Hi Jeff,

mri_extract_label -t transforms/talairach.m3z...

will do most of what you want (it will also jacobian correct the label so that you get a "mass" image). We never put this together into a pipeline because it is of course well-known that interpreting the results from a neurobiological perspective is fraught with difficulty (which will always be the case when the quantity you are using to drive the registration is also the one you are correlating with e.g. disease effects). Nevertheless, tons of people do it so the tools are around.

cheers Bruce

On Wed, 13 Apr 2011, Jeff Sadino wrote:

Hello,

I found a couple of scripts that might work, namely the mri_hausdorff_dist, mri_distance_transform, the mri_compute commands, and the mri_seg_diff. They all seem to do one part of what I want, but none all together. Has anyone done this before and could they point me in the right direction?

Thank you, Jeff Sadino

On Mon, Apr 11, 2011 at 1:07 PM, Jeff Sadino jsadino.queens@gmail.comwrote:

...

Hello,

I am interested in a way to visualize the differences in the volume in subcortical structures, preferably in 3D. For example, I would like to view the Thalamus of controls. And then I would like to overlay a color-coded map that shows the difference between the volume of the Control Thalamus and the Study Thalamus. I have seen a couple of different ways to do this, but they all seem rather clunky. Can anyone recommend a method for this?

Thank you very much, Jeff Sadino