Dear experts,
fmriprep is running into an error during the execution of 3dQwarp.
Here the command:
singularity run --cleanenv -B /myfolder fmriprep-20.2.3.simg /myfolder/mydataset /myfolder/output participant --participant-label sub-002 --fs-license-file /myfolder/license.txt --output-spaces anat func fsnative fsaverage MNI152NLin6Asym --use-aroma --aroma-melodic-dimensionality 16 --nthreads 4 --omp-nthreads 4 --work-dir /myfolder/tmp
Here the error (the same for each run) from the HTML report:
Node Name: fmriprep_wf.single_subject_002_wf.func_preproc_task_sism_dir_AP_run_9_wf.sdc_estimate_wf.pepolar_unwarp_wf.qwarp
File: /myfolder/output/fmriprep/sub-002/log/20211104-134131_91cf71f7-fc4b-4822-a9da-3d055247b2d9/crash-20211104-140030-user-qwarp-d77fd53a-0371-44d9-9d16-82b689c90404.txt
Working Directory: /myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp
Inputs:
Qfinal:
Qonly:
allineate:
allineate_opts:
allsave:
args: -noXdis -noZdis
ballopt:
base_file:
baxopt:
blur: [-1.0, -1.0]
duplo:
emask:
environ: {'OMP_NUM_THREADS': '4'}
expad:
gridlist:
hel:
in_file:
inilev:
iniwarp:
iwarp:
lpa:
lpc:
maxlev:
mi:
minpatch: 9
nmi:
noXdis:
noYdis:
noZdis:
noneg:
nopad:
nopadWARP: True
nopenalty:
nowarp:
noweight: True
num_threads: 4
out_file: Qwarp.nii.gz
out_weight_file:
outputtype: AFNI
overwrite:
pblur: [0.05, 0.05]
pear:
penfac:
plusminus: True
quiet:
resample:
source_file:
verb:
wball:
weight:
wmask:
workhard:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 125, in _run_interface
runtime, correct_return_codes
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 753, in raise_exception
).format(**runtime.dictcopy())
RuntimeError: Command:
3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/uni_xform_masked.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05
Standard output:
Standard error:
++ OpenMP thread count = 4
++ 3dQwarp: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as /myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/transform_Warped.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:/myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz is 9.536010 degrees from plumb.
++ Oblique dataset:/myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/uni_xform_masked.nii.gz is 9.536010 degrees from plumb.
++ Dataset zero-pad: xbot=437701747 xtop=32440 ybot=437735012 ytop=32440 zbot=1643987507 ztop=32681 voxels
e[7m** ERROR:e[0m EDIT_volpad: Can't malloc space for new array
e[7m** ERROR:e[0m EDIT_volpad: Can't malloc space for new array
Fatal Signal 11 (SIGSEGV) received
3dQwarp
Bottom of Debug Stack
** Command line was:
3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /myfolder/tmp/fmriprep_wf/single_subject_002_wf/func_preproc_task_sism_dir_AP_run_9_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/uni_xform_masked.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05
** AFNI version = Debian-16.2.07~dfsg.1-5~nd16.04+1 Compile date = Jun 12 2017
** [[Precompiled binary Debian-x86_64-1-gnu: Jun 12 2017]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Crash log is appended to file /home/user/.afni.crashlog
Return code: 1
Any feedback would be really helpful! Let me know if I can share more details.
Thank you,
Valeria