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!