Hi,

You have a continuous variable "age" in your fsgd file. As far as i know, permutation can't have continuous variables.

Try mc-z that should work.

pratap

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer