Dear Eelco

years ago i posed a similar question on the FS email list

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021386.html

a part of the response is below

>>> The other question is how mri_glmfit estimates the variance. Because I have
>>> only one subject in the patient group, there is not variance in that group
>>> and therefore I guess mri_glmfit used pooled (across both groups) estimates
>>> of variance, isn't it?
>>>   
>>>       
>> Yes, it uses pooled estimates.
>>
>> doug
if you are concerned with respect to the variance estimates, it does not matter 
because variance is estimated pooledly, i.e. across both groups.
hope this helps

Cheers
Jürgen

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Am 13.10.2016 um 15:56 schrieb Eelco van Duinkerken:

> Hi all,
> 
> I am using FS with data from 2 different studies that were acquired on the 
> same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the 
> group sizes are not very balanced, with 31 controls, 16 obese and 32 diabetes 
> patients.
> 
> Is the GLM for thickness used in FS very sensitive to this unequal group size?
> 
> 
> Thanks for the help,
> 
> Eelco
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