Hi, a question resulting from this this suggestion. I removed --fs-no-reconall and specified pre-run freesurfer outputs using --fs-subjects-dir. I see how that changed some of the registration methods, which is fine. However, the output reports from the same command list freesurfer reconstruction as “pre-existing directory” or “run by fmriprep” inconsistently across subjects.
As far as I can tell, there are no new freesurfer outputs in derivatives or in the pre-run directory for the latter case. And I didn’t see anything in the log suggesting reconall was run (each took ~1 hour). I was not keeping the tmp files in a working directory, but testing that now with subjects from each case. Last, the pre-run freesurfer file trees for subjects from both cases look similar except in the freesurfer tmp dir (tree_fs_sub-0005.txt (13.3 KB) is “pre-exist” and tree_fs_sub-0010.txt (15.7 KB) is “run by fmriprep”). This thread had a similar question. All in all, safe to assume the pre-run freesurfer outputs were being used for all subjects regardless of what the report states?