Thanks for your answer.

I want to correlate TMS values in 17 stroke patients. Following the instructions provided to Anders in this link https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+flipping+surface+data%22&o=newest&f=1 I created the --y file that joins the affected hemispheres together and the unaffected hemispheres together. I omitted the --paired-diff flag. When I run mri_glmfit with --fsgd it asks for 34 inputs. I am guessing those are for the 34 hemispheres of the patients in the order mentioned in my first email. Would this be the right way to correlate the variables?

In short, I am trying to test if there is a difference in cortical thickness, while adding covariates, between the affected and unaffected hemispheres in stroke patients.

Thanks in advance

On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

What are you trying to test? Usually you don't have lh and rh in the same glm

On 10/17/19 7:09 AM, Jose Graterol wrote:
        External Email - Use Caution

Dear Freesurfer Community,

I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi.

First the --y file was created as previously explained in another discussion (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63965.html). That is, mris_preproc with --xhemi and no --fsgd flag.

If I understood correctly, that would create a mgh file with the following order: sub01lh, sub01rh, sub02lh, sub02rh...

Then the FSGD file while running mri_glmfit would be:

GroupDescriptorFile 1

Title xxx

Class sub

Variables   var1

Input   sub01lh   sub   var1_lh_sub01

Input   sub01rh   sub   var1_rh_sub01

Input   sub02lh   sub   var1_lh_sub02

Input   sub02rh   sub   var1_rh_sub02

Would this be correct? If so, what would be the best case for specifying a variable like age? Just repeating the value 2 times?

As always, thanks in advance

Kind Regards

José
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