Hi Anita
the problem is that the cortex is not well aligned in the avg152 space, and
so a volume-defined ROI will not follow the contours of the cortex well.
Not sure that there's much you can do about this except possibly map the
ROI back to the individual subjects, and recreate it in fsaverage space
using surface-based tools. Perhaps Doug will chime in after the trytophan
wears off....
Bruce
On
Fri, 29 Nov 2013, Anita van Loenhoud wrote:
Dear Freesurfer experts,
I want to use volume-defined ROIs (obtained in a VBM study) to extract mean
thickness and surface area, in a total group of 138 participants. I followed
the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few
questions regarding this analysis:
1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1
and fsaverage. After the vol2surf-step, however, a few problems arise. The
new ROIs look very different: one ROI actually consists of two clusters
close to each other, one is very small and two ROIs have completely
disappeared. Does anyone know why this happened?
2. When I want to obtain surface area data instead of thickness data, is it
sufficient to replace 'thickness' with 'area' in the surf2surf command (it
seems to work, but I want to check)? So:
--sval lh.area \
--tval lh.area.fsaverage.mgh \
3. mri_segstats creates separate files for each ROI in each participant.
When I want to have all thickness and area ROI data in one file, can I use
asegstats2table, meas mean (it seems to work, but I want to check)?
Any help would be very much appreciated!
Anita
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