Yes!! this worked. Thank you so much!

I was afraid of that. You will need to either map wmparc to the brainstem space or the brainstem into the wmparc. Probably better to do the first. You can use mri_label2vol with --seg wmparc.mgz --temp brainstem.mgz --regheader wmparc.mgz --o wmparc.in-brainstem.mgz

swif�,7�&

-------- Original Message --------
Subject: Re: combining masks
Local Time: January 10, 2018 11:54 AM
UTC Time: January 10, 2018 4:54 PM
From: John.anderso@protonmail.com
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

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