Volumetric measurments and difference between results from "recon_all" and "mri_segstats"
Hello Folks,
I used the recon-all -i -all -segmentation for the structural image. FreeSurfer makes several folder and one of them is "stats". In this folder, there is aseg.stats that includes volume of different brain regions. Also, I found "mri_segstats" command line that gives us the volume of the same brain regions. But, there is significant difference between reported numbers from these two methods . I would say the difference is approximately 200 mm3 for each brain region. Do you know what is correct way to measure volume of segmented brain regions using FreeSurfer?
Cheers, Saeed
Hi all,
I’m trying to open a couple aseg.mgz labels and color code them. I thought I’d do this by making my own ColorLUT table, setting the color of my regions, and then making every other region in the table be completely transparent by fiddling with the opacity value. I can’t figure out what number I want in the opacity column to make a region totally transparent, and on the wiki it says something about “255-alpha” for that column, but I don’t know what that means. In the opacity column I’ve tried values 0, 1, and 255, and it all looks the same (completely opaque) - anyone know what value I want there?
Attached is my ColorLUT table, which currently gives me yellow caudate and green amyg and hippo (what I want), and the rest of the aseg.mgz labels are all black (I’m trying to change all the black to 100% transparent so they don’t show up at all and all I see are my yellow and green regions). Thanks!!
(If it’s relevant, I’m loading the fsaverage orig.mgz and aseg.mgz into freeview and loading my ColorLUT table onto the aseg.mgz there, because I can’t figure out how to get this working in tkmedit).
Best, Stephanie
Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: (617) 724-3283 Fax: (617) 726-4078
Hi Stephanie,
I think you will need to use the dev version of Freeview for the "alpha" value to work properly.
hth d
On Thu, May 5, 2016 at 12:08 PM, DeCross, Stephanie N. SDECROSS@mgh.harvard.edu wrote:
Hi all,
I’m trying to open a couple aseg.mgz labels and color code them. I thought I’d do this by making my own ColorLUT table, setting the color of my regions, and then making every other region in the table be completely transparent by fiddling with the opacity value. I can’t figure out what number I want in the opacity column to make a region totally transparent, and on the wiki it says something about “255-alpha” for that column, but I don’t know what that means. In the opacity column I’ve tried values 0, 1, and 255, and it all looks the same (completely opaque) - anyone know what value I want there?
Attached is my ColorLUT table, which currently gives me yellow caudate and green amyg and hippo (what I want), and the rest of the aseg.mgz labels are all black (I’m trying to change all the black to 100% transparent so they don’t show up at all and all I see are my yellow and green regions). Thanks!!
(If it’s relevant, I’m loading the fsaverage orig.mgz and aseg.mgz into freeview and loading my ColorLUT table onto the aseg.mgz there, because I can’t figure out how to get this working in tkmedit).
Best, Stephanie
Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: (617) 724-3283 Fax: (617) 726-4078
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http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Whatgoesint...
On 05/05/2016 11:59 AM, Saeed Mahdizadeh Bakhshmand wrote:
Hello Folks,
I used the recon-all -i -all -segmentation for the structural image. FreeSurfer makes several folder and one of them is "stats". In this folder, there is aseg.stats that includes volume of different brain regions. Also, I found "mri_segstats" command line that gives us the volume of the same brain regions. But, there is significant difference between reported numbers from these two methods . I would say the difference is approximately 200 mm3 for each brain region. Do you know what is correct way to measure volume of segmented brain regions using FreeSurfer?
Cheers, Saeed
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freesurfer@nmr.mgh.harvard.edu
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DeCross, Stephanie N. -
dgw -
Douglas N Greve -
Saeed Mahdizadeh Bakhshmand