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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, age and sex.

My FSGD file is: 

GroupDescriptorFile 1

Title Func

Class HC

Class CMT

Variables  Age gender

Input fs_VF HC      46 Female

Input fs_RF HC         24 Female

.......

My group.diff.mtx is:

1 -1 0 0 0 0     0 

My command line:

 mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir 

But unfortunately I get this wrong message: 

RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

--------------------------------

Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

If you seek help with this problem, make sure to send:

  1. Your command line:

    mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir 

  2. The FSGD file (if using one)

  3. And the design matrix above

Attempting to diagnose further 

SumSq: Min=0.000000 (col 5), Max=146.140350 (col 3)

 The scale is much different between columns 5 and 3, you may want to 

 normalize by subtracting the mean and dividing by the standard deviation.

Column 5,  all values are 0

Column 6,  all values are 0

Columns 5 and 6 are the same

Can you please help me?

Thank you very much

Raf

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