On Sun, 22 Mar 2009, Avram Holmes wrote:
All,
I have generated a mask of the cingulate regions for each of my participants
from their aparc+aseg.mgz files (see attached image) and I would like see how
these masks overlay with the group average brain I have generated for my
study. Is there a simple way to transform a mask from an individual subjects
space to the group average volume space? I made my group average with the
make_average_subject command.
You can create a mask of the cingulate with mri_binarize --match XXX,
then convert that into the average space with mri_vol2vol (for
command-line ops see how the aseg is done in make_average_subject),
then concatenate all of your masks together with mri_concat, adding
--mean to compute the mean. The value at each voxel will then be the
fraction of your subjects that had a cingualte mask at that voxel. You
can display this as an overlay, or you can threshold it to turn it
back into a mask.
In a related question is it possible to generate a group average
aparc+aseg.mgz file? I can see the surface labels in the average and the
aseg.mgz cortical labels. However, I don't know of a way to generate the
aparc+aseg.mgz file.
I did write software to do this, but it turned into a real
mess. Cortex is so thin and the location of the indivdual cortical
regions so variable, that the final map ended up with all kinds of
strange holes (a good advertisement against talairach!). If you just
want it for display, you should be able to run "mri_aparc2aseg --s
avgsubject --volmask", but this won't reflect the actual labels from
your group of subjects.
doug
Thanks for any help you can offer,
Avram
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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