Re: [Freesurfer] recon all with optiBET brain mask

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Dear Yujing, Thank you for your reply. Would there be a way to just use the mask created with optiBET for the recon-all process to mask the brain? At the moment we are segmenting 2 images at once (mprage and mp2rage) to improve the quality of the segmentation and we have the skull-stripped images only for one of them so the solution below might not be ideal.

Thanks again.

Best, Irene

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: venerdì 29 dicembre 2023 15:44 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all with optiBET brain mask

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

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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

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