Hi everyone,

I get this error when running group analysis of cortical thickness by command-line:

xin-fa@xinfa--PC:/media/E/FREESURFER/VisualData$ mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir

gdfReadHeader: reading group_differ.fsgd

INFO: gd2mtx_method is dods

Reading source surface /media/E/FREESURFER/VisualData/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces    327680

Total area         65416.648438

AvgVtxArea       0.399267

AvgVtxDist       0.721953

StdVtxDist       0.195470

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /media/E/FREESURFER/VisualData

cmdline mri_glmfit --y lh.group_differ.thickness.10.mgh --fsgd group_differ.fsgd dods --C con.mtx --surf fsaverage lh --cortex --glmdir lh.group_differ.glmdir 

sysname  Linux

hostname xinfa--PC

machine  x86_64

user     xin-fa

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh

logyflag 0

usedti  0

FSGD group_differ.fsgd

labelmask  /media/E/FREESURFER/VisualData/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.group_differ.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.group_differ.glmdir

Loading y from /media/E/FREESURFER/VisualData/lh.group_differ.thickness.10.mgh

INFO: gd2mtx_method is dods

Saving design matrix to lh.group_differ.glmdir/Xg.dat

Normalized matrix condition is 1

Matrix condition is 1.04762

Found 149955 points in label.

Pruning voxels by thr: 0.000000

Found 149953 voxels in mask

Saving mask to lh.group_differ.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 74612.446501

ERROR: dimension mismatch between X and contrast con.mtx       X has 2 cols, C has 1 cols

The data is altogether 43 subjects,including 22 subjects in expert group.I just want to explore the difference between both groups.

Attached is the FSGD file ,which is two groups ,zero covariates . The contrast matrix is 1 -1 .

Subsequently I try it only with a few subjects ,and it succeeds. 

Can you help me ?

Best wishes.

Xin-Fa .

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