Hi Karishma

if you draw an ROI and save it in label format you can use mri_label_vals to generate a text file with the value of every voxel in the label. That can then be imported into matlab to do whatever you want.

cheers Bruce

On Fri, 19 Sep 2014, Karishma Smart wrote:

Dear all, Is there a way to get a count of the voxels in a manually drawn ROI while retaining each voxel's intensity value?  In particular, I would like to get a count of how many voxels in this manually drawn ROI fall above and below an assigned intensity threshold.

I have used mri_segstats to quantify the number of voxels in a particular ROI that I have drawn manually (i.e. not using aseg).  However, in doing so (I created a label for the ROI and used mri_segstats to count the number of voxels in the label), I assigned each voxel the intensity of the label, thus losing the intensity information.

Any guidance or assistance would be greatly appreciated.  Preferably, it would be helpful if anybody knows a way to do this that is not modality-dependent.

Thank you in advance for your help, Karishma

--Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015