You will need to create a new color table. It is currently referencing FreeSurferColorLUT.txt. If you load the segmentation as both a segmentation and the aux volume, you can see the number associated with the color. You will need to create a table similar to FreeSurferColorLUT.txt doug

On 05/28/2013 01:51 PM, Gonzalo Rojas Costa wrote:

Hi Doug:

It is labeled as wm-rh-fusiform and wm-lh-fusiform

Sincerely,

Gonzalo Rojas Costa

On Tue, May 28, 2013 at 1:47 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

...

what is is labled?

On 05/28/2013 01:42 PM, Gonzalo Rojas Costa wrote:

...

Hi Doug:

I use the instructions that you told me... But, why I get the gray

colored region (red arrow) ?...

Sincerely,

Gonzalo Rojas Costa

...

Message: 15 Date: Mon, 27 May 2013 22:41:41 -0400 From: Douglas Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] white matter volume per lobe... To: freesurfer@nmr.mgh.harvard.edu Message-ID: 51A41965.6050808@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed

you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug

-- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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