The contrast is not correct for your design. Your design matrix will
have 3 columns, one for HC, one for CMT, and one for
rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a
DOSS kind of way. If you want to test for a difference in
thickness-meylin slopes between the two groups, you will need to have
two PVRs, one where the value is the thickness for HC subjects and 0 for
CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1.
If you just want to remove thickness as a nuisance, then you can stick
with what you have and just use a contrast of 1 -1 0

On 12/25/18 5:05 AM, Raffaele Dubbioso wrote:
>
>         External Email - Use Caution
>
> Dear Freesurfer team,
>
> I'm running a group analysis where I'd like to compare myelination
> between two groups regressing out cortical thickness.
> Unfortunately I get always the same error message:
> dimension mismatch between X and contrast group.diff.mtx       X has 3
> cols, C has 4 cols. Is my group.mtx correct?
>
> My command line is:
> mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd
> thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C
> group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf
> fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir
>
> My group_diff.mtx: 1 -1 0 0
>
> This is my FSGD FILE:
> GroupDescriptorFile 1
> Title Myelin
> Class HC
> Class CMT
> Inputfs_VFHC
> ........
>
>
>  Thank you very much for your help
>
> Best regards,
> Raffaele
>
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