Options when reuse FreeSurfer outputs

Software Support
1

Dear experts,

I’m sorry if this has already been asked somewhere. I’m afraid this is a basic question, but let me make sure my understanding is correct.

I have already run recon-all my subjects, so I would like to reuse the FreeSurfer outputs when I perform fMRIPrep (the FreeSurfer outputs are in /derivatives/sourcedata/freesurfer/sub-XXXX).
In this case, would the skull-stripped images in FreeSurfer be used for spatial normalization and brain tissue segmentation and would the options for ANTs Registration (--skull-strip-template, --skull-strip-fixed-seed) be unnecessary?
If yes, should I use the flag --skull-strip-t1w skip right?

Best regards,

2

Reusing FreeSurfer derivatives just means fMRIPrep won’t try to run FreeSurfer for you. If your T1w images are not skull-stripped, you will still want fMRIPrep to skull-strip them. In general, you shouldn’t need to use --skull-strip-template unless you want to use something other than the ANTs default of OASIS30, and you should only use --skull-strip-fixed-seed if you are concerned about getting the exact same result when rerunning fMRIPrep (in which case you should also use --omp-nthreads 1).

3

Dear @effigies ,

Thank you for the clear answers! Sorry for the late reply.
Yes, my T1w are not skull-stripped, so I will use --skull-strip-fixed-seed.

Best,