El lun, 5 abr 2021 a las 15:50, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:

What are your command lines?

On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
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Thanks a lot, It works!, now I have obtained values to ctx and wm volumes for each area. However when I look at the gray matter volume values calculated by mri_anatomical stats, the results are pretty similar to the ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In that case what measure will be more suitable?
El lun, 29 mar 2021 a las 5:22, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:
You'll need to create your own color table by adding 3000 to the left hemi structures and 4000 to the right hemi structures. Look at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt

On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
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Hello Douglas, i tried but when i look at the wmparc.mgz created by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names from FreeSurferColorLUT instead of the names in the colorLUT associated with myAAL.annot then the ROIs are disorganized. Could you help me with this problem?
El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:
Look in recon-all.log to find the command that creates the wmparc.mgz. Run that command changing the aparc annot to your annot and the output to a new file name. Look in wmparc.stats; at the top will be an mri_segstats command line. Copy that command line changing the file names as needed.

On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
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Thanks!, how can I obtain the white matter volume stats using my annotation file?
El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (<dgreve@mgh.harvard.edu>) escribió:
I think they will give very similar results, but my guess is that #1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
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I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

1. Convert the annotation file to each subject space using mri_sur2surf and using mri_anatomical_stats in each subject

2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (<BFISCHL@mgh.harvard.edu>) escribió:

Hi Alberto

And 4. Are not properties of single surfaces – they are computed from the white and the pial. For 2 and 3 that is really up to you

Cheers
Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alberto Del Cerro Leon
Sent: Monday, March 8, 2021 7:02 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Problem with freesurfer measures

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Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures:

1. Gray and White Matter Volume

2. Folding Index

3. Curvature measures

4. Thickness

However I don't know what surface in the surf folder of each subject I have to use. Could u help me?

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