Update - Solved the issue. A better way to extract values from a surface overlay is by using mri_segstats with --annot subject hemi parc.

Thanks

On Sat, Oct 7, 2017 at 11:45 AM, Yash Patel ypatel@research.baycrest.org wrote:

Hi,

I have a MT and T1W volume (processed through recon-all). I would like to extract all MT values that lie in the middle surface of the cortex, and run that through mri_segstats so I get average MT values for each cortical region in the DK-atlas.

My workflow is as follows:

1. mri_vol2suf --mov <MT_vol> --hemi lh --projfrac 0.5 -- regheader <id>

--reg <MT_reg_to_T1W.dat> --o <vol2surf.output.mgh> --interp nearest

2. mri_surf2vol --surfval <vol2surf.output.mgh> --hemi lh --fillribbon

--identity <id> --template <T1W> --o <surf2vol.output.mgh.

3. mri_segstats --seg <aparc+aseg for subid.mgz> --i <surf2vol.output.mgh>

--ctab --id <list of regions> --o <output.stats>

Is this the correct way of going about it? I was wonder if its alright to use mri_vol2surf to get MT values on a T1W surface, and then mri_surf2vol to get the output from vol2surf into a T1W cortical ribbon. And finally run mri_segstats on the output of mri_surf2vol using the aprac+aseg for that subject.

Thank you,

Yash RRI, Baycrest Health Sciences University of Toronto