Hi Jeff, you should use mris_preproc to stack the subjects into one file, mri_surf2surf to smooth them, and mri_glmfit to analyze them (including computing the difference between groups and other stats). See the group tutorial on the web page. You could probably do what you are suggesting, but it takes you off the usual pipeline and would be a dead end in the case that you wanted to take the next step such as computing p-values.

doug

On 2/14/12 9:15 AM, Bruce Fischl wrote:

Hi Jeff,

I think you want to use Doug's tools for this (mri_glm and such). He'll probably comment in an hour or two

cheers
Bruce

On Mon, 13 Feb 2012, Jeff Sadino wrote:

Hello FreeSurfers,
I want to compare cortical thickness differences between my two groups. Is
this the correct pipeline?

I ran make_average_subject on each group.

To get the study thickness file in control space, I did this: mri_surf2surf
--srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control
--trgsurfval control/surf/study.thickness.mgh --hemi lh

And then to calculate the differences, I used: mris_thickness_diff -out
diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial
control/surf/study.thickness.mgh. Is this the right way to do this?
mris_thickness_diff says it should only be used on the same subject.
mris_diff says it is still being tested. I also see
mris_thickness_comparison. Which command is the best to use to get a
thickness difference map?

Thank you very much,
Jeff Sadino
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