Hi Lindsay
you can use the m-file read_curv.m to read in the thickness file (lh.thickness or rh.thickness). You can also load .mgf files with either load_mgh.m or MRIread.m, then compute the mean in any subset of the vertices you want.
cheers Bruce
On Fri, 4 Jan 2019, lindsay hanford wrote:
External Email - Use Caution
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