Hi all,
I’m running fmriprep (version 20.2.5, using singularity) and getting the following errors on a couple of subjects:
indexed_gzip.indexed_gzip.CrcError: CRC/size validation failed - the GZIP data might be corrupt (file: /scratch/users/mayay/work/LMB_fmriprep/fmriprep_wf/single_subject_309_wf/func_preproc_ses_1_task_rest_run_1_wf/bold_std_trans_wf/_std_target_MNI152NLin2009cAsym.resnative/bold_to_std_transform/vol0343_xform-00343.nii.gz)
Node Name: fmriprep_wf.single_subject_309_wf.func_preproc_ses_1_task_rest_run_1_wf.bold_std_trans_wf.bold_to_std_transform
Looking at the html report, it seems that the pipeline ran smoothly until the AROMA step.
The error suggests that one of my nifti files is corrupted, but I’m confused since it doesn’t refer to my input files but for some intermediate derivative in the work folder, created by the fmriprep pipeline itself. Any ideas of where the problem might be? Happy to provide the log file and more details if anyone can help!
Thanks!
Maya
This is the command I’m running:
singularity run --cleanenv MYPATH/singularity_images/fmriprep-20.2.5.simg
/scratch/MYPATH/input
/scratch/MYPATH/derivatives participant --participant-label sub-309
-w /MYPATH/work/fmriprep
–output-spaces anat fsnative fsaverage MNI152NLin2009cAsym
–dummy-scans 4
–use-aroma \
–bids-filter-file /home/users/mayay/myScripts/filter_T1w.json
(the filter file selects a specific T1w image from the anat folder)