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
On 01/10/2018 11:54 AM, John Anderson wrote:
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
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