18fri.r01.tshift+orig \
-epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off" \
./mprage-s18-obl_al_junk+orig
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_pb01.sub18fri.r01.tshift*
#Script is running:
\rm -f ./__tt_mprage-s18-obl*
# Finished alignment successfully
@auto_tlrc -base TT_N27+tlrc -input mprage-s18-obl_ns+orig -no_ss
*********** Warning *************
Dataset centers are 58.261184 mm
apart. If registration fails, or if
parts of the original anatomy gets
cropped, try adding option
-init_xform AUTO_CENTER
to your @auto_tlrc command.
*********************************
Padding ...
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ output dataset: ./__ats_tmp__ref_TT_N27_40pad+tlrc.BRIK
Resampling ...
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp_step+orig.BRIK
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__resamp+tlrc.BRIK
Clipping -0.000100 3693.000100 ...
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__ats_tmp___rs_mprage-s18-obl_ns+tlrc.BRIK
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___rs_mprage-s18-obl_ns+tlrc.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_NN+tlrc.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp__resamp_edge_art+tlrc.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Registration (linear final interpolation) ...
++ 3dWarpDrive: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
RMS[0] = 83.2858 50.3984 ITER = 10/137
83.2858
Warping has converged.
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
Applying brain mask
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp__reg_braintlrcstep+orig.BRIK
++ 3dWarp: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ 3drename: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ THD_rename_dataset_files: rename __ats_tmp___pad40_mprage-s18-obl_ns+orig.HEAD -> __ats_tmp___pad40_mprage-s18-obl_ns.skl+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___pad40_mprage-s18-obl_ns+orig.BRIK -> __ats_tmp___pad40_mprage-s18-obl_ns.skl+orig.BRIK
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__ats_tmp___pad40_mprage-s18-obl_ns+orig.BRIK
Unpadding ...
++ 3dZeropad: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ output dataset: ./__ats_tmp___upad40_mprage-s18-obl_ns+orig.BRIK
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_mprage-s18-obl_ns+orig
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of transformed anatomy
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_mprage-s18-obl_ns+orig.HEAD
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
Setting parent with 3drefit -wset mprage-s18-obl_ns+orig __ats_tmp___upad40_mprage-s18-obl_ns+tlrc
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset __ats_tmp___upad40_mprage-s18-obl_ns+tlrc
++ 3drefit processed 1 datasets
++ 3drename: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Warning: ignoring +tlrc on new_prefix.
++ THD_rename_dataset_files: rename __ats_tmp___upad40_mprage-s18-obl_ns+tlrc.HEAD -> mprage-s18-obl_ns+tlrc.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___upad40_mprage-s18-obl_ns+tlrc.BRIK -> mprage-s18-obl_ns+tlrc.BRIK
Cleanup ...
cat_matvec mprage-s18-obl_ns+tlrc::WARP_DATA -I
if ( ! -f mprage-s18-obl_ns+tlrc.HEAD ) then
foreach run ( 01 )
3dvolreg -verbose -zpad 1 -base pb01.sub18fri.r01.tshift+orig[2] -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 -cubic -1Dmatrix_save mat.r01.vr.aff12.1D pb01.sub18fri.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb01.sub18fri.r01.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.sub18fri.r01.tshift+orig.BRIK is 1.882632 degrees from plumb.
++ Reading in base dataset ./pb01.sub18fri.r01.tshift+orig.BRIK
++ Oblique dataset:./pb01.sub18fri.r01.tshift+orig.BRIK is 1.882632 degrees from plumb.
++ Reading input dataset ./pb01.sub18fri.r01.tshift+orig.BRIK
++ Edging: x=4 y=4 z=2
++ Creating mask for -maxdisp
+ Automask has 55631 voxels
+ 7777 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 362 sub-bricks: 0..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..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..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..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359..360..361..
++ CPU time for realignment=19 s [=0.0526 s/sub-brick]
++ Min : roll=-0.062 pitch=-0.040 yaw=-0.086 dS=-0.217 dL=-0.028 dP=-0.192
++ Mean: roll=-0.022 pitch=+0.089 yaw=-0.019 dS=-0.050 dL=+0.011 dP=-0.104
++ Max : roll=+0.010 pitch=+0.260 yaw=+0.059 dS=+0.097 dL=+0.054 dP=+0.014
++ Max displacements (mm) for each sub-brick:
0.05 0.08 0.00 0.05 0.12 0.20 0.21 0.19 0.22 0.17 0.17 0.18 0.17 0.19 0.13 0.12 0.15 0.13 0.11 0.09 0.06 0.07 0.08 0.12 0.15 0.14 0.11 0.10 0.09 0.11 0.11 0.11 0.07 0.10 0.11 0.08 0.08 0.07 0.07 0.09 0.09 0.07 0.07 0.10 0.12 0.12 0.12 0.11 0.12 0.16 0.13 0.08 0.11 0.13 0.18 0.14 0.13 0.13 0.14 0.16 0.11 0.21 0.24 0.28 0.25 0.26 0.31 0.37 0.41 0.35 0.39 0.42 0.43 0.40 0.34 0.39 0.39 0.39 0.40 0.34 0.33 0.35 0.36 0.34 0.34 0.41 0.34 0.37 0.36 0.43 0.38 0.37 0.38 0.39 0.35 0.35 0.38 0.33 0.27 0.30 0.29 0.26 0.27 0.26 0.25 0.27 0.27 0.27 0.28 0.33 0.31 0.28 0.31 0.29 0.28 0.27 0.25 0.22 0.25 0.21 0.27 0.27 0.31 0.27 0.31 0.30 0.30 0.29 0.27 0.29 0.33 0.29 0.28 0.28 0.30 0.32 0.36 0.36 0.37 0.36 0.32 0.33 0.40 0.33 0.31 0.33 0.35 0.34 0.34 0.33 0.28 0.28 0.34 0.27 0.31 0.29 0.32 0.31 0.31 0.25 0.23 0.17 0.25 0.21 0.21 0.20 0.26 0.24 0.24 0.24 0.22 0.27 0.23 0.19 0.20 0.20 0.23 0.18 0.17 0.21 0.23 0.25 0.26 0.23 0.22 0.21 0.22 0.23 0.22 0.24 0.21 0.21 0.25 0.23 0.22 0.22 0.22 0.24 0.22 0.22 0.21 0.19 0.19 0.21 0.20 0.19 0.18 0.18 0.19 0.19 0.17 0.19 0.22 0.18 0.19 0.19 0.18 0.16 0.22 0.22 0.25 0.17 0.18 0.17 0.21 0.18 0.22 0.19 0.24 0.20 0.20 0.25 0.17 0.19 0.24 0.26 0.24 0.27 0.24 0.35 0.37 0.40 0.40 0.33 0.36 0.34 0.35 0.23 0.30 0.29 0.24 0.29 0.24 0.26 0.24 0.26 0.28 0.25 0.28 0.26 0.31 0.27 0.31 0.32 0.34 0.33 0.34 0.33 0.37 0.37 0.34 0.32 0.36 0.39 0.38 0.39 0.38 0.42 0.41 0.38 0.33 0.36 0.37 0.35 0.32 0.30 0.36 0.32 0.35 0.36 0.33 0.27 0.31 0.35 0.34 0.34 0.28 0.22 0.22 0.24 0.21 0.23 0.20 0.28 0.33 0.32 0.26 0.23 0.26 0.23 0.24 0.32 0.36 0.36 0.34 0.30 0.27 0.30 0.24 0.21 0.27 0.24 0.25 0.23 0.30 0.26 0.28 0.22 0.28 0.26 0.31 0.24 0.28 0.22 0.31 0.25 0.33 0.36 0.27 0.28 0.21 0.31 0.31 0.32 0.34 0.29 0.30 0.31 0.41 0.29 0.33 0.25 0.37 0.35 0.40 0.24 0.24 0.33 0.29 0.31 0.28 0.21
++ Max displacement in automask = 0.43 (mm) at sub-brick 72
++ Wrote dataset to disk in ./rm.epi.volreg.r01+orig.BRIK
3dcalc -overwrite -a pb01.sub18fri.r01.tshift+orig -expr 1 -prefix rm.epi.all1
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: input 'a' is not used in the expression
++ Output dataset ./rm.epi.all1+orig.BRIK
cat_matvec -ONELINE mprage-s18-obl_ns+tlrc::WARP_DATA -I mprage-s18-obl_al_junk_mat.aff12.1D -I mat.r01.vr.aff12.1D
3dAllineate -base mprage-s18-obl_ns+tlrc -input pb01.sub18fri.r01.tshift+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r01
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./pb01.sub18fri.r01.tshift+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./pb01.sub18fri.r01.tshift+orig.BRIK is 1.882632 degrees from plumb.
++ Source dataset: ./pb01.sub18fri.r01.tshift+orig.HEAD
++ Base dataset: ./mprage-s18-obl_ns+tlrc.HEAD
++ Loading datasets
++ master dataset for output = base
++ changing output grid spacing to 3.0000 mm
++ OpenMP thread count = 4
++ ========== Applying transformation to 362 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=1.3 s]
++ ========== sub-brick #1 ========== [total CPU to here=1.4 s]
++ ========== sub-brick #2 ========== [total CPU to here=1.4 s]
++ ========== sub-brick #3 ========== [total CPU to here=1.5 s]
++ ========== sub-brick #4 ========== [total CPU to here=1.6 s]
++ ========== sub-brick #5 ========== [total CPU to here=1.7 s]
++ ========== sub-brick #6 ========== [total CPU to here=1.8 s]
++ ========== sub-brick #7 ========== [total CPU to here=1.8 s]
++ ========== sub-brick #8 ========== [total CPU to here=1.9 s]
++ ========== sub-brick #9 ========== [total CPU to here=1.9 s]
++ ========== sub-brick #10 ========== [total CPU to here=2.0 s]
++ ========== sub-brick #11 ========== [total CPU to here=2.1 s]
++ ========== sub-brick #12 ========== [total CPU to here=2.1 s]
++ ========== sub-brick #13 ========== [total CPU to here=2.2 s]
++ ========== sub-brick #14 ========== [total CPU to here=2.3 s]
++ ========== sub-brick #15 ========== [total CPU to here=2.4 s]
++ ========== sub-brick #16 ========== [total CPU to here=2.4 s]
++ ========== sub-brick #17 ========== [total CPU to here=2.5 s]
++ ========== sub-brick #18 ========== [total CPU to here=2.6 s]
..
..
++ Output dataset ./rm.epi.nomask.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 26.1 sec Elapsed = 20.5
++ ###########################################################
3dAllineate -base mprage-s18-obl_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./rm.epi.all1+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./rm.epi.all1+orig.BRIK is 1.882632 degrees from plumb.
++ Output dataset ./rm.epi.1.r01+tlrc.BRIK
++ 3dAllineate: total CPU time = 18.1 sec Elapsed = 18.6
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.epi.min.r01+tlrc.BRIK
end
cat dfile.r01.1D
3dcopy rm.epi.min.r01+tlrc mask_epi_extents
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
foreach run ( 01 )
3dcalc -a rm.epi.nomask.r01+tlrc -b mask_epi_extents+tlrc -expr a*b -prefix pb02.sub18fri.r01.volreg
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb02.sub18fri.r01.volreg+tlrc.BRIK
end
3dcopy mprage-s18-obl_ns+tlrc anat_final.sub18fri
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
3dAllineate -source mprage-s18-obl+orig -master anat_final.sub18fri+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped
++ 3dAllineate: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Zhark the Registrator
++ -1Dmatrix_apply: converting input 3x4 array to 1 row of 12 numbers
++ Source dataset: ./mprage-s18-obl+orig.HEAD
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=5.0 s]
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset ./anat_w_skull_warped+tlrc.BRIK
++ 3dAllineate: total CPU time = 22.6 sec Elapsed = 11.1
++ ###########################################################
foreach run ( 01 )
3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.sub18fri.r01.blur pb02.sub18fri.r01.volreg+tlrc
++ 3dmerge: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ default -1dindex = 0
++ default -1tindex = 1
Program 3dmerge
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (119.3 MB)
-- Wrote edited dataset: ./pb03.sub18fri.r01.blur+tlrc.BRIK
Editing sub-brick 0
Editing sub-brick 1
Editing sub-brick 2
Editing sub-brick 3
Editing sub-brick 4
....
.....
....
end
foreach run ( 01 )
3dAutomask -dilate 1 -prefix rm.mask_r01 pb03.sub18fri.r01.blur+tlrc
++ 3dAutomask: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset pb03.sub18fri.r01.blur+tlrc
++ Forming automask
+ Fixed clip level = 1593.594360
+ Used gradual clip level = 1364.120850 .. 1839.525879
+ Number voxels above clip level = 50128
+ Clustering voxels ...
+ Largest cluster has 49833 voxels
+ Clustering voxels ...
+ Largest cluster has 49272 voxels
+ Filled 235 voxels in small holes; now have 49507 voxels
+ Filled 4 voxels in large holes; now have 49511 voxels
+ Clustering voxels ...
+ Largest cluster has 49508 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 123292 voxels
+ Mask now has 49508 voxels
++ Dilating automask
+ Clustering voxels ...
+ Largest cluster has 115236 voxels
++ 57564 voxels in the mask [out of 172800: 33.31%]
++ first 1 x-planes are zero [from R]
++ last 4 x-planes are zero [from L]
++ first 2 y-planes are zero [from A]
++ last 5 y-planes are zero [from P]
++ first 4 z-planes are zero [from I]
++ last 0 z-planes are zero [from S]
++ Output dataset ./rm.mask_r01+tlrc.BRIK
++ CPU time = 0.650000 sec
end
3dmask_tool -inputs rm.mask_r01+tlrc.HEAD -union -prefix full_mask.sub18fri
++ processing 1 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 57564 survived, 115236 were zero
++ writing result full_mask.sub18fri...
++ Output dataset ./full_mask.sub18fri+tlrc.BRIK
3dresample -master full_mask.sub18fri+tlrc -input mprage-s18-obl_ns+tlrc -prefix rm.resam.anat
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.sub18fri
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 53959 survived, 118841 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_anat.sub18fri...
++ Output dataset ./mask_anat.sub18fri+tlrc.BRIK
3dABoverlap -no_automask full_mask.sub18fri+tlrc mask_anat.sub18fri+tlrc
tee out.mask_ae_overlap.txt
++ 3dOverlap: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
#A=./full_mask.sub18fri+tlrc.BRIK B=./mask_anat.sub18fri+tlrc.BRIK
#A #B #(A uni B) #(A int B) #(A \ B) #(B \ A) %(A \ B) %(B \ A) Rx(B/A) Ry(B/A) Rz(B/A)
57564 53959 63938 47585 9979 6374 17.3355 11.8127 0.8654 0.9116 0.9924
3ddot -demean full_mask.sub18fri+tlrc mask_anat.sub18fri+tlrc
tee out.mask_ae_corr.txt
0.784506
3dresample -master full_mask.sub18fri+tlrc -prefix ./rm.resam.group -input /Users/sdb99/abin/TT_N27+tlrc
3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 5 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 55366 survived, 117434 were zero
++ filled 0 holes (0 voxels)
++ writing result mask_group...
++ Output dataset ./mask_group+tlrc.BRIK
foreach run ( 01 )
3dTstat -prefix rm.mean_r01 pb03.sub18fri.r01.blur+tlrc
++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./rm.mean_r01+tlrc.BRIK
3dcalc -a pb03.sub18fri.r01.blur+tlrc -b rm.mean_r01+tlrc -c mask_epi_extents+tlrc -expr c * min(200, a/b*100)*step(a)*step(b) -prefix pb04.sub18fri.r01.scale
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./pb04.sub18fri.r01.scale+tlrc.BRIK
end
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D
1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_sub18fri
total number of censored TRs = 0
3dDeconvolve -input pb04.sub18fri.r01.scale+tlrc.HEAD -censor motion_sub18fri_censor.1D -polort 5 -num_stimts 16 -stim_times 1 stimuli/s18-dis-der-sndpwr.txt GAM -stim_label 1 dis-der-sndpwr -stim_times 2 stimuli/s18-heart.txt GAM -stim_label 2 heart -stim_times 3 stimuli/s18-lungs.txt GAM -stim_label 3 lungs -stim_times 4 stimuli/s18-sndpwr.txt GAM -stim_label 4 sndpwr -stim_file 5 motion_demean.1D[0] -stim_base 5 -stim_label 5 roll_01 -stim_file 6 motion_demean.1D[1] -stim_base 6 -stim_label 6 pitch_01 -stim_file 7 motion_demean.1D[2] -stim_base 7 -stim_label 7 yaw_01 -stim_file 8 motion_demean.1D[3] -stim_base 8 -stim_label 8 dS_01 -stim_file 9 motion_demean.1D[4] -stim_base 9 -stim_label 9 dL_01 -stim_file 10 motion_demean.1D[5] -stim_base 10 -stim_label 10 dP_01 -stim_file 11 motion_deriv.1D[0] -stim_base 11 -stim_label 11 roll_02 -stim_file 12 motion_deriv.1D[1] -stim_base 12 -stim_label 12 pitch_02 -stim_file 13 motion_deriv.1D[2] -stim_base 13 -stim_label 13 yaw_02 -stim_file 14 motion_deriv.1D[3] -stim_base 14 -stim_label 14 dS_02 -stim_file 15 motion_deriv.1D[4] -stim_base 15 -stim_label 15 dL_02 -stim_file 16 motion_deriv.1D[5] -stim_base 16 -stim_label 16 dP_02 -gltsym SYM: sndpwr-1*heart-1*dis-der-sndpwr -1*lungs -glt_label 1 sndpwr_contrast -gltsym SYM: dis-der-sndpwr -lungs -glt_label 2 dis-der-sndpwr-lungs -gltsym SYM: heart -lungs -glt_label 3 heart-lungs -gltsym SYM: 0.333*dis-der-sndpwr +0.333*heart +0.333*lungs -glt_label 4 mean.DHL -gltsym SYM: dis-der-sndpwr -0.5*heart -0.5*lungs -glt_label 5 D-HL -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -errts errts.sub18fri -bucket stats.sub18fri
*+ WARNING: '-stim_times 3' didn't read any good times from file 'stimuli/s18-lungs.txt'
++ 3dDeconvolve: AFNI version=AFNI_2011_12_21_1014 (May 8 2015) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset pb04.sub18fri.r01.scale+tlrc.HEAD
++ STAT automask has 150911 voxels (out of 172800 = 87.3%)
++ Skipping check for initial transients
++ Input polort=5; Longest run=724.0 s; Recommended minimum polort=5 ++ OK ++
++ -stim_times using TR=2 s for stimulus timing conversion
++ -stim_times using TR=2 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using GLOBAL times
*+ WARNING: '-stim_times 1' (GLOBAL) has 360 times outside range 0 .. 722 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
-0.00033521 -0.00080065 -0.00031457 -0.00075729 -0.001189 -0.0011157 -0.0011393 -0.0009936 -0.00039896 -0.0012745 -0.001677 -0.00078611 -0.00090805 -0.0015619 -0.0021151 -0.0013384 -0.0012254 -0.0014131 -0.0013692 -0.0022498 -0.0013194 -0.0012966 -0.0012612 -0.0014383 -0.0017519 -0.0020166 -0.0018996 -0.0016561 -0.0016934 -0.0023928 -0.0017936 -0.001478 -0.0017891 -0.001319 -0.00093228 -0.0018412 -0.0016798 -0.0012272 -0.0017156 -0.0010843 -0.001368 -0.0014586 -0.0013864 -0.0017816 -0.00097647 -0.00074393 -0.0011494 -0.001874 -0.0013458 -0.0012806 -0.00098596 -0.0010554 -0.0012612 -0.0016581 -0.0016946 -0.00086249 -0.00090011 -0.0012635 -0.0013297 -0.0015283 -0.0018435 -0.00094732 -0.0010019 -0.0016497 -0.0010593 -0.00041586 -0.0016805 -0.0011409 -0.0011641 -0.0012335 -0.0014618 -0.00072225 -0.0010285 -0.001572 -0.001169 -0.00047179 -0.00075702 -0.0013343 -0.0011784 -0.00054674 -0.0006481 -0.0009147 -0.0014466 -0.00055693 -0.00063124 -0.0018422 -0.0014234 -0.00090477 -0.0017458 -0.0011796 -0.00028771 -0.0020169 -0.0022075 -0.0015181 -0.0015074 -0.0017257 -0.0021419 -0.0019365 -0.0009708 -0.0011883 -0.0012868 -0.0011995 -0.0015956 -0.00058397 -0.00050529 -0.0013771 -0.001331 -0.00091854 -0.0011353 -0.0017077 -0.0012412 -0.0010625 -0.0012855 -0.00087241 -0.0012668 -0.00176 -0.0014228 -0.00077562 -0.0016853 -0.00089719 -0.00053753 -0.0013926 -0.00078348 -0.0017391 -0.0017018 -0.00098777 -0.0017562 -0.001285 -0.0011263 -0.00077809 -0.0012755 -0.0021087 -0.001539 -0.00018512 -0.0013921 -0.00095747 -0.0009337 -0.0023318 -0.0012434 -0.00068321 -0.001643 -0.0016882 -0.001388 -0.0011987 -0.0018013 -0.0013577 -0.0010807 -0.0011451 -0.00071461 -0.0010498 -0.00089263 -0.00082241 -0.00079144 -0.00040043 -0.0010156 -0.0014817 -0.00065941 -0.0010021 -0.0011768 -0.0014355 -0.001407 -0.0012132 -0.0010416 -0.0012322 -0.0011426 -0.0015412 -0.0012513 -0.00042612 -0.00087084 -0.0008127 -0.0012559 -0.0010876 -0.0012375 -0.0014603 -0.0010197 -0.0011795 -0.0021858 -0.0013803 -0.0011851 -0.0017416 -0.0012107 -0.0016088 -0.0013057 -0.0013119 -0.001527 -0.0017342 -0.0014097 -0.00088016 -0.0015783 -0.0018108 -0.0013308 -0.0019654 -0.0018034 -0.0010704 -0.001406 -0.0011312 -0.0015329 -0.0012809 -0.0017147 -0.001838 -0.00073073 -0.001048 -0.0016941 -0.001416 -0.0009804 -0.0015934 -0.00075055 -0.0011214 -0.0012941 -0.00099531 -0.0017494 -0.0013531 -0.0010363 -0.001196 -0.0016989 -0.0015519 -0.00070721 -0.0016278 -0.0021144 -0.00086777 -0.0010911 -0.001824 -0.0016726 -0.0011928 -0.0018075 -0.0012007 -0.00083597 -0.0017495 -0.0015741 -0.0014518 -0.0015369 -0.0018104 -0.0018114 -0.00077776 -0.0020599 -0.0017328 -0.0011388 -0.0014981 -0.001736 -0.00094106 -0.0011598 -0.0014084 -0.0013401 -0.0009457 -0.0011199 -0.00079298 -0.00021199 -0.0013639 -0.0021085 -0.0010829 -0.00064974 -0.0019349 -0.0019064 -0.001331 -0.0015279 -0.001426 -0.0016878 -0.0009596 -0.0011862 -0.00089052 -0.0011737 -0.0014053 -0.00094183 -0.00086661 -0.00077598 -0.0012326 -0.0012317 -0.00082557 -0.00074735 -0.0014462 -0.00086694 -0.00079106 -0.00078837 -0.00081753 -0.00091292 -0.0011294 -0.0006283 -0.00081676 -0.00082247 -0.00077335 -0.0016144 -0.00048817 -0.00074297 -0.0015748 -0.0012727 -0.0014331 -0.001844 -0.0013343 -0.0016193 -0.0019768 -0.0014983 -0.0011643 -0.00098428 -0.0011579 -0.0018035 -0.0013473 -0.00074985 -0.0013867 -0.0018602 -0.0010332 -0.00082867 -0.0020013 -0.001693 -0.00047956 -0.0011509 -0.0018467 -0.0013535 -0.0011524 -0.0011984 -0.0015431 -0.0019434 -0.0011064 -0.00053092 -0.0009897 -0.0010925 -0.00097376 -0.00078873 -0.00033222 -0.0019131 -0.00082683 -0.00027045 -0.0017654 -0.0011477 -0.0011111 -0.00085222 -0.0018299 -0.0016863 -0.00060763 -0.0010158 -0.0011903 -0.00090387 -0.001572 -0.0012238 -0.00024587 -0.0010557 -0.0013312 -0.0020034 -0.00092383 -0.00060547 -0.0010234 -0.0015 -0.0017718 -0.00075465 -0.00085238 -0.00081407 -0.0011766 -0.0015139 -0.00093331 -0.00062086 -0.0010944 -0.0013375 -0.0011193 -0.0014382 -0.0016644 -0.00069853 -0.00089108 -0.0013167 -0.00078364 -0.00082634 -0.0010653
*+ WARNING: '-stim_times 1' file 'stimuli/s18-dis-der-sndpwr.txt' has 0 duplicate and 1 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
++ ** GUESSED ** -stim_times 2 using GLOBAL times
*+ WARNING: '-stim_times 2' (GLOBAL) has 116 times outside range 0 .. 722 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
-0.279 -3.229 -3.5957 -3.3176 -0.034927 -2.2409 -6.678 -3.4342 -1.9999 -8.3584 -0.62135 -2.0644 -1.7942 -0.59761 -3.614 -5.5434 -11.403 -4.7095 -0.58027 -5.7555 -0.1233 -6.8775 -0.9493 -0.046737 -11.127 -9.3933 -9.6199 -0.62529 -1.192 -1.246 -1.7678 -1.3375 -0.23264 -0.40082 -0.68628 -0.43081 -0.80747 -4.6299 -4.6098 -7.6304 -4.744 -6.2811 -4.2214 -0.36617 -0.095402 -0.94951 -2.5717 -0.42375 -3.8442 -5.7512 -0.69589 -6.9687 -1.8901 -4.6272 -9.9362 -0.091347 -1.571 -3.2272 -0.84451 -4.8573 -1.0034 -3.4041 -2.6522 -2.5115 -6.6941 -6.546 -0.86224 -0.71194 -9.218 -12.415 -2.4015 -4.246 -0.13364 -8.8978 -1.2167 -2.8001 -2.4707 -0.43889 -6.1311 -8.0479 -3.5204 -8.7851 -1.8118 -1.3603 -1.1307 -5.394 -5.2664 -3.1067 -3.2471 -28.448 -10.959 -0.45195 -12.707 -5.4603 -1.4005 -5.7206 -10.505 -1.7241 -11.749 -0.89892 -0.7275 -2.4604 -5.1116 -3.0717 -2.9136 -1.3719 -2.8084 -11.051 -2.4584 -0.26153 -18.588 -9.7706 -2.3536 -0.55641 -24.231 -14.8
*+ WARNING: '-stim_times 2' file 'stimuli/s18-heart.txt' has 0 duplicate and 5651 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
++ ** GUESSED ** -stim_times 3 using GLOBAL times
*+ WARNING: '-stim_times 3' (GLOBAL) has 362 times outside range 0 .. 722 [PSFB syndrome]
+ dataset TR being used is 2 s -- unusable times follow
-1159.6 -2818.3 -2466 -2655.2 -2392.8 -2495.8 -2363.6 -2590.5 -2424.1 -2159.6 -2563.3 -2372.1 -2489.6 -2555.9 -2606.6 -2656.7 -2662.3 -2473.2 -2536.1 -2620.6 -2505.6 -2196.9 -2191.2 -2603.4 -2331.7 -2623.2 -2607.3 -2711.5 -2610.3 -2682.5 -2635.7 -2763.4 -2421 -2865.1 -1647.8 -2300 -2776 -2549.5 -2784.9 -2435.2 -2661.1 -2587.8 -2442.6 -2624 -2123.7 -1921.5 -2819 -2489.1 -2646.1 -2608.2 -2466.8 -2387.5 -3197.3 -1529.3 -2540.3 -2128.8 -2587.9 -2055 -2426.7 -2573 -2479.5 -2664.8 -1218.8 -3025 -2315.2 -2657.2 -2364.1 -2602.2 -2213 -2524.7 -2539.3 -2189.9 -2399.1 -2694.5 -2350.8 -2736.4 -2254 -2471.2 -2403.2 -2413.9 -2551.5 -2413.8 -2743.6 -2720.2 -2410.5 -2508.5 -2291.8 -2423.3 -2148.6 -2614.2 -2278.7 -2798.2 -2514.2 -2568.6 -2659.8 -2338.5 -2382.9 -2604.7 -2548.8 -2847.5 -2105.1 -2245.1 -2660.1 -2580.1 -2766.3 -2616.9 -2632.1 -2563.6 -2461.5 -2574.4 -2387.8 -2698.5 -2268.6 -2437.6 -2557.9 -2540.6 -2489.2 -2541.7 -2426.9 -2488.2 -2522.3 -2276.4 -2766.1 -2283.6 -2666.9 -2067.9 -2824 -2395.9 -2507.6 -2771.9 -2161.6 -2311.4 -2599.5 -2598.9 -2395.4 -2376.7 -2433.6 -2280.6 -2624.1 -2476 -2497 -2871.1 -2068 -2711.3 -2705.9 -2345.8 -2626.5 -2416 -2463.2 -2627.1 -2457.5 -2739.5 -1770.6 -2122.2 -3046.5 -1910.4 -2952.4 -2292.7 -2774.1 -2485.5 -2574.2 -2391.8 -2411.5 -1814 -2841.9 -2294.1 -2710.4 -2385.4 -2670.5 -2428.6 -2530.2 -2446.4 -2233.7 -2571.2 -2740.9 -2289.1 -2572.7 -2434.8 -2637.1 -2551.6 -2487.4 -2620.9 -2300.3 -2611.9 -2475.7 -2560 -2574.4 -2454.3 -2532.3 -2626.6 -2491.1 -2601.2 -2617.7 -2439.7 -2537.1 -2480.8 -2427.2 -2580.4 -2483.3 -2439.5 -2490.3 -2580.6 -2512.2 -2530.3 -2544.6 -2574.4 -2406.8 -2639.3 -2412.9 -1803.4 -2694.7 -2502.5 -2560 -2636.4 -2812 -2303.1 -2648.4 -2528.3 -2568.6 -2580.4 -2587.2 -2308.4 -2956 -2107.4 -2750.2 -2370.2 -2696.5 -1253.8 -2566.2 -2608.2 -2461.8 -2508.7 -2441.7 -2880.9 -1625.5 -2420 -2703.9 -2494.4 -2418.6 -2530.8 -2071 -2376 -2618 -2562.7 -2591.1 -2381.4 -2793.7 -2320.6 -2741.4 -1601.7 -2338.3 -2908.4 -1058.7 -3010.9 -2325.2 -2773.6 -2487.1 -2472.8 -2592.3 -2301.7 -2919.4 -2237.2 -2815.6 -2450.4 -2573.4 -2334.2 -2694.7 -2394.9 -2733.3 -2211.9 -2738.6 -2529.9 -2351.5 -2588.4 -2379 -2604.2 -2412.9 -2450.4 -2446 -2395.1 -2510.3 -2572 -2467.1 -2524.4 -2535.3 -2570.6 -2353.4 -2506.8 -2685.8 -2229.1 -2744.4 -2636.6 -2571.1 -2202.9 -2561.5 -2462.8 -2536 -2500.3 -2547 -2469.4 -2442.2 -2779.9 -2314 -2782.5 -1771.3 -2335 -2733.7 -2410.7 -2795.7 -2231.5 -2799.3 -2286 -2016.5 -2766.2 -2418.4 -2604.9 -2428.9 -2730.4 -2579.7 -2778.5 -2489.6 -2033.9 -2715.2 -2257.4 -2831.8 -1809.2 -2825.5 -2313.7 -2541.7 -2292.5 -2737.3 -2101.9 -2600.6 -2195 -2601.4 -1918.7 -2933.7 -597.79 -2275.8 -3064.2 -2190.5 -2994.3 -1811 -2924.1 -2405.2 -2643 -2748.8 -2289.2 -2788.2 -2037.8 -2933.1 -1597.1 -2761.6 -1786.7 -2860 -2305 -2994.6 -484.42 -1582.7 -3130.2 -2198.7 -3280.2
*+ WARNING: !! '-stim_times 3' file 'stimuli/s18-lungs.txt' has no good stimulus time values
++ ** GUESSED ** -stim_times 4 using GLOBAL times
*+ WARNING: '-stim_times 4' file 'stimuli/s18-sndpwr.txt' has 2 duplicate and 65339 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
*+ WARNING: -gltsym: Can't interpret '*' scale factor in 'sndpwr-1*heart-1*dis-der-sndpwr' -- replaced by 1
*+ WARNING: -gltsym: '*' scale factor in 'sndpwr-1*heart-1*dis-der-sndpwr' not at start of string?
** ERROR: -gltsym: can't match symbolic name 'heart-1*dis-der-sndpwr'
------------------------------------------------------------
GLT matrix from 'SYM: sndpwr-1*heart-1*dis-der-sndpwr -1*lungs':
0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
** ERROR: -gltsym errors immediately above from file 'SYM: sndpwr-1*heart-1*dis-der-sndpwr -1*lungs'
------------------------------------------------------------
GLT matrix from 'SYM: dis-der-sndpwr -lungs':
0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: heart -lungs':
0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: 0.333*dis-der-sndpwr +0.333*heart +0.333*lungs':
0 0 0 0 0 0 0.333 0.333 0.333 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: dis-der-sndpwr -0.5*heart -0.5*lungs':
0 0 0 0 0 0 1 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0
** FATAL ERROR: Can't continue after the above -gltsym problems!
** Program compile date = May 8 2015
| Subject | Author | Posted |
|---|---|---|
|
sdb99 | May 22, 2015 06:00PM |
|
rick reynolds | May 24, 2015 10:04PM |
