It will be easier not to use make_average_subject. Just use mris_preproc as if you are doing a group analysis. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 The output of mris_preproc (lh.gender_age.thickness.00.mgh) can be compressed to an average with mri_concat lh.gender_age.thickness.00.mgh --mean --o lh.gender_age.thickness.00.mean.mgh
You can do the same thing for volume and area
On 7/28/2020 5:06 AM, Oana Georgiana Rus wrote:
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Dear Doug,
Thanks for the fast reply. Well we calculated the measures surface area (SA) , thickness (THK), volume (VOL) in each participant (in surf folder) of our groups and evaluated the differences between them using Monte Carlo.
Now we wanted just for descriptive purposes to be able to see the average THK, VOL and SA in each of the 3 groups mentioned before projected on the group average.
So yes every voxel in the map would contain the average value of eg. Thickness in that voxel in the group.
To obtain that we created an average brain of every group using the following command:
make_average_subject —subjects A1 B2.. —out Group_average
After this we had an average of each of our 3 groups, (in the groups space I assume). In the surf folder of every group I could find the average thickness and area map.
here an example : in freeview we loaded the surface inflated and took the overalay lh.thickness in one of our groups.
*Now I would like to have the same for the average volume in the group, however I am not quite sure how to obtain that, as there is no lh.volume file in the average brain of our group.*
I think this question was asked before see: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05874.html
However I could not really follow the instructions there.
Thanks !
Georgiana
On 27. Jul 2020, at 16:43, Douglas N. Greve <dgreve@MGH.HARVARD.EDU mailto:dgreve@MGH.HARVARD.EDU> wrote:
What do you mean by "gray matter Volume"? Do you just want a map where the value at a voxel is the fraction of GM in that voxel? What space (eg, cvs, fsaverage, mni305) are you planning to make the average in?
On 7/27/2020 4:33 AM, Oana Georgiana Rus wrote:
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Dear Freesurfer Community,
I want to have an image of the average gray matter Volume in each of my 3 groups, and I did not find a good way to do it.
I easily obtained an image from the GM thickness and area by using make_average_subject in each of my 3 groups (young musicians, old musicians and old nonmusicians). Thereby in the surf subfolder I could find an image of these 2 measures.
Could anybody give some helpful hint.
I am using FreeSurfer 6.0 on an Ubuntu Machine.18.04.4 LTS.
Best regards, Georgiana
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Oana Georgiana Rus-Oswald PhD, Dipl.-Psych.
Postdoctoral researcher
University of Zurich University Hospital Zurich Department of Neuroradiology Clinical Neuroscience Center Frauenklinikstrasse 10 CH-8091 Zürich Switzerland
Phone: +41 44 2555603 OanaGeorgiana.Rus@uzh.ch mailto:OanaGeorgiana.Rus@uzh.ch
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