Hi Bruce,

Thank you, I didn't realize it would be so simple in matlab!

To help others who might be looking for a solution:

I was able to use MRIread for both my data.mgh file (created using mri_surf2surf, resampled to template space for the thickness values) and mask file (which i inverted using mri_binarize --binval 0 --binvalnot 1). Then I was able to use a simple multiplication across the two vectors (as they have the same number of vertices) to conserve the thickness values from vertices of interest and remove values from vertices I wanted to exclude.

matlab code:

datafile_lh=MRIread('data_lh.mgh')

maskfile_lh=MRIread('mask_lh.mgh')

newmatrix=datafile.vol.*mask.vol).

Thanks again!

Lindsay

On Fri, Jan 4, 2019 at 10:05 AM lindsay hanford <lindsay.hanford@gmail.com> wrote:

Hi Bruce,
Sorry for the late reply. I have been searching the forum and the freesurfer wiki. Are there instructions somewhere on how to do this in matlab?
Thanks,
Lindsay

On Thu, Dec 20, 2018 at 2:41 PM lindsay hanford <lindsay.hanford@gmail.com> wrote:
Hello Freesurfer Community,

I am wondering if it is possible to recalculate cortical thickness metrics (perhaps using mri_segstats or aparcstats2table) while including either a SD threshold or an exclusion mask.

Using mri_surf2surf to register scans to the same space and then mri_surface_stats to create the std maps I have been comparing the variability of cortical thickness across the cortex for multiple scans across the same subject. From this I can determine a SD threshold point (0.5 say) or create a mask that includes all regions above that threshold.

I would like to use this to threshold the regions showing the highest variability out of my calculations for mean hemispheric thickness and also regional thickness.
Is there a way to use an SD threshold within mri_segstats or aparcstats2table? Otherwise apply a mask image to exclude specific vertices?

Thank you in advance,

Lindsay

--
Lindsay Hanford, PhD
The Buckner Laboratory | Harvard University
280 Northwest Laboratory, 52 Oxford St | Cambridge, MA 02138
412-218-4368 | lindsay.hanford@gmail.com