Please see below the output logs from tcsh -xef proc.sub-08 with the same data with the three different ways.
- Log from tcsh -xef proc.sub-08 when using local cmake built:
echo auto-generated by afni_proc.py, Fri Jul 28 16:49:17 2023
auto-generated by afni_proc.py, Fri Jul 28 16:49:17 2023
echo (version 7.58, June 22, 2023)
(version 7.58, June 22, 2023)
echo execution started: `date`
date
execution started: Fri Jul 28 16:49:33 CDT 2023
afni -ver
Precompiled binary 1: Jul 8 2023 (Version AFNI_23.1.10 'Publius Helvius Pertinax')
afni_history -check_date 14 Nov 2022
-- is current: afni_history as new as: 14 Nov 2022
most recent entry is: 26 Jun 2023
if ( 0 ) then
if ( 0 > 0 ) then
set subj = sub-08
endif
set output_dir = sub-08.results
if ( -d sub-08.results ) then
set runs = ( `count -digits 2 1 2` )
count -digits 2 1 2
mkdir -p sub-08.results
mkdir sub-08.results/stimuli
3dcopy /work/project/npavlovikj/afni/Flanker/sub-08/anat/sub-08_T1w.nii.gz sub-08.results/sub-08_T1w
++ 3dcopy: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
3dcopy /work/HCC/BCRF/app_specific/afni/afni_atlases_dist/MNI_avg152T1+tlrc.HEAD sub-08.results/MNI_avg152T1+tlrc.HEAD
++ 3dcopy: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
3dTcat -prefix sub-08.results/pb00.sub-08.r01.tcat /work/project/npavlovikj/afni/Flanker/sub-08/func/sub-08_task-flanker_run-1_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ elapsed time = 0.7 s
3dTcat -prefix sub-08.results/pb00.sub-08.r02.tcat /work/project/npavlovikj/afni/Flanker/sub-08/func/sub-08_task-flanker_run-2_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ elapsed time = 0.7 s
set tr_counts = ( 146 146 )
cd sub-08.results
tee out.vlines.pb00.tcat.txt
find_variance_lines.tcsh -polort 2 -nerode 2 -rdir vlines.pb00.tcat pb00.sub-08.r01.tcat+orig.HEAD pb00.sub-08.r02.tcat+orig.HEAD
++ have nslices : 40 40
++ copying pb00.sub-08.r01.tcat+orig.HEAD[0..$] to ts.0.orig.r01.nii.gz
++ 3dTcat: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ elapsed time = 18.4 s
++ copying pb00.sub-08.r02.tcat+orig.HEAD[0..$] to ts.0.orig.r02.nii.gz
++ 3dTcat: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ elapsed time = 11.9 s
++ creating automask from first dset
++ 3dAutomask: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ts.0.orig.r01.nii.gz
++ Forming automask
+ Fixed clip level = 343.908478
+ Used gradual clip level = 328.785889 .. 363.965637
+ Number voxels above clip level = 39446
+ Clustering voxels ...
+ Largest cluster has 38882 voxels
+ Clustering voxels ...
+ Largest cluster has 38556 voxels
+ Filled 356 voxels in small holes; now have 38912 voxels
+ Filled 3 voxels in large holes; now have 38915 voxels
+ Clustering voxels ...
+ Largest cluster has 38915 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 124925 voxels
+ Mask now has 38915 voxels
++ 38915 voxels in the mask [out of 163840: 23.75%]
++ first 11 x-planes are zero [from L]
++ last 11 x-planes are zero [from R]
++ first 0 y-planes are zero [from P]
++ last 5 y-planes are zero [from A]
++ first 1 z-planes are zero [from I]
++ last 3 z-planes are zero [from S]
++ Output dataset ./mask.nii.gz
++ CPU time = 0.000000 sec
-- will apply mask mask.nii.gz
++ eroding mask.nii.gz by 2 voxels
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 23179 survived, 140661 were zero
++ writing result mask.nii.gz...
++ Output dataset ./mask.nii.gz
++ requiring 5 voxels in mask columns
++ 3dLocalstat: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: Emperor Zhark
** AFNI can't deal with 5 dimensional NIfTI(/lustre/work/project/npavlovikj/afni/Flanker/sub-08.results/vlines.pb00.tcat/mask.nii.gz)
** FATAL ERROR: Can't open dataset 'mask.nii.gz'
** Program compile date = Jul 8 2023
++ 3dcalc: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset tmp.mask.col.count.nii.gz
** Program compile date = Jul 8 2023
-- detrend -polort 2, new eset = ts.1.det.r01.nii.gz
++ 3dTproject: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ Setting up regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
++ 146 retained time points MINUS 3 regressors ==> 143 D.O.F. left
++ no -mask option ==> processing all 163840 voxels in dataset
*+ WARNING: 3dTproject input data :: 2561 vectors are constant
++ 3dTstat: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./tmp.stdev.nii.gz
++ 3dcalc: AFNI version=AFNI_23.1.10 (Jul 8 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./var.0.orig.r01.nii.gz
** FATAL ERROR: Can't open dataset 'mask.nii.gz'
** Program compile date = Jul 8 2023
- Log from tcsh -xef proc.sub-08 when using the Docker image built with cmake with Apptainer (apptainer shell docker://afni/afni_cmake_build:AFNI_23.1.10):
echo auto-generated by afni_proc.py, Fri Jul 28 16:56:00 2023
auto-generated by afni_proc.py, Fri Jul 28 16:56:00 2023
echo (version 7.58, June 22, 2023)
(version 7.58, June 22, 2023)
echo execution started: `date`
date
execution started: Fri Jul 28 16:56:10 CDT 2023
afni -ver
Precompiled binary 1: Jun 30 2023 (Version AFNI_99.99.99 'Alexios V Doukas the Bushy-eyebrowed')
afni_history -check_date 14 Nov 2022
-- is current: afni_history as new as: 14 Nov 2022
most recent entry is: 26 Jun 2023
if ( 0 ) then
if ( 0 > 0 ) then
set subj = sub-08
endif
set output_dir = sub-08.results
if ( -d sub-08.results ) then
set runs = ( `count -digits 2 1 2` )
count -digits 2 1 2
mkdir -p sub-08.results
mkdir sub-08.results/stimuli
3dcopy /work/project/npavlovikj/afni/Flanker/sub-08/anat/sub-08_T1w.nii.gz sub-08.results/sub-08_T1w
++ 3dcopy: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
3dcopy /work/HCC/BCRF/app_specific/afni/afni_atlases_dist/MNI_avg152T1+tlrc.HEAD sub-08.results/MNI_avg152T1+tlrc.HEAD
++ 3dcopy: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
3dTcat -prefix sub-08.results/pb00.sub-08.r01.tcat /work/project/npavlovikj/afni/Flanker/sub-08/func/sub-08_task-flanker_run-1_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ elapsed time = 0.7 s
3dTcat -prefix sub-08.results/pb00.sub-08.r02.tcat /work/project/npavlovikj/afni/Flanker/sub-08/func/sub-08_task-flanker_run-2_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ elapsed time = 0.7 s
set tr_counts = ( 146 146 )
cd sub-08.results
tee out.vlines.pb00.tcat.txt
find_variance_lines.tcsh -polort 2 -nerode 2 -rdir vlines.pb00.tcat pb00.sub-08.r01.tcat+orig.HEAD pb00.sub-08.r02.tcat+orig.HEAD
++ have nslices : 40 40
++ copying pb00.sub-08.r01.tcat+orig.HEAD[0..$] to ts.0.orig.r01.nii.gz
++ 3dTcat: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ elapsed time = 4.3 s
++ copying pb00.sub-08.r02.tcat+orig.HEAD[0..$] to ts.0.orig.r02.nii.gz
++ 3dTcat: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ elapsed time = 4.2 s
++ creating automask from first dset
++ 3dAutomask: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ts.0.orig.r01.nii.gz
++ Forming automask
+ Fixed clip level = 343.908478
+ Used gradual clip level = 328.785889 .. 363.965637
+ Number voxels above clip level = 39446
+ Clustering voxels ...
+ Largest cluster has 38882 voxels
+ Clustering voxels ...
+ Largest cluster has 38556 voxels
+ Filled 356 voxels in small holes; now have 38912 voxels
+ Filled 3 voxels in large holes; now have 38915 voxels
+ Clustering voxels ...
+ Largest cluster has 38915 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 124925 voxels
+ Mask now has 38915 voxels
++ 38915 voxels in the mask [out of 163840: 23.75%]
++ first 11 x-planes are zero [from L]
++ last 11 x-planes are zero [from R]
++ first 0 y-planes are zero [from P]
++ last 5 y-planes are zero [from A]
++ first 1 z-planes are zero [from I]
++ last 3 z-planes are zero [from S]
++ Output dataset ./mask.nii.gz
++ CPU time = 0.000000 sec
-- will apply mask mask.nii.gz
++ eroding mask.nii.gz by 2 voxels
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 23179 survived, 140661 were zero
++ writing result mask.nii.gz...
++ Output dataset ./mask.nii.gz
++ requiring 5 voxels in mask columns
++ 3dLocalstat: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ Authored by: Emperor Zhark
** AFNI can't deal with 5 dimensional NIfTI(/work/project/npavlovikj/afni/Flanker/sub-08.results/vlines.pb00.tcat/mask.nii.gz)
** FATAL ERROR: Can't open dataset 'mask.nii.gz'
** Program compile date = Jun 30 2023
++ 3dcalc: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset tmp.mask.col.count.nii.gz
** Program compile date = Jun 30 2023
-- detrend -polort 2, new eset = ts.1.det.r01.nii.gz
++ 3dTproject: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ Setting up regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
++ 146 retained time points MINUS 3 regressors ==> 143 D.O.F. left
++ no -mask option ==> processing all 163840 voxels in dataset
*+ WARNING: 3dTproject input data :: 2561 vectors are constant
++ 3dTstat: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./tmp.stdev.nii.gz
++ 3dcalc: AFNI version=AFNI_99.99.99 (Jun 30 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./var.0.orig.r01.nii.gz
** FATAL ERROR: Can't open dataset 'mask.nii.gz'
** Program compile date = Jun 30 2023