georgias-mbp:CMTX georgina$ mri_glmfit --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir

gdfRead(): reading CMTX_b.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 age 45.2083 12.1603

Class Means of each Continuous Variable

1 patientmale  38.7778 

2 patientfemale  53.0000 

3 controlmale  40.1667 

4 controlfemale  51.8462 

INFO: gd2mtx_method is dods

Reading source surface /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces    327680

Total area         65416.984375

AvgVtxArea       0.399269

AvgVtxDist       0.721953

StdVtxDist       0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX

cmdline mri_glmfit.bin --y lh.CMTX_b.thickness.10.mgh --fsgd CMTX_b.fsgd --C Contrasts/age_sim.mtx --surf fsaverage lh --cortex --glmdir lh.CMTX_b_thickness.glmdir 

sysname  Darwin

hostname 192.168.1.32

machine  x86_64

user     georgina

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

OneSampleGroupMean 0

y    /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh

logyflag 0

usedti  0

FSGD CMTX_b.fsgd

labelmask  /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.CMTX_b_thickness.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.CMTX_b_thickness.glmdir

Loading y from /Users/georgina/Dropbox/UP_TO_DATE/CMTX_STUDY/CMTX/lh.CMTX_b.thickness.10.mgh

   ... done reading.

INFO: gd2mtx_method is dods

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

Computing normalized matrix

Normalized matrix condition is 160.248

Matrix condition is 182721

Found 149955 points in label.

Pruning voxels by thr: 1.175494e-38

Found 148239 voxels in mask

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

Reshaping mriglm->mask...

search space = 73702.448371

ERROR: dimension mismatch between X and contrast Contrasts/age_sim.mtx       X has 8 cols, C has 5 cols