So I am at a point where I need help with fmriprep. Please note, I am running it with Singularity and have run it successfully many times. However I have discovered I needed to add the “IntendedFor:” field into my fmap json files in the BIDS data(which has passed bids validator), to account for SDC. After doing this I tested it and it HAS run succesfully. After running a batch script to get all subjects done, most of the subjects are partially finishing (the ~/func directory and the report sub-X.html is not being completed). When looking at my error output the strange thing is the errors aren’t consistent, sometimes I am getting out of memory errors(which I highly doubt because the memory allocated for this is beyond sufficient and because some subjects run successfully) but for instance that error looks like…
OSError: [Errno 28] No space left on device:
or I get something like…
FileNotFoundError: No such file: '/home_dir/projects/niblab/bids_projects/Experiments/Bevel/fmriprep/sub-005/fmriprep_wf/single_subject_005_wf/func_preproc_task_prob_run_1_wf/bold_mni_trans_wf/bold_to_mni_transform/vol0112_xform-00112.nii.gz'
and for reference the command looks like…
singularity exec -B /:/home_dir /projects/niblab/bids_projects/Singularity_Containers/fmriprep.simg \ fmriprep /home_dir/projects/niblab/bids_projects/Experiments/Bevel/BIDS /home_dir/projects/niblab/bids_projects/Experiments/Bevel/fmriprep/sub-001 \ participant \ --participant-label sub-001 \ --fs-license-file /home_dir/projects/niblab/bids_projects/freesurfer/license.txt \ --fs-no-reconall \ --omp-nthreads 16 --n_cpus 16 \ --ignore slicetiming \ --bold2t1w-dof 12 \ --output-space template --template MNI152NLin2009cAsym \ --debug \ -w /home_dir/projects/niblab/bids_projects/Experiments/Bevel/fmriprep/sub-001 \ --resource-monitor --write-graph --stop-on-first-crash
Like I mentioned above, this command had worked before I modified the json files and even after the modification some of my subjects have run successfully(and I cannot notice a difference in the BIDS data between successful and unsuccessful runs). That being said I do not think it is a singularity or BIDS issue. My next guess is possibly a package issue or possibly something I may need the cluster administrators to adjust but I am not sure. I am really at a loss here, any help is appreciated. Thank you.