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Longitudinal fmriprep with pre-run Freesurfer #21
I've run Freesurfer's recon all for my participants. When I run fmriprep, should I use the --no-fs-reconall option. When I include the flag, the process crashes out with an error (see attached crash text file). When I do not include the flag, the process runs but it's not clear if the freesurfer output is being incorporated.
My call to fmriprep was:
where $OUTDIR already contains a "freesurfer" folder built from my $INDIVDIR. The --no-fs-reconall was included for one participant and excluded for one participant. The one where it was included completed.
Please let me know what other files might be needed to identify if freesurfer is getting incorporated as intended.
You should not use
Looking at that error, it's finding your FreeSurfer directory, but for some reason not identifying it as being complete. This is most likely a lapse in Nipype's ability to detect a completed directory. I'm not sure what all differences there are in such a directory.
Could you give a full listing of the commands you ran directly with FreeSurfer? If I can replicate your situation, I should be able to get ReconAll to correctly detect that your directory has already been run.
where $FSOUT is my BIDS derivatives folder/freesurfer.
Attached is a truncated text file with the file tree that gets created from running this. This is the same participant for the crash file I attached previously. The only thing I'm not sure of is whether I needed the "steps" flag in the recon-all call, but it looks like it doesn't. It appears that the cross-sectional, base, and longitudinal folders all got created.
I have a follow-up tangential question for OP. I see that you have run the freesurfer scans through the longitudinal pipeline. How do you specify for fmriprep for them to use the longitudinally processed directories for each timepoint and not the original cross-sectional freesurfer output directories?