Fmriprep running recon-all but freesurfer outputs exist (and are detected)

1

Hi,

I have completed fMRIprep on a directory that includes task fMRI data for a group of participants. I did not include the IntendedFor key in the fieldmap json file, and so I am rerunning fMRIprep (with updated jsons) to ensure SDC is completed. I want to use the existing freesurfer outputs rather than rerun everything, and fMRIprep has detected the freesurfer folder in the output directory. I get a message to say recon-all complete : Not running, but then certain recon-all steps do seem to be running: “resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-101 -sd /outputfolder/freesurfer” and taking quite a long time (looking at the logs it seems like the parcellation/normalization steps are re-completed). It then appears to be hanging after completion of the FS steps. I am wondering if this is the intended process, and whether it is possible to avoid it and still obtain the required preprocessed outputs? For info, I have removed the func folder from derivatives/fmriprep/sub/ses-001 directory to encourage rewriting files (which may have been unnecessary, but I don’t think the source of the problem).

Thank you very much!

Caitlin

2

What version of FreeSurfer were your existing FreeSurfer outputs generated by? Unfortunately, FreeSurfer’s steps changed between v5.3 and v6.0, so 5.3-reconstructed subjects will not be detected as complete by FreeSurer 6.0.

3

Thank you for your response. Both attempts were run under freesurfer 6.0, so I don’t think that is the issue. It looks like it might be related to this discussion: https://github.com/poldracklab/fmriprep/issues/1875. I am now getting many messages saying outdated cache are found (e.g. ‘Outdated cache found for “fmriprep_wf.single_subject_102_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol”’). Do you know if there is a workaround other than the hack proposed in the linked thread (i.e. --use-plugin)? Thank you!

4

Hi,
I seem to be having a similar issue, recon-all is rerun even when existing freesurfer output is provided. How did you manage to solve this in the end?