Dear fmriprep experts,
Hi! I’m running fmriprep on the Healthy Brain Network dataset for preprocessing, and keep running into a same problem in a random manner.
I am using the following command:
fmriprep-docker my/input/directory my/output/directory participant --participant-label NDAREU890CYJ --skull-strip-template MNIPediatricAsym:cohort-1 --output-spaces MNIPediatricAsym:cohort-1:res-2 --skip_bids_validation --fs-license-file Desktop/license.txt --nthreads 12 --low-mem --work-dir Desktop/HBN/MRI/temp
and I have added the pediatric template as the output space since I am using a developmental dataset.
fmriprep has been working with most of the subject data pretty well, except for some where it says that it failed and the workflow did not execute cleanly. This is the error description I found in the html :
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/fixes.py", line 64, in _run_interface
runtime = super(FixHeaderApplyTransforms, self)._run_interface(
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
antsApplyTransforms --default-value 0 --float 0 --input
/scratch/fmriprep_wf/single_subject_NDAREU890CYJ_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/resample/
--interpolation MultiLabel --output seg_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-
MNIPediatricAsym/cohort-1/tpl-MNIPediatricAsym_cohort-1_res-2_T1w.nii.gz --transform
/scratch/fmriprep_wf/single_subject_NDAREU890CYJ_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsymcohort-
1/registration/ants_t1_to_mniComposite.h5
Standard output:
Standard error:
Exception caught during reference file reading
itk::ImageFileReaderException (0x3d74740)
Location: "unknown"
File: /src/ants/build/staging/include/ITK-5.1/itkImageFileReader.hxx
Line: 133
Description: Could not create IO object for reading file /home/fmriprep/.cache/templateflow/tpl-
MNIPediatricAsym/cohort-1/tpl-MNIPediatricAsym_cohort-1_res-2_T1w.nii.gz
Tried to create one of the following:
BMPImageIO
BioRadImageIO
Bruker2dseqImageIO
GDCMImageIO
GE4ImageIO
GE5ImageIO
GiplImageIO
HDF5ImageIO
JPEGImageIO
JPEG2000ImageIO
LSMImageIO
MGHImageIO
MINCImageIO
MRCImageIO
MetaImageIO
NiftiImageIO
NrrdImageIO
PNGImageIO
StimulateImageIO
TIFFImageIO
VTKImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
file /home/fmriprep/.cache/templateflow/tpl-MNIPediatricAsym/cohort-1/tpl-MNIPediatricAsym_cohort-1_res-2_T1w.nii.gz
Segmentation fault
Return code: 139
I am suspecting that it’s an issue about ANTS using a non-default template (according to https://neurostars.org/t/moving-images-from-mni-to-bold-epi-native-space/ and https://neurostars.org/t/fmriprep-potentially-antsapplytransforms-and-hd5-issue/ ),
but what is puzzling is that when I remove all output files and rerun fmriprep on the same data with the same commands, it sometimes works.
So, I am growing suspicions that it might be a memory issue since I have been encountering some lately.
Would anyone have any suggestions about the problem? It would be a big help.
Thank you in advance!
Sujin.
