Hi Sabrina

if you have drawn the label in freeview you can use mri_label_vals to generate a file of the value of each voxel in the label in whatever volume you specify. You can then do whatever you want with them (e.g. fit a Gaussian to it, etc...)

Bruce On Tue, 24 May 2016, Sabrina Yu wrote:

Hello,

I have created my own subcortical ROI in freesurfer (saved as .label file), and am trying to generate an intensity stats file for this ROI. Reading the mailing list, I think that the best way to do this is to:

1. mri_label2vol to convert my ROI to a volume file

2. mri_label_volume to generate stats on this volume

I was able to achieve the first step, but am unable to generate a stats file with intensity info for the volume. This is the command I tried to use:

cd /freesurfer/subjects/<subjectname>/mri

mri_label_volume -s <subjectname> stroke_area.mgz label 1

Any help would be much appreciated! Thank you in advance.

Sabrina