Dear FreeSurfer experts,

I get this error message when running group analysis on cortical thickness using glmfit:

ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx X has 9 cols, C has 10 cols

Please find attached the FSGD file, the contrast file and the terminal output below.

I want to do ANCOVA with three groups (ADHD, COM and TD) controlling for the effects of age and IQ.

So I assume the regressors would be ADHD COM TD age IQ and my contras matrix 1 -1 0 0 0 1 0 -1 0 0 according to information from these two tutorials: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V and https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V.

Can anybody help me out? Where am I wrong? Why does glmfit assume X has 9 cols?

Any help would be much appreciated, thank you in advance!

Best

Lea

Terminal Output:

mri_glmfit --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
gdfRead(): reading FSGD/ADHD_COM_TD_orig_age_IQ.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 13.6015 1.73148
1 IQ 107.288 11.1649
Class Means of each Continuous Variable
1 ADHD  13.7193 104.3478
2 COM  12.8657 105.3929
3 TD  14.0119 112.3784
INFO: gd2mtx_method is dods
Reading source surface /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces    327680
Total area         65020.839844
AvgVtxArea       0.396851
AvgVtxDist       0.717994
StdVtxDist       0.193566

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS
cmdline mri_glmfit.bin --y rh.thickness.ADHD_COM_TD_orig.15.mgh --fsgd FSGD/ADHD_COM_TD_orig_age_IQ.fsgd --C Contrasts/ADHD_COM_TD_age_IQ.mtx --surf fsaverage rh --cortex --glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
sysname  Darwin
hostname edr06188.dip.tu-dresden.de
machine  x86_64
user     Lea
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh
logyflag 0
usedti  0
FSGD FSGD/ADHD_COM_TD_orig_age_IQ.fsgd
labelmask  /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir
Loading y from /Volumes/Elements/ADHS_MRI/T1/FreeSurfer/Auswertung_cortical/Lea_2018/SUBJECTS/rh.thickness.ADHD_COM_TD_orig.15.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1027
Matrix condition is 4.07619e+06
Found 149926 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149926 voxels in mask
Saving mask to rh.thickness.ADHD_COM_TD_orig_age_IQ.15.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 74490.844410
ERROR: dimension mismatch between X and contrast Contrasts/ADHD_COM_TD_age_IQ.mtx       X has 9 cols, C has 10 cols