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