Martina,
For a single roi, it should not be necessary to create an annotation file. An annotation file is generally only useful for collections of labels (typically composing an atlas). Even for multiple roi, working with label files is easier.
mris_thickness_diff works with pairs of subjects because it is necessary to have a registration from one to the other. For multiple scans, you could use mris_surf2surf to sample the subject data onto either a common average surface, or in your case where you are using one subject, you could sample onto the first scan. Then mris_anantomical_stats can give you thickness stats for a label. Or you could use mri_concat to compute some stats (add --help to each of these utils for help and examples).
Nick
On Fri, 2009-03-13 at 16:49 +0100, Campanella Martina wrote:
Hi,
We would like to test the thickness repeatibility in a particular region of interest from 6 scans of the same subject in the same session and from the same subject in 6 different sessions to compute the overall statistics of them.
We are trying to follow the protocol described in the wiki page about Thickness Repeatibility (http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility) but we're encountering some problems.
We defined with tksurfer tools the label corresponding to the roi intended, afterwards we converted it in an annotation. The tutorial suggests the use of mris_thickness_diff but we have 6 scans, rather than only 2. So what can we do?
Anyway we tried to find the thickness difference map using the first scan as the reference surface and the others as the input surfaces but, since we'd like to analyze the thickness deviation standard in a specific region, we used the option flag “-annotation” and the results seem wrong: we tried to use several annot files, specifing different label names but we found always the same error:“ total 0 vertices involved in thickness comparison”.
Any suggestions for our data?
Thanks,
Elisa Molinari, Martina Campanella
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