Hi Jason,

You can use mri_binarize to extract a wm-hypointensities.mgz volume and view that over the orig.mgz. The following will make a binary volume called wm-hypointensities.mgz from all voxels in the aseg.mgz with an intensity of 77 - all voxels labeled wm-hypointensities:

mri_binarize --i mri/aseg.mgz --o mri/wm-hypointensities.mgz --match 77

Then view the new wm-hypointensities volume over the orig.mgz like this:

freeview mri/orig.mgz mri/wm-hypointensities.mgz:colormap=heat

Best,

Bram

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ledesma, Jason <jason.ledesma@labiomed.org>
Sent: Wednesday, February 21, 2018 1:53:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Lookup Table

Hi,

When viewing MRI mgz images in Freeview, is it possible to only look at certain structures specified in the look up table? That is, to only view colorization of one structure to view it more concisely? Specifically, we want to look at wm-hypointensities to see lesion approximations. Thanks.

Sincerely,

Jason Ledesma

Staff Research Associate
Phone: 1(424)571-7755
E-mail: jason.ledesma@labiomed.org

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