for the annot, it should get the color table from the annot itself. for the output, there is not an option to change the colortable, but you can just
mri_convert -ctab your.ctab file.mgz file.mgz


On 2/14/2022 3:49 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

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Is there an argument to put in a custom LUT? I don’t see it in the options for mri_surf2volseg. I’m assuming I have to put in average/colortable_vpnl.txt and average/colortable_BA.txt
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Sunday, February 13, 2022 10:42:41 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] [External] Re: white matter measurements for labels/annotations
 
You'll have to create an annotation first (maybe with mris_label2annot), then use mri_surf2volseg to create the segmentation. Look at the command line to create wmparc.mgz

On 2/4/2022 10:03 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

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Yes but instead of DKT regions, it would have brodmann area for example
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Friday, February 4, 2022 7:10:17 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] white matter measurements for labels/annotations
 
Do you mean something like wmparc.mgz and wmparc.stats?

On 2/1/2022 1:10 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:

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Hi, 

is it possible to extract white matter volume estimations for labels/annotations? I am specifically wondering about the brodmann atlas and the stanford atlas that is already included in latest FS.

Thanks,

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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