Hi Bruce, Thank you very much for your quick answer, The output of those command lines are left and right cerebellum white matter. How can I create a mask for the whole cerebellum white matter?

Thanks Mohamad ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 28, 2014 11:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

Hi Mohamad

you can use mri_binarize --match or mri_extract_label on the aseg.mgz.

cheers Bruce On Mon, 28 Jul 2014, Alshikho, Mohamad J. wrote:

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation?

Thanks mohamad

Thanks Doug

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 28, 2014 11:54 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

With mri_binarize you can give it multiple match options to merge different segments

On 07/28/2014 11:50 AM, Alshikho, Mohamad J. wrote:

Hi Bruce, Thank you very much for your quick answer, The output of those command lines are left and right cerebellum white matter. How can I create a mask for the whole cerebellum white matter?

Thanks Mohamad ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, July 28, 2014 11:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cerebellum white matter mask {Disarmed}

Hi Mohamad

you can use mri_binarize --match or mri_extract_label on the aseg.mgz.

cheers Bruce On Mon, 28 Jul 2014, Alshikho, Mohamad J. wrote:

...

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation?

Thanks mohamad

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