On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

If you are trying to determine whether the hemispheres are different,
then you need to do the subtraction between the hemis (ie, the
--paired-diff). If you want to look at the hemispheres separately, then
don't combine them in a single file

On 10/21/19 4:58 AM, Jose Graterol wrote:
>
>         External Email - Use Caution
>
> 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 <mailto: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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