Hi,

using version 4.0.5

i ran the command:
mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/

it worked.

then i did:

mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh --glmdir stats/newperm_lh/

output:

gdfReadHeader: reading qdec/qdec.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 15.4819
Class Means of each Continuous Variable
1 control 15.0882
2 patient 15.7551
INFO: gd2mtx_method is doss
Reading source surface /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white
reading group avg surface area 822 cm^2 from file
Reading in average area /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh
simbase stats/perm_lh
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 1.138.2.1 2007/09/12 15:38:19 nicks Exp $
cwd /home/neuro/joost/redes/maranon/freesurfer
cmdline mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh  --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/perm_lh --glmdir stats/
sysname  Linux
hostname fedoraneuro.lim.local
machine  x86_64
user     neuro
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh
logyflag 0
usedti  0
FSGD qdec/qdec.fsgd
glmdir stats/
DoFFx 0
Loading y from /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh
Matrix condition is 404.504
search space = 82220
ERROR: design matrix is not orthogonal, cannot be used with permutation.
If this something you really want to do, run with --perm-force

mri_info N83_only_boys.mgh gives 83 frames.
 
what´s wrong with my design matrix?

thanks!
-joost