frmiprep for one subject

[smithaka2024]

I encountered the following error while I executed the cammand

sudo fmriprep-docker /home/virus/smith1/BIDS/derivatives --participant-label sub-01 --fs-license-file /home/virus/smith1/BIDS/freesurfer.txt --ignore fieldmaps --output-spaces MNI152NLin6Asym:res-2.

The error was

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-01 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot 

	setting seed for random number generator to 1234
	using ../mri/aseg.presurf.mgz aseg volume to correct midline
	7.3.2
	  7.3.2
	Killed
	Linux 7681d14f07fe 5.15.0-126-generic #136~20.04.1-Ubuntu SMP Thu Nov 14 16:38:05 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux

	recon-all -s sub-01 exited with ERRORS at Sun Dec 22 16:49:21 UTC 2024

	For more details, see the log file /out/sourcedata/freesurfer/sub-01/scripts/recon-all-rh.log
	To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Stderr:

Traceback:
	RuntimeError: subprocess exited with code 1.

241222-16:49:25,545 nipype.workflow ERROR:
	 could not run node: fmriprep_24_1_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm
2024-12-22 16:49:25,545 [   ERROR] could not run node: fmriprep_24_1_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.fsnative2t1w_xfm
241222-16:49:25,555 nipype.workflow ERROR:
	 could not run node: fmriprep_24_1_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
2024-12-22 16:49:25,555 [   ERROR] could not run node: fmriprep_24_1_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
241222-16:49:25,558 nipype.workflow ERROR:
	 could not run node: fmriprep_24_1_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
2024-12-22 16:49:25,558 [   ERROR] could not run node: fmriprep_24_1_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
2024-12-22 16:49:25,622 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2024-12-22 16:49:25,638 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
2024-12-22 16:49:25,647 [ WARNING] WARNING: sentry_sdk.push_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-pushing
241222-16:49:25,672 nipype.workflow CRITICAL:
	 fMRIPrep failed: 3 raised. Re-raising first.
2024-12-22 16:49:25,672 [CRITICAL] fMRIPrep failed: 3 raised. Re-raising first.
Sentry is attempting to send 6 pending events
Waiting up to 2 seconds
Press Ctrl-C to quit
fMRIPrep: Please report errors to https://github.com/nipreps/fmriprep/issues

I am using fMRIprep for the first time. Please help to resolve the issue.

Thanks and Regards
Smitha

[tsalo]

@smithaka2024 there is a specific template for bug reports, which I would recommend using in the future if you want to report a bug. The template has a number of fields that make it easier for the fMRIPrep developers to figure out what the problem is. I would also recommend starting by posting on Neurostars for issues like this.

In any case, the error seems to be that Freesurfer was killed, which I would guess stems from the process not having enough memory. I recommend increasing the amount of memory your Docker container is allowed (which can be set in the Docker app settings) and using that limit in your fMRIPrep call via the --mem and --nprocs arguments.