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lnnrtwttkhn / highspeed-fast-preproc

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Error with FSL: `Error: short read, file may be truncated` #3

Open lnnrtwttkhn opened 1 month ago

lnnrtwttkhn commented 1 month ago 
RuntimeError: Command:
fslmaths /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold.nii.gz -mas /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-brain_mask.nii.gz /mnt/beegfs/home/wittkuhn/highspeed-fast/highspeed-fast-preproc/work/preproc/susan_smooth/_subject_id_sub-03/mask/mapflow/_mask4/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold_mask.nii.gz
Standard output:

Standard error:
Image Exception : #22 :: Failed to read volume /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold.nii.gz
Error : Error: short read, file may be truncated
terminate called after throwing an instance of 'std::runtime_error'
  what():  Failed to read volume /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold.nii.gz
Error : Error: short read, file may be truncated
Aborted
Return code: 134

When creating this crashfile, the results file corresponding
to the node could not be found.
lnnrtwttkhn commented 1 month ago

See here: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;3ae9d96c.1902

lnnrtwttkhn commented 1 month ago

Attempt 1:

datalad unlock /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold.nii.gz
xxd /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold.nii.gz > hexfile.hex
sed -i 's/\(^00000150:.*\)\(..\)\(.*$\)/\100 \3/' hexfile.hex
xxd -r hexfile.hex /home/mpib/wittkuhn/highspeed-fast/highspeed-fast-preproc/inputs/fmriprep/sub-03/ses-01/func/sub-03_ses-01_task-rest_rec-prenorm_space-T1w_desc-preproc_bold.nii.gz
lnnrtwttkhn commented 1 month ago

I think the issues is related to this: https://github.com/datalad/datalad/issues/7408

FSL is trying to operate on the files in-place and this does not play well when DataLad has the files locked.