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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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
External Email - Use Caution
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
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