Hi Maria,
Here are the responses:
1. Can you send us a screenshot of what you mean with "it doesn't hug the contours of the brain mask"? You can use: tkmedit <SUBJ> T1.mgz lh.pial -aux-surface lh.pial-outer-smoothed (or the corresponding in freeview) and it should give you what correspond to the top image in the wiki page.
2. The color code including many colors as you see in the wiki was created using scuba. With free view / tksurfer you'll rather have a binary color scale. You have to set the minimum at 1, and you will see minimum values around the medial prefrontal regions, and maximal ones around the insula. You can use the following command: tksurfer <SUBJ> ?h pial -overlay /surf/?h.pial_lgi -fthresh 1. See as well the jove video explaining the process here: http://www.jove.com/video/3417 (subscription required)
3. Yes you can get all of that: numerical values for each vertex are stored in the ?h.pial_lgi (curv format). Otherwise, average lGI over the entire hemisphere should be written at the end of the lGI process in your command line (or in your log). And you can get statistics in ROI using: mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats
Hope it helps,
Marie
On Oct 27, 2014, at 10:02 PM, Maria Holland <mholla@stanford.edumailto:mholla@stanford.edu> wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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