Re: [Freesurfer] ROI analyses

On 03/28/2014 08:51 AM, Emily Boeke wrote:

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?

No, it is done in native space. The voxelwise analysis is done in fsaverage/mni305 space, but the ROI boundaries used to compute the ROI averages are computed in native space and mapped to fsaverage/mni305 space.

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)?

You can still use mri_segstats, just spec --slabel instead of seg doug

Thanks!

Emily