Hi Freesurfers,
I have some questions about ROI analyses.
1. I use the mni305 and fsaverage flags during preprocessing. Does this mean that when I run funcroi-config, funcroi-sess, etc, the analysis is being done for each subject in mni305 space, as opposed to native space? Meaning, If I specify -seg aseg.mgz 18 in funcroi-config, the analysis will not be done using the left amygdala from that individual's aseg, but instead will be done in mni305 space with the fsaverage left amygdala ROI?
2. I sometimes want to use labels I've created on fsaverage from averaged group activation to do ROI analyses. If the ROI is in the volume, I convert the label to a mask and run:
mri_segstats --i cespct.nii.gz --seg mymask.mgz --id 1 --avgwf ces.mymask.dat
In the appropriate contrast folder. What should I do if I want to do the same thing, but with a surface label (in a lh or rh surface analysis, not an mni305 analysis)?
Thanks!
Emily