Hi all,
I'm trying to get gyrification information about a single subject. I've run the -localGI process but I have a few questions about the results:
1. When I try to plot the smoothed out pial surface over the brainmask in freeview, I use the command
freeview -v subject/mri/brainmask.mgz -f subject/surf/lh.pial-outer-smoothed
but it appears to be an inflated surface of some sort. It doesn't hug the contours of the brain mask as I expected (or as shown in the top image here: https://surfer.nmr.mgh.harvard.edu/fswiki/LGI). How can I see that surface?
2. I see very little variation in the local GI. I'm wondering if the third image in the link above is typical, and also how to get the blue to red color scale as shown? I can only get red to yellow, which doesn't show as much variation.
3. There is information on how to run analysis on a group of subjects, but I'm wondering if it's possible to get numerical data on a single subject. For instance: average GI in a given ROI, global GI, distribution (min, max, std dev, etc.). If nothing else, can I get the numerical values for each vertex?
Thanks for your help!
~ Maria Holland Stanford University