Dear all,

I am trying to run a group analysis through the terminal using an .fsgd file, with no additional covariates.

GroupDescriptorFile 1 Title PDPLUS2 Class PD Class MSA Class PSP Input PDPLUS007/ PD Input PDPLUS005/ MSA Input PDPLUS004/ PSP etc...

When I try to run a command similar to the example fsgd analysis on the freesurfer wiki:

mri_glmfit \ --glmdir pdplus \ --y y.mgh \ --fsgd g3v0.fsgd \ --C PD-MSA.mtx \ --C PD-PSP.mtx \ --C MSA-PSP.mtx \ --C group.effect.mtx \ --C PD+MSA-vs-ad.mtx

I have received the following error message:

Creating output directory pdplus2 Loading y from /home/k1204763/images/PDPLUS/y.mgh mghRead(/home/k1204763/images/PDPLUS/y.mgh, -1): could not open file ERROR: loading y /home/k1204763/images/PDPLUS/y.mgh

I am not too sure whether y.mgh actually exists, is there a way that I can create this file for the three groups? Any other thoughts on this error would very much be appreciated.

Thanks in advance,

Amanda