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Dear Doug,
Thanks for the fast reply. I tried it out as you mentioned and it worked out. At the end of the email are the details of my analysis for people which might want to do the same analysis.
Now I have a question with respect to the output and its colorbar in freeview (so loading the output images from mri_concat command obtained before in freeview).
The outputs for the 3 measures would be: - lh.gender_age.thickness.00.mean.mgh, - lh.gender_age.volume.00.mean.mgh - lh.gender_age.area.00.mean.mgh
I loaded them in freeview on the inflated surface of the group as an overlay(load generic) I also configure the overlay using the color wheel option. Then I click the color scale option to see the colorbar in the image (see example below) with my configurations.
While for the thickness the colorscale looks logical values going from 1.28 -3.99 (assuming these are mm). For volume and surface area they look not intuitive i.e. 0.239-4.39 in volume and 0.206-1.13 in surface area.
Is there a way to show the colorscale bar in the units of the respective measure i.e. volume in mm3 and surface area in mm2 ? Or asked in another way: what range or unit is the colorscale which i see now.
To make it more clear here one screenshots of the settings for for the volume : Thanks a lot in advance for your reply.
Georgi
average volume image in a group:
***** For others: How I computed the average volume, surface area or thickness in a group For this I did the mris_preoproc command for each one of the groups i had (young musicians, old musicians and old non-musicians), therefore using the respective fsgd file. This I run for each of the 3 measures. thickness, volume, surface area. Then i used each one of the output files (eg lh.gender_age.thickness.00.mgh, lh.gender_age.volume.00.mgh, lh.gender_age.area.00.mgh) in the mri_concat command to obtain the average thickness, volume and area map of the groups.
On 28. Jul 2020, at 16:14, Douglas N. Greve dgreve@MGH.HARVARD.EDU wrote:
It will be easier not to use make_average_subject. Just use mris_preproc as if you are doing a group analysis. Seehttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 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:
External Email - Use CautionDear 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.
<OM.lh.thickness.png>
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 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:
External Email - Use CautionDear 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
