Dear Dr Greeve,

Thank you very much for the quick and detailed response.

Before your response, I tried fslmaths instead of fslcalc and I got error message complains about misorientation between the input masks.

Now, I tried fslcalc and it failed as well to combine the masks due to a mismatch sizes!

Any suggestions are highly appreciated?

you'll need to do it in 3 steps

mri_binarize --i wmparc.mgz --match 1024 2024 3024 4024 --o wmparc.mask.mgz

mri_binarize --i brainstemSsLabels.v10.mgz --match 173 --o bs.mask.mgz

fscalc wmparc.mask.mgz and bs.mask.mgz -o final.mask.mgz

The only problem will be if the brainstem seg is higher res than wmpar

On 01/10/2018 11:10 AM, John Anderson wrote:

> Dear Freesurfer experts,

> I want to create mask for the midbrain and the precentral gyrus.

> I used FSV6 to do the reconstruction. Then I used the flag

> -brainstem-structures in recon-all to segment the brain stem.

> How can I create _one mask_ that include structures from wmpac.mgz and

> brainstemSsLabels.v10.mgz for instance I want to use mri_binarize to

> create one mask contains the following labels

> 1024 2024 3024 4024 from wmpar.mgz and 173 from

> brainstemSsLabels.v10.mgz

> Any advice you provide is highly appreciated.

> Thanks

> John

-------- Original Message --------
Subject: combining masks
Local Time: January 10, 2018 11:10 AM
UTC Time: January 10, 2018 4:10 PM
From: John.anderso@protonmail.com
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Dear Freesurfer experts,
I want to create mask for the midbrain and the precentral gyrus.
I used FSV6 to do the reconstruction. Then I used the flag -brainstem-structures in recon-all to segment the brain stem.
How can I create one mask that include structures from wmpac.mgz and brainstemSsLabels.v10.mgz for instance
I want to use mri_binarize to create one mask contains the following labels
1024 2024 3024 4024 from wmpar.mgz and 173 from brainstemSsLabels.v10.mgz

Any advice you provide is highly appreciated.
Thanks
John