that's in make_average_volume
doug
Avram Holmes wrote:
Doug,
I'm having some trouble tracking down the command line that you suggest I find (where teh aseg file is transformed in make_average_subject). Do you think you could give me a pointer in the right direction? Once again I'm trying to convert individual subjects cingulate masks into the group average space.
Thanks, Avram
On 3/22/2009 3:34 PM, Doug Greve wrote:
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