afni.nimh.nih.gov
| June 08, 2021 10:10AM | |
Registered: 2 years ago Posts: 19 |
Thank you for your help with this. I updated my afni binaries but unfortunately I'm still encountering the same problems. Here is the log from the redo_apqc script (copied in 2 parts because of the message character limit):
1/2:
[Michaels-MacBook-Pro-6:AFNI_data6/FT_analysis/FT.NL.results] michaelspilka% tcsh redo_apqc.tcsh
++ REDOing APQC
++ Going to re-run APQC in this dir only: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results
++ Found 41 files for QCing.
++ Done making (executable) script to generate HTML QC:
./@ss_review_html
*+ Found main dset (template): /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ My command:
@chauffeur_afni -ulay vr_base_min_outlier+orig.HEAD -olay vr_base_min_outlier+orig.HEAD -ulay_range_nz 0 1751.000000 -func_range 1751.000000 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim QC_FT.NL/media/qc_00_vorig_EPI.pbar.jpg -pbar_comm_range 98%ile in vol -pbar_for dset -prefix QC_FT.NL/media/qc_00_vorig_EPI -save_ftype JPEG -blowup 4 -opacity 9 -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
++ 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, 1751.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_bbULaIX34j9/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_bbULaIX34j9/tmp_olay.nii
++ User-entered function range value value (1751.000000)
++ Dimensions (xyzt): 80 80 33 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 8 3
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=vr_base_min_outlier+orig.HEAD[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_6sTfbGnj_VZMWRtARIWKNA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_6sTfbGnj_VZMWRtARIWKNA+orig.BRIK
++ 211200 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 40 40 16
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :611
[1] 45065
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_bbULaIX34j9*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean gray_scale'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.axi.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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:3:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean gray_scale -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 1751.000000 -com SET_FUNC_RANGE 1751.000000 -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_IJK 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_00_vorig_EPI.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_00_vorig_EPI.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_00_vorig_EPI.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_bbULaIX34j9'.\n
++ DONE (good exit)
see: QC_FT.NL/media/qc_00_vorig_EPI*
ERROR: QC_FT.NL/media/qc_00_vorig_EPI.pbar.txt not found!!
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) to workdir
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_0_cp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_0_cp.nii
++ Base dataset: (not given)
++ Loading datasets into memory
+ -cmass x y z shifts = 0.000 0.000 0.000
+ shift search range is +/- = 60.990 73.028 60.990
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ 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 QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_1_grid2olay.nii
++ 3dAllineate: total CPU time = 28.1 sec Elapsed = 8.6
++ ###########################################################
++ Output dataset ./eac_2_ulay_shrp.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_3_cp.nii
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_3_cp.nii
++ Forming automask
+ Fixed clip level = 457.476471
+ Used gradual clip level = 444.055969 .. 462.343231
+ Number voxels above clip level = 1751345
+ Clustering voxels ...
+ Largest cluster has 1751228 voxels
+ Clustering voxels ...
+ Largest cluster has 1735652 voxels
+ Filled 25607 voxels in small holes; now have 1761259 voxels
+ Filled 88085 voxels in large holes; now have 1849344 voxels
+ Clustering voxels ...
+ Largest cluster has 1849333 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6679560 voxels
+ Mask now has 1850461 voxels
++ 1850461 voxels in the mask [out of 8530021: 21.69%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 25 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 5 z-planes are zero [from I]
++ last 31 z-planes are zero [from S]
++ Output dataset ./eac_4_mask.nii
++ CPU time = 1.870000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Output dataset ./eac_5_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_2_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_6_edgy.nii -ulay_range_nz 2% 98% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 17.745312 -opacity 9 -prefix ../qc_01_ve2a_epi2anat -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: eac_2_ulay_shrp.nii
++ Found input file: eac_6_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_mB1CFMIc4np
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1683.303589]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_mB1CFMIc4np/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_mB1CFMIc4np/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 245.202560
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_2_ulay_shrp.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_XGAxa3qRzo9hHcisRjjjiw argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_XGAxa3qRzo9hHcisRjjjiw+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :225
[1] 45280
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_mB1CFMIc4np*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1683.303589 -com SET_FUNC_RANGE 245.202560 -com SET_THRESHNEW 17.745312 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage ../qc_01_ve2a_epi2anat.sag blowup=2 -com SAVE_PNG coronalimage ../qc_01_ve2a_epi2anat.cor blowup=2 -com SAVE_PNG axialimage ../qc_01_ve2a_epi2anat.axi blowup=2 -com QUITT ../__tmp_chauf_mB1CFMIc4np
\n+* Removing temporary image directory '../__tmp_chauf_mB1CFMIc4np'.\n
++ DONE (good exit)
see: ../qc_01_ve2a_epi2anat*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_01_ve2a_epi2anat
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) to workdir
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/eac_0_cp.nii
++ Output dataset ./eac_1_ulay_shrp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets into memory
*+ WARNING: -1D*_apply '1D: 12@0'': 1 isn't enough rows for source dataset -- last row will repeat
+ -cmass x y z shifts = -0.008 -0.005 0.029
+ shift search range is +/- = 61.632 73.188 61.632
++ OpenMP thread count = 4
++ ========== Applying transformation to 5 sub-bricks ==========
volume 0..1*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #1
..2*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #2
..3*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #3
..4
*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #4
++ Output dataset QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/eac_2_res.nii
++ 3dAllineate: total CPU time = 5.0 sec Elapsed = 4.4
++ ###########################################################
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_2_res.nii
++ Forming automask
+ Fixed clip level = 866.280640
+ Used gradual clip level = 839.463562 .. 889.332031
+ Number voxels above clip level = 1839751
+ Clustering voxels ...
+ Largest cluster has 1839749 voxels
+ Clustering voxels ...
+ Largest cluster has 1839644 voxels
+ Filled 2255 voxels in small holes; now have 1841899 voxels
+ Filled 40056 voxels in large holes; now have 1881955 voxels
+ Clustering voxels ...
+ Largest cluster has 1881949 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6644410 voxels
+ Mask now has 1885611 voxels
++ 1885611 voxels in the mask [out of 8530021: 22.11%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 24 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 6 z-planes are zero [from I]
++ last 32 z-planes are zero [from S]
++ Output dataset ./eac_3_mask.nii
++ CPU time = 2.850000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
*+ WARNING: Only processing sub-brick #0
++ Output dataset ./eac_4_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_1_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_5_edgy.nii -ulay_range 0% 120% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 22.371048 -opacity 9 -prefix ../qc_02_va2t_anat2temp -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: eac_1_ulay_shrp.nii
++ Found input file: eac_5_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_kCrlzLJwrjM
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1127.647339]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_kCrlzLJwrjM/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_kCrlzLJwrjM/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 344.516327
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_1_ulay_shrp.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_mMcw3A-Fv9qWTkpJrJtZFw argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.172907
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_mMcw3A-Fv9qWTkpJrJtZFw+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :623
[1] 45495
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_kCrlzLJwrjM*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1127.647339 -com SET_FUNC_RANGE 344.516327 -com SET_THRESHNEW 22.371048 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage ../qc_02_va2t_anat2temp.sag blowup=2 -com SAVE_PNG coronalimage ../qc_02_va2t_anat2temp.cor blowup=2 -com SAVE_PNG axialimage ../qc_02_va2t_anat2temp.axi blowup=2 -com QUITT ../__tmp_chauf_kCrlzLJwrjM
\n+* Removing temporary image directory '../__tmp_chauf_kCrlzLJwrjM'.\n
[1] Done Xvfb :623 -screen 0 1024x768x24
++ DONE (good exit)
see: ../qc_02_va2t_anat2temp*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_02_va2t_anat2temp
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay stats.FT.NL+tlrc.HEAD -cbar Plasma -pbar_posonly -ulay_range 0% 120% -func_range 243.879257 -thr_olay 23.285336 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.jpg -pbar_comm_range 99%ile in mask -pbar_comm_thr 90%ile in mask, alpha+boxed on -prefix QC_FT.NL/media/qc_03_vstat_Full_Fstat -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: stats.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1059.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL/tmp_olay.nii
++ User-entered function range value value (243.879257)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_iIEqlfFAe1ogWogEqzqX4w argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_iIEqlfFAe1ogWogEqzqX4w+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :35
[1] 45687
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean Plasma'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean Plasma -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 243.879257 -com SET_THRESHNEW 23.285336 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL'.\n
[1] Done Xvfb :35 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_03_vstat_Full_Fstat*
ERROR: QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.txt not found!!
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
++ Done! Figure created:
QC_FT.NL/media/qc_04_mot_enormoutlr.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: dfile_rall.1D: 6 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
++ Done! Figure created:
QC_FT.NL/media/qc_05_mot_VR6.jpg
++ 3dGrayplot: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
+ Loading dataset ./errts.FT.NL+tlrc.HEAD
+ Number of voxels in mask = 93399
+ 3dGrayplot: Elapsed = 30.1 s
++ My command:
@chauffeur_afni -ulay mask_epi_anat.FT.NL+tlrc.HEAD -olay mask_epi_anat.FT.NL+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar gray_scale -func_range 3.29 -blowup 1 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_06_mot_grayplot.pbar.jpg -pbar_comm_range for normal distr, bounds of 0.001 prob tail -prefix __tmp_ZXCV_img -save_ftype JPEG -montx 1 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Using blowup factor: 1
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_FeFJxDdgsc6
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_FeFJxDdgsc6/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_FeFJxDdgsc6/tmp_olay.nii
++ User-entered function range value value (3.29)
++ Dimensions (xyzt): 77 92 77 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 10 8
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=mask_epi_anat.FT.NL+tlrc.HEAD[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_dk6pqsxyELKZhRcoPE7y_g argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 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
++ 545468 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 37 45 38
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :470
[1] 45908
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/__tmp_chauf_FeFJxDdgsc6*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean gray_scale'
++ Writing one 276x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.sag.png'
++ Writing one 231x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.cor.png'
++ Writing one 231x276 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.axi.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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:10:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean gray_scale -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 3.29 -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_IJK 37 45 38 -com SAVE_PNG sagittalimage ./__tmp_ZXCV_img.sag blowup=1 -com SAVE_PNG coronalimage ./__tmp_ZXCV_img.cor blowup=1 -com SAVE_PNG axialimage ./__tmp_ZXCV_img.axi blowup=1 -com QUITT ./__tmp_chauf_FeFJxDdgsc6
\n+* Removing temporary image directory './__tmp_chauf_FeFJxDdgsc6'.\n
++ DONE (good exit)
see: ./__tmp_ZXCV_img*
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
*+ No ylabels entered
*+ No input x-axis; making values based on length of data: [0..449]
++ Will scale each time series by censor_hline
++ Apply scale: 3.3333333333333335
++ Apply scale: 20.0
++ Will apply same y-axis range '[0.0, 3.0]' to all dsets
++ Plotting:
++ Plotting:
++ Done! Figure created:
__tmp_img_enorm.jpg
\n+* Removing temporary files '__tmp_gluing*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_06_mot_grayplot.jpg
rm: No match.
ERROR: QC_FT.NL/media/qc_06_mot_grayplot.pbar.txt not found!!
++ FOR: sum_ideal.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: regressor sum
++ Done! Figure created:
QC_FT.NL/media/qc_07_regr_ideal.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: X.stim.xmat.1D: 2 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: aud#0
++ Plotting: vis#0
++ Done! Figure created:
QC_FT.NL/media/qc_08_regr_stims.jpg
++ Check summary of degrees of freedom in: QC_FT.NL/media/qc_09_regr_df.dat
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay corr_brain+tlrc.HEAD -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_10_regr_corr_errts.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_FT.NL/media/qc_10_regr_corr_errts -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: corr_brain+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1059.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_s51H8xERyU7XnMhwQSAAPQ argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_s51H8xERyU7XnMhwQSAAPQ+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :948
[1] 46169
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_10_regr_corr_errts.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_10_regr_corr_errts.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_10_regr_corr_errts.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7'.\n
[1] Done Xvfb :948 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_10_regr_corr_errts*
ERROR: QC_FT.NL/media/qc_10_regr_corr_errts.pbar.txt not found!!
++ Prepare for running adjunct_apqc_tsnr_general (ver = 1.1)
++ MODE: 10
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay TSNR.FT.NL+tlrc.HEAD -ulay_range 0% 120% -func_range 322 -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -set_subbricks 0 0 0 -pbar_posonly -blowup 2 -cbar 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -cbar_ncolors 8 -cbar_topval EMPTY -opacity 4 -olay_alpha No -olay_boxed No -thr_olay 0 -pbar_saveim QC_FT.NL/media/qc_11_regr_tsnr_fin.pbar -pbar_comm_range 95%ile in mask -pbar_comm_gen cbar: hot color range (5-95%ile TSNR in mask): 84 - 322 -prefix QC_FT.NL/media/qc_11_regr_tsnr_fin -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: TSNR.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1059.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B/tmp_olay.nii
++ User-entered function range value value (322)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_N0u5gfOjMnNaKFqHj1TT0Q argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_N0u5gfOjMnNaKFqHj1TT0Q+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :638
[1] 46712
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.axi.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 322 -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_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_11_regr_tsnr_fin.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B'.\n
[1] Done Xvfb :638 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_11_regr_tsnr_fin*
1/2:
[Michaels-MacBook-Pro-6:AFNI_data6/FT_analysis/FT.NL.results] michaelspilka% tcsh redo_apqc.tcsh
++ REDOing APQC
++ Going to re-run APQC in this dir only: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results
++ Found 41 files for QCing.
++ Done making (executable) script to generate HTML QC:
./@ss_review_html
*+ Found main dset (template): /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ My command:
@chauffeur_afni -ulay vr_base_min_outlier+orig.HEAD -olay vr_base_min_outlier+orig.HEAD -ulay_range_nz 0 1751.000000 -func_range 1751.000000 -box_focus_slices AMASK_FOCUS_ULAY -cbar gray_scale -pbar_posonly -pbar_saveim QC_FT.NL/media/qc_00_vorig_EPI.pbar.jpg -pbar_comm_range 98%ile in vol -pbar_for dset -prefix QC_FT.NL/media/qc_00_vorig_EPI -save_ftype JPEG -blowup 4 -opacity 9 -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Found input file: vr_base_min_outlier+orig.HEAD
++ Using blowup factor: 4
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
++ 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, 1751.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_bbULaIX34j9/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_bbULaIX34j9/tmp_olay.nii
++ User-entered function range value value (1751.000000)
++ Dimensions (xyzt): 80 80 33 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 8 3
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=vr_base_min_outlier+orig.HEAD[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_6sTfbGnj_VZMWRtARIWKNA argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_6sTfbGnj_VZMWRtARIWKNA+orig.BRIK
++ 211200 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 40 40 16
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :611
[1] 45065
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_bbULaIX34j9*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean gray_scale'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.sag.png'
++ Writing one 960x432 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.cor.png'
++ Writing one 960x960 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_00_vorig_EPI.axi.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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:3:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean gray_scale -com DO_NOTHING -com SET_SUBBRICKS -1 -1 -1 -com SET_ULAY_RANGE A.all 0.000000 1751.000000 -com SET_FUNC_RANGE 1751.000000 -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_IJK 40 40 16 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_00_vorig_EPI.sag blowup=4 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_00_vorig_EPI.cor blowup=4 -com SAVE_PNG axialimage QC_FT.NL/media/qc_00_vorig_EPI.axi blowup=4 -com QUITT QC_FT.NL/media/__tmp_chauf_bbULaIX34j9
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_bbULaIX34j9'.\n
++ DONE (good exit)
see: QC_FT.NL/media/qc_00_vorig_EPI*
ERROR: QC_FT.NL/media/qc_00_vorig_EPI.pbar.txt not found!!
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) to workdir
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_0_cp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_0_cp.nii
++ Base dataset: (not given)
++ Loading datasets into memory
+ -cmass x y z shifts = 0.000 0.000 0.000
+ shift search range is +/- = 60.990 73.028 60.990
++ OpenMP thread count = 4
++ ========== Applying transformation to 1 sub-bricks ==========
++ 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 QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_1_grid2olay.nii
++ 3dAllineate: total CPU time = 28.1 sec Elapsed = 8.6
++ ###########################################################
++ Output dataset ./eac_2_ulay_shrp.nii
++ Just copy olay, bc ulay will get regridded
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B/eac_3_cp.nii
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_3_cp.nii
++ Forming automask
+ Fixed clip level = 457.476471
+ Used gradual clip level = 444.055969 .. 462.343231
+ Number voxels above clip level = 1751345
+ Clustering voxels ...
+ Largest cluster has 1751228 voxels
+ Clustering voxels ...
+ Largest cluster has 1735652 voxels
+ Filled 25607 voxels in small holes; now have 1761259 voxels
+ Filled 88085 voxels in large holes; now have 1849344 voxels
+ Clustering voxels ...
+ Largest cluster has 1849333 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6679560 voxels
+ Mask now has 1850461 voxels
++ 1850461 voxels in the mask [out of 8530021: 21.69%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 25 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 5 z-planes are zero [from I]
++ last 31 z-planes are zero [from S]
++ Output dataset ./eac_4_mask.nii
++ CPU time = 1.870000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Output dataset ./eac_5_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_2_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_6_edgy.nii -ulay_range_nz 2% 98% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 17.745312 -opacity 9 -prefix ../qc_01_ve2a_epi2anat -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: eac_2_ulay_shrp.nii
++ Found input file: eac_6_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_mB1CFMIc4np
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1683.303589]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_mB1CFMIc4np/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_mB1CFMIc4np/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 245.202560
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_2_ulay_shrp.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_XGAxa3qRzo9hHcisRjjjiw argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.087659
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_XGAxa3qRzo9hHcisRjjjiw+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :225
[1] 45280
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_mB1CFMIc4np*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_01_ve2a_epi2anat.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1683.303589 -com SET_FUNC_RANGE 245.202560 -com SET_THRESHNEW 17.745312 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage ../qc_01_ve2a_epi2anat.sag blowup=2 -com SAVE_PNG coronalimage ../qc_01_ve2a_epi2anat.cor blowup=2 -com SAVE_PNG axialimage ../qc_01_ve2a_epi2anat.axi blowup=2 -com QUITT ../__tmp_chauf_mB1CFMIc4np
\n+* Removing temporary image directory '../__tmp_chauf_mB1CFMIc4np'.\n
++ DONE (good exit)
see: ../qc_01_ve2a_epi2anat*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_Zafa5dlo38B*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_01_ve2a_epi2anat
++ Prepare for running @djunct_edgy_align_check (ver = 1.45)
++ Copy refbox (/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz) to workdir
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/REFBOX.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/eac_0_cp.nii
++ Output dataset ./eac_1_ulay_shrp.nii
++ 3dAllineate: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Zhark the Registrator
++ Source dataset: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Base dataset: (not given)
++ Loading datasets into memory
*+ WARNING: -1D*_apply '1D: 12@0'': 1 isn't enough rows for source dataset -- last row will repeat
+ -cmass x y z shifts = -0.008 -0.005 0.029
+ shift search range is +/- = 61.632 73.188 61.632
++ OpenMP thread count = 4
++ ========== Applying transformation to 5 sub-bricks ==========
volume 0..1*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #1
..2*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #2
..3*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #3
..4
*+ WARNING: Re-using final row of -1D*_apply '1D: 12@0'' for sub-brick #4
++ Output dataset QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf/eac_2_res.nii
++ 3dAllineate: total CPU time = 5.0 sec Elapsed = 4.4
++ ###########################################################
++ 3dAutomask: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset eac_2_res.nii
++ Forming automask
+ Fixed clip level = 866.280640
+ Used gradual clip level = 839.463562 .. 889.332031
+ Number voxels above clip level = 1839751
+ Clustering voxels ...
+ Largest cluster has 1839749 voxels
+ Clustering voxels ...
+ Largest cluster has 1839644 voxels
+ Filled 2255 voxels in small holes; now have 1841899 voxels
+ Filled 40056 voxels in large holes; now have 1881955 voxels
+ Clustering voxels ...
+ Largest cluster has 1881949 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 6644410 voxels
+ Mask now has 1885611 voxels
++ 1885611 voxels in the mask [out of 8530021: 22.11%]
++ first 24 x-planes are zero [from L]
++ last 24 x-planes are zero [from R]
++ first 24 y-planes are zero [from P]
++ last 23 y-planes are zero [from A]
++ first 6 z-planes are zero [from I]
++ last 32 z-planes are zero [from S]
++ Output dataset ./eac_3_mask.nii
++ CPU time = 2.850000 sec
++ 3dMedianFilter: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
*+ WARNING: Only processing sub-brick #0
++ Output dataset ./eac_4_mfilt.nii
++ 3dedge3: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ My command:
@chauffeur_afni -ulay eac_1_ulay_shrp.nii -box_focus_slices REFBOX.nii -olay eac_5_edgy.nii -ulay_range 0% 120% -func_range_perc_nz 33 -cbar Reds_and_Blues_Inv -set_subbricks 0 0 0 -olay_alpha No -olay_boxed No -thr_olay 22.371048 -opacity 9 -prefix ../qc_02_va2t_anat2temp -montx 7 -monty 1 -montgap 1 -montcolor black -save_ftype JPEG -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: eac_1_ulay_shrp.nii
++ Found input file: eac_5_edgy.nii
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ../__tmp_chauf_kCrlzLJwrjM
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1127.647339]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_kCrlzLJwrjM/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./../__tmp_chauf_kCrlzLJwrjM/tmp_olay.nii
++ For olay, the 33%ile value leads to
--> upper range value: 344.516327
++ Dimensions (xyzt): 193 229 193 1
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=eac_1_ulay_shrp.nii[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_mMcw3A-Fv9qWTkpJrJtZFw argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.172907
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_mMcw3A-Fv9qWTkpJrJtZFw+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :623
[1] 45495
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_kCrlzLJwrjM*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > ../qc_02_va2t_anat2temp.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -pass Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1127.647339 -com SET_FUNC_RANGE 344.516327 -com SET_THRESHNEW 22.371048 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage ../qc_02_va2t_anat2temp.sag blowup=2 -com SAVE_PNG coronalimage ../qc_02_va2t_anat2temp.cor blowup=2 -com SAVE_PNG axialimage ../qc_02_va2t_anat2temp.axi blowup=2 -com QUITT ../__tmp_chauf_kCrlzLJwrjM
\n+* Removing temporary image directory '../__tmp_chauf_kCrlzLJwrjM'.\n
[1] Done Xvfb :623 -screen 0 1024x768x24
++ DONE (good exit)
see: ../qc_02_va2t_anat2temp*
\n+* Removing temporary workdir 'QC_FT.NL/media/__workdir_EAC_JATZ4xJK2Wf*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_02_va2t_anat2temp
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay stats.FT.NL+tlrc.HEAD -cbar Plasma -pbar_posonly -ulay_range 0% 120% -func_range 243.879257 -thr_olay 23.285336 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.jpg -pbar_comm_range 99%ile in mask -pbar_comm_thr 90%ile in mask, alpha+boxed on -prefix QC_FT.NL/media/qc_03_vstat_Full_Fstat -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: stats.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1059.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL/tmp_olay.nii
++ User-entered function range value value (243.879257)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_iIEqlfFAe1ogWogEqzqX4w argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_iIEqlfFAe1ogWogEqzqX4w+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :35
[1] 45687
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +99 -do_clean Plasma'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_03_vstat_Full_Fstat.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +99 -do_clean Plasma -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 243.879257 -com SET_THRESHNEW 23.285336 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_03_vstat_Full_Fstat.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_T9OLFqLeRxL'.\n
[1] Done Xvfb :35 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_03_vstat_Full_Fstat*
ERROR: QC_FT.NL/media/qc_03_vstat_Full_Fstat.pbar.txt not found!!
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: enorm (~mm)
++ Plotting: outlier frac
++ Done! Figure created:
QC_FT.NL/media/qc_04_mot_enormoutlr.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: dfile_rall.1D: 6 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: dP
(mm)
++ Plotting: dL
(mm)
++ Plotting: dS
(mm)
++ Plotting: yaw
(deg)
++ Plotting: pitch
(deg)
++ Plotting: roll
(deg)
++ Done! Figure created:
QC_FT.NL/media/qc_05_mot_VR6.jpg
++ 3dGrayplot: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
+ Loading dataset ./errts.FT.NL+tlrc.HEAD
+ Number of voxels in mask = 93399
+ 3dGrayplot: Elapsed = 30.1 s
++ My command:
@chauffeur_afni -ulay mask_epi_anat.FT.NL+tlrc.HEAD -olay mask_epi_anat.FT.NL+tlrc.HEAD -box_focus_slices AMASK_FOCUS_OLAY -cbar gray_scale -func_range 3.29 -blowup 1 -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_06_mot_grayplot.pbar.jpg -pbar_comm_range for normal distr, bounds of 0.001 prob tail -prefix __tmp_ZXCV_img -save_ftype JPEG -montx 1 -monty 1 -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Found input file: mask_epi_anat.FT.NL+tlrc.HEAD
++ Using blowup factor: 1
++ Using opacity: 9
++ Making temporary work directory to copy vis files: ./__tmp_chauf_FeFJxDdgsc6
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_FeFJxDdgsc6/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././__tmp_chauf_FeFJxDdgsc6/tmp_olay.nii
++ User-entered function range value value (3.29)
++ Dimensions (xyzt): 77 92 77 1
++ (initial) Slice spacing ordered (x,y,z) is: 8 10 8
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=mask_epi_anat.FT.NL+tlrc.HEAD[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_dk6pqsxyELKZhRcoPE7y_g argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 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
++ 545468 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 37 45 38
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :470
[1] 45908
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/__tmp_chauf_FeFJxDdgsc6*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean gray_scale'
++ Writing one 276x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.sag.png'
++ Writing one 231x231 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.cor.png'
++ Writing one 231x276 image to filter '/usr/local/bin/pnmtopng -compression 9 > ./__tmp_ZXCV_img.axi.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=9 mont=3x3:8:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:10:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:8:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean gray_scale -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1.000000 -com SET_FUNC_RANGE 3.29 -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_IJK 37 45 38 -com SAVE_PNG sagittalimage ./__tmp_ZXCV_img.sag blowup=1 -com SAVE_PNG coronalimage ./__tmp_ZXCV_img.cor blowup=1 -com SAVE_PNG axialimage ./__tmp_ZXCV_img.axi blowup=1 -com QUITT ./__tmp_chauf_FeFJxDdgsc6
\n+* Removing temporary image directory './__tmp_chauf_FeFJxDdgsc6'.\n
++ DONE (good exit)
see: ./__tmp_ZXCV_img*
++ FOR: motion_FT.NL_enorm.1D: 1 arrays with 450 pts
++ FOR: outcount_rall.1D: 1 arrays with 450 pts
*+ No ylabels entered
*+ No input x-axis; making values based on length of data: [0..449]
++ Will scale each time series by censor_hline
++ Apply scale: 3.3333333333333335
++ Apply scale: 20.0
++ Will apply same y-axis range '[0.0, 3.0]' to all dsets
++ Plotting:
++ Plotting:
++ Done! Figure created:
__tmp_img_enorm.jpg
\n+* Removing temporary files '__tmp_gluing*'\n
++ DONE! Image output:
QC_FT.NL/media/qc_06_mot_grayplot.jpg
rm: No match.
ERROR: QC_FT.NL/media/qc_06_mot_grayplot.pbar.txt not found!!
++ FOR: sum_ideal.1D: 1 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: regressor sum
++ Done! Figure created:
QC_FT.NL/media/qc_07_regr_ideal.jpg
/Users/michaelspilka/abin/afnipy/lib_plot_1D.py:373: UserWarning: FixedFormatter should only be used together with FixedLocator
pp.set_xticklabels(['']*nlabs)
++ FOR: X.stim.xmat.1D: 2 arrays with 450 pts
++ Lists of names and yvars match length
*+ No input x-axis; making values based on length of data: [0..449]
++ Plotting: aud#0
++ Plotting: vis#0
++ Done! Figure created:
QC_FT.NL/media/qc_08_regr_stims.jpg
++ Check summary of degrees of freedom in: QC_FT.NL/media/qc_09_regr_df.dat
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay corr_brain+tlrc.HEAD -cbar Reds_and_Blues_Inv -ulay_range 0% 120% -func_range 0.6 -thr_olay 0.3 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 0 0 -opacity 9 -pbar_saveim QC_FT.NL/media/qc_10_regr_corr_errts.pbar.jpg -pbar_comm_range Pearson r -pbar_comm_thr alpha+boxed on -prefix QC_FT.NL/media/qc_10_regr_corr_errts -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: corr_brain+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1059.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7/tmp_olay.nii
++ User-entered function range value value (0.6)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_s51H8xERyU7XnMhwQSAAPQ argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_s51H8xERyU7XnMhwQSAAPQ+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :948
[1] 46169
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_10_regr_corr_errts.axi.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=9 mont=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=9 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=9 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL -99 -do_clean Reds_and_Blues_Inv -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 0.6 -com SET_THRESHNEW 0.3 * -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_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_10_regr_corr_errts.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_10_regr_corr_errts.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_10_regr_corr_errts.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_BLZD0SdnOo7'.\n
[1] Done Xvfb :948 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_10_regr_corr_errts*
ERROR: QC_FT.NL/media/qc_10_regr_corr_errts.pbar.txt not found!!
++ Prepare for running adjunct_apqc_tsnr_general (ver = 1.1)
++ MODE: 10
++ My command:
@chauffeur_afni -ulay /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -olay TSNR.FT.NL+tlrc.HEAD -ulay_range 0% 120% -func_range 322 -box_focus_slices /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz -set_subbricks 0 0 0 -pbar_posonly -blowup 2 -cbar 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -cbar_ncolors 8 -cbar_topval EMPTY -opacity 4 -olay_alpha No -olay_boxed No -thr_olay 0 -pbar_saveim QC_FT.NL/media/qc_11_regr_tsnr_fin.pbar -pbar_comm_range 95%ile in mask -pbar_comm_gen cbar: hot color range (5-95%ile TSNR in mask): 84 - 322 -prefix QC_FT.NL/media/qc_11_regr_tsnr_fin -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 3 -do_clean -pass -pass
\n------------------ start of optionizing ------------------\n
++ Found input file: /Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz
++ Found input file: TSNR.FT.NL+tlrc.HEAD
++ Using blowup factor: 2
++ Using opacity: 4
++ Making temporary work directory to copy vis files: QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
++ Converted 0 to labels
++ Final subbrick indices: 0 0 0
++ Copy ulay to visualize (volumetric) within user's range:
++ Ulay to be visualized within user range:
[0%, 98%] -> [0.000000, 1059.000000]
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B/tmp_olay.nii
++ User-entered function range value value (322)
++ Dimensions (xyzt): 193 229 193 5
++ (initial) Slice spacing ordered (x,y,z) is: 21 25 21
++ 3dmaskdump: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Executing 3dcalc()
argv[0]=3dcalc argv[1]=-a argv[2]=/Users/michaelspilka/abin/MNI152_2009_template_SSW.nii.gz[0] argv[3]=-expr argv[4]=a argv[5]=-byte argv[6]=-session argv[7]=/var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/ argv[8]=-prefix argv[9]=3dcalc_AFN_N0u5gfOjMnNaKFqHj1TT0Q argv[10]=-verbose
++ 3dcalc: AFNI version=AFNI_21.1.09 (May 29 2021) [64-bit]
++ Authored by: A cast of thousands
++ Computing sub-brick 0
++ Scaling output to type byte brick(s)
++ Sub-brick 0 scale factor = 0.162420
++ Computing output statistics
++ Output dataset /var/folders/c0/n_1q183x17df518zrf8bpr_m0000gn/T/3dcalc_AFN_N0u5gfOjMnNaKFqHj1TT0Q+tlrc.BRIK
++ 8530021 voxels in the entire dataset (no mask)
++ 1 voxels in the boxes and/or balls
++ Using only the boxes+balls mask
++ Will have: SET_IJK 95 114 96
\n------------------- end of optionizing -------------------\n
-- trying to start Xvfb :638
[1] 46712
+/Volumes/Seagate/UGA/AfniBootcamp/AFNI_data6/FT_analysis/FT.NL.results/QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B*+ WARNING: Bad drive AFNI result from 'SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none'
++ Writing one 1374x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.sag.png'
++ Writing one 1158x1158 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.cor.png'
++ Writing one 1158x1374 image to filter '/usr/local/bin/pnmtopng -compression 9 > QC_FT.NL/media/qc_11_regr_tsnr_fin.axi.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=3x3:21:0:black crop=0:0,0:0 -com OPEN_WINDOW coronalimage opacity=4 mont=3x3:25:0:black crop=0:0,0:0 -com OPEN_WINDOW axialimage opacity=4 mont=3x3:21:0:black crop=0:0,0:0 -com SET_PBAR_ALL +8 -pass 322=red 282=oran-red 242=orange 203=oran-yell 163=yell-oran 123=yellow 84=lt-blue2 52=blue 0=none -com DO_NOTHING -com SET_SUBBRICKS 0 0 0 -com SET_ULAY_RANGE A.all 0.000000 1059.000000 -com SET_FUNC_RANGE 322 -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_IJK 95 114 96 -com SAVE_PNG sagittalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.sag blowup=2 -com SAVE_PNG coronalimage QC_FT.NL/media/qc_11_regr_tsnr_fin.cor blowup=2 -com SAVE_PNG axialimage QC_FT.NL/media/qc_11_regr_tsnr_fin.axi blowup=2 -com QUITT QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B
\n+* Removing temporary image directory 'QC_FT.NL/media/__tmp_chauf_ac7ziXX1U2B'.\n
[1] Done Xvfb :638 -screen 0 1024x768x24
++ DONE (good exit)
see: QC_FT.NL/media/qc_11_regr_tsnr_fin*
| Subject | Author | Posted |
|---|---|---|
|
mjss | June 07, 2021 05:35PM |
|
ptaylor | June 07, 2021 05:56PM |
|
mjss | June 07, 2021 08:49PM |
|
ptaylor | June 07, 2021 09:53PM |
|
mjss | June 08, 2021 10:10AM |
|
mjss | June 08, 2021 10:11AM |
|
mjss | June 08, 2021 06:01PM |
|
ptaylor | June 09, 2021 05:02PM |
|
mjss | June 10, 2021 11:49AM |
|
ptaylor | June 10, 2021 06:23PM |
