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.ande...@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
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