Will fMRIPrep 25.x work with FreeSurfer 8.x?

Software Support
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1

Hello,

I’m wondering if fMRIPrep 25.x will accept precomputed FreeSurfer 8.x subject directories (via --fs-subjects-dir). The container (25.x.x) includes FreeSurfer 7.3.2 — so I suspect that fMRIPrep might not recognize 8.x and could try to rerun recon-all?

I would appreciate any insights or experiences on whether this setup would work.

Thanks!

2

Hi @sreeniva,

As long as the file output structure has not drastically changed between versions it should work fine. If it does throw an error you can try with the --fs-no-resume option.

Best,
Steven

3

Hi Steven,

Thank you so for the response. I am running fMRIPrep using FS 8.1 data, both with and without the -fs-no-resume flag, and have not errored out yet.

The run (run1) without the -fs-no-resume flag invoked a new recon-all using freesurfer 7.3.2 in the container (based on recon-all.log in the folder mentioned via --fs-subjects-dir), while I do not see this for the other run (run2 with the -fs-no-resume flag).

I do not see any modifications in the FS folder for run2. However, the T1 summary for both shows that freesurfer is run by fMRIPrep. So would that mean the FS8.x is not being recognized, but since the structure is similar/same, the processing might go through since all the files are present (?). Thanks again.

4

If you do not see evidence of recon-all being executed in the output logs, then you should be good in assuming fMRIPrep is not rerunning anything.

5

Tried a few weeks ago, i can confirm that it works without --fs-no-resume .

I actually compared running fMRIprep 25.2.3 on freesurfer 8.1.0 vs freesurfer 7.4.1 precomputed output. When ran on freesurfer 8.1.0, it took 1-2 hours longer to complete, there were some additional anat processing which wasn’t required if i ran on freesurfer 7.4.1

for what’s its worth, i also ran fMRIprep on a manually prepared environment with a freesurfer 8.1.0 installation, without any precomputed freesurfer output— it crashed out somewhere during the anat/sMRIprep processing. This wasnt an issue with freesurfer 7.4.1

So i’m not sure if its worthwhile to upgrade to freesurfer 8.x at the moment if you are using it primarily for fMRIprep