Hi, FreeSurfer Users.

 

I am comparing cortical thickness of 2 groups controlled for certain variables of no interest.

 

My contrast matrix is

1 -1 0 0 0 0 0 0 0 0 0 0  to check for group 1 thickness > group 2 thickness

 

I get my sig.mgh and I want to run mri_surfcluster command to correct for FDR.

 

I am confused as to whether I should use –no-adjust in mri_surfcluster. According to the help mri_surfcluster (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster) :

I have to use –no-adjust if my sig.mgh is not a log(10) map and sig.mgh was created using a one-tailed test.

 

Since my contrast is group1>group2 ; I am thinking my sig.mgh is a log(10) but a one-tailed. Hence I have to use –no-adjust.

 

But then again, mri_glmfit (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit) says if #of rows in Contrast matrix is 1 (which is true in my case), then the F-test reduces to a two-tailed t-test which means I should not use –no-adjust.

 

I would appreciate any response regarding this.

 

Thanks


Regards

 

Virendra

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