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:
External Email - Use Caution
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
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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
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*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Friday, February 4, 2022 7:10:17 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto: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:
External Email - Use Caution
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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