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Q. I have already skull-stripped data. Can I submit it to recon-all?

A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently.

First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s <subjid>

Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all:
recon-all -autrecon2 -autorecon3 -s <subjid>

Hope it helps.

 Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of BALBONI Irene
Sent: Tuesday, December 19, 2023 3:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon all with optiBET brain mask

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Hello,

I would like to run recon all on a batch of subjects using 2 inputs (mprage and mp2rage). I would also like to run recon all using as brain mask not the standard brain mask generated by recon-all itself but a previously created optiBET. Would you have any suggestion on how to proceed? I tried simply replacing the brainmask file with the optiBET but it did not work.

Just for context all my participants (150) have been already segmented using recon-all but we noticed during quality control that we still have skull stripping and pial surface errors for the majority of them and that is why we would like to implement the optiBET mask.

Thanks for your help,

Irene Balboni

PhD student

She/Her

Institute de plurilinguisme | Université de Fribourg

&

Brain and Language Lab | Université de Genève

c/o Campus Biotech

Chemin des Mines 9 – 1202

Université de Genève, CH

+41(0)223790141

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