On 02/06/2013 12:49 PM, Gabriel Gonzalez Escamilla wrote:

Dear Doug and FreeSurfer experts,

Thnak you so much for all your lasts responses!.

I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions:

given the command for interhemispheric comparisons: mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir glm.lh.lh-rh.thickness.sm05 --osgm --surf fsaverage_sym lh;

A) This read all subjects to construct X and C as one-sample group mean, this means that as result I get the difference across hemispheres and across my subjects in a population, right?

Correct.

B) But, what if I have two groups? controls and patients, I'm wondering if is it possible to examine regional differences of thickness asymmetries between those two groups? or more?

This just becomes a standard two group analysis as described in the tutorials. You create an FSGD file with two classes and list your input subjects.

C) If I want to examine effects of group or sex, while controlling for age and other factors how do I introduce them into the glm model? If so, do I set the contrasts as normally for mri_glmfit? I mean as any other thickness study? or there is any other thing that I should do?

You do not need to do anything different than with a normal thickness study.

The command for multiple comparisons correction is: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 Which performs only cluster-wise corrections,

D) is there any other way to correct for multiple comparisons, something like permutation tests or anything else?

Yes, you can run something like mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm05 --cwpvalthresh .5 --sim perm 10000 2 csdperm --sim-sign abs You should run mri_glmfit-sim --help to see what these options mean as you may need to change the voxelwise threshold (the "2" value)

doug

Many thanks in advanced, Gabriel