Re-running fmriprep after using the -anat-only flag

Dear experts,

I’ve run fmriprep with the -anat-only flag; then, I’ve manually edited the segmentation with FreeSurfer. Now I want to run again fmriprep to complete the preprocessing, using the new surfaces.
Here (Fmriprep: correction of surface extracted from Freesurfer (--anat-only)) I’ve found very clear guidelines on how to do it, but I still have a doubt.
Running fmriprep with the -anat-only flag created the /some/output/folder/freesurfer directory, but also the /some/output/folder/fmriprep directory. What should I do with this last directory? Can I simply re-run fmriprep without changing my /some/output/folder/ structure or is it better to remove the fmriprep directory and run the preprocessing just keeping the /some/output/folder/freesurfer directory?

Thank you for your precious help, and sorry for my naive question.


It should be fine to use the same output fmriprep folder. Just make sure the freesurfer folder you want to use (that is, corrected one) is either 1) in the same level of the fmriprep folder with the name freesurfer or 2) manually specified with --fs-subjects-dir. You may want to specify a new cache directory (-w) to ensure that everything (besides freesurfer) will be recomputed as new. Hope this helps!