AFNI version info (afni -ver):
23.1
code text # or delete if not needed
Hello AFNI users!
I am trying to run the following code (proc.py script) over a HPC server:
#!/bin/tcsh
#Set up afni_proc.py
#add the path to where your individual subject folders are located below between the single quotes
setenv expdir '/work/dietschlab/rahulk/Strength_Skill_NP'
setenv subdir ${expdir}
setenv resdir ${subdir}/results
mkdir ${resdir}
#add your subject numbers separated by a space
foreach subject (TC001_Baseline)
cd ${subdir}/${subject}
afni_proc.py \
-script ${expdir}/proc.${subject}_swallow_block \
-scr_overwrite \
-subj_id ${subject} \
-out_dir ${expdir}/${subject}.results_swallow.block \
-dsets ${subdir}/${subject}/${subject}_swallow1_epi.nii.gz \
${subdir}/${subject}/${subject}_swallow2_epi.nii.gz \
${subdir}/${subject}/${subject}_swallow3_epi.nii.gz \
-copy_anat ${subdir}/${subject}/${subject}_t1.nii.gz \
-anat_has_skull yes \
-blocks despike tshift align tlrc volreg blur mask scale regress \
-despike_new yes \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-align_opts_aea \
-giant_move \
-cost lpc+ZZ \
-volreg_align_to MIN_OUTLIER \
-volreg_tlrc_warp \
-volreg_align_e2a \
-blur_in_automask \
-regress_stim_times \
${subdir}/stimfiles/swallow_run.1D \
-regress_stim_labels \
SWALLOW \
-regress_basis \
'BLOCK(20,1)' \
-mask_apply anat \
-regress_motion_per_run \
-test_stim_files no \
-regress_opts_3dD \
-GOFORIT 8 \
-jobs 6 \
-regress_censor_motion 0.3 \
-regress_apply_mot_types demean deriv \
-regress_censor_first_trs 3 \
-regress_est_blur_errts \
-remove_preproc_files \
-execute
end
I am getting the following issue:
++ 3dLocalstat: AFNI version=AFNI_99.99.99 (Jun 22 2023) [64-bit]
++ Authored by: Emperor Zhark
** AFNI can't deal with 5 dimensional NIfTI(/lustre/work/dietschlab/rahulk/Strength_Skill_NP/TC001_Baseline.results_swallow.block/vlines.pb00.tcat/mask.nii.gz)
** FATAL ERROR: Can't open dataset 'mask.nii.gz'
** Program compile date = Jun 22 2023
++ 3dcalc: AFNI version=AFNI_99.99.99 (Jun 22 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 22 2023
-- detrend -polort 5, new eset = ts.1.det.r01.nii.gz
++ 3dTproject: AFNI version=AFNI_99.99.99 (Jun 22 2023) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /lustre/work/dietschlab/rahulk/Strength_Skill_NP/TC001_Baseline.results_swallow.block/vlines.pb00.tcat/ts.0.orig.r01.nii.gz,
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:/lustre/work/dietschlab/rahulk/Strength_Skill_NP/TC001_Baseline.results_swallow.block/vlines.pb00.tcat/ts.0.orig.r01.nii.gz is 9.303011 degrees from plumb.
++ Setting up regressors
++ 1 Blocks * 6 polynomials -- 6 polort regressors
++ 646 retained time points MINUS 6 regressors ==> 640 D.O.F. left
++ no -mask option ==> processing all 359856 voxels in dataset
*+ WARNING: 3dTproject input data :: 4285 vectors are constant
++ 3dTstat: AFNI version=AFNI_99.99.99 (Jun 22 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /lustre/work/dietschlab/rahulk/Strength_Skill_NP/TC001_Baseline.results_swallow.block/vlines.pb00.tcat/ts.1.det.r01.nii.gz,
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:/lustre/work/dietschlab/rahulk/Strength_Skill_NP/TC001_Baseline.results_swallow.block/vlines.pb00.tcat/ts.1.det.r01.nii.gz is 9.303011 degrees from plumb.
++ Output dataset ./tmp.stdev.nii.gz
++ 3dcalc: AFNI version=AFNI_99.99.99 (Jun 22 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 22 2023
Thanks!
- RK