Hi Kenza, (I added the freesurfer mailing list in copy, please post there)
You have to set the min threshold at 1 when you overlay the lGI, then you should not see any gray regions anymore.
Not sure I understood your problem with the statistical analyses, maybe there is simply no significant difference? If you could complete the lGI without problem (which is the case if you have the ?h.pial_lgi files), and if you are certain of your statistical design, then it simply means that there is nothing which is more significant than the given significance threshold (you can play with the significance threshold to explore that as well, and visualize the data in plots at some vertices in qdec).
Best,
Marie
On Apr 3, 2014, at 4:57 AM, Kenza Drissi-kaïtouni kenza.drissi-kaitouni@polymtl.ca wrote:
Dear Marie,
I have been trying to use the lgi implemented in Freesurfer. I was able to obtain results, but unfortunately, when I overlay visualize them as an overlay of ?h.pial_lgi on the ?h.pial surface in tksurfer, I still see gray regions which shouldnt be... What can I do to fix this problem?
Also, when I perform a statistical analysis on the data I obtained, only 2 small spots appear for lh and none for rh. I strongly suspect this is because of the gray regions where no lgi was apparently calculated/retained. Is it so?
Thank you very much for you time, Kenza Drissi-Kaitouni B.Sc. Biomedical Engineering Ecole Polyetchnique de Montreal
D.E.S.S Biomedical Engineering