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:
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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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