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