If you don't have any covariates, you can use --osgm. If you have covariates, then they need to go into an FSGD file. doug

On 11/15/2013 04:12 PM, Govindarajan, Koushik Athreya wrote:

Hi all,

 I am trying to compute differences between 2 runs of my same set 

of subjects (repeatability) using the steps from the paired analysis wiki page. After I finish the mris_preproc and the mri_surf2surf steps, when I do the glmfit, should I be using the osgm option ? Since it is the same subject, I do not need the age variable as mentioned in the 2^nd fsgd file. If I should still be using the 2^nd fsgd file and not osgm, what would my contrast file look like?

Thanks for the help

Koushik

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