Hi Bruce,
Thanks for your answer!
I tried mris_anatomical_stats command, but I met problems: (1) I would like to get the mean intensity ratio of the superior temporal, so I need a label of this region. I first used mri_annotation2label to get lh.superiortemporal.label file.
(2) Then I used mris_anatomical_stats command as following (I saved GM/WM intensity ratio as lh.gm_wm.mgh): mris_anatomical_stats -l label/lh.superiortemporal.label -t subj1/surf/lh.gm_wm.mgh -b -f ./lh.intensity.stats subj1 lh
I didn't get intensity results, rather than mean thickness, area and curvature in this region. I got the same results in above command using "-t lh.thickness" instead of "-t subj1/surf/lh.gm_wm.mgh".
It looks like it didn't read the information of "lh.gm_wm.mgh", even I used "-t subj1/surf/lh.gm_wm.mgh".
I didn't find other appropriate flags which could instead of "-t".
Do you know how to fix this problem?
Thanks for your help!
Regards
Li
________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, December 03, 2012 2:51 PM To: Kong, Li Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Calculating the mean intensity ratio in one specific region
Hi Li
save it as a .mgz volume and use mris_anatomical_stats with the parcellation you want.
cheers Bruce On Mon, 3 Dec 2012, Kong, Li wrote:
Hello everyone,
I got grey matter/ white matter intensity ratio at each vertex across the cortex. I would like to know the mean intensity ratio in one region (ex, superior temporal gyrus).
Anyone knows how to get it?
Thanks in advance!
Li
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