Dear Doug,

I was running the 

 mri_glmfit-sim \
--glmdir GroupAnalysis_abs.glmdir \
--sim perm 1000 3 permcsd \
--sim-sign abs \
--cwpvalthresh .05

just to get an idea of how my FA Group Analysis data is looking and I got an error before to get the permcsd.sig.cluster.summary file from the mri_volcluster:

mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh
ERROR: cannot find /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS/fsaverage/mri/aparc+aseg.mgz


I replaced the fsaverage/mri/aparc+aseg.mgz with the cvs_avg35/mri/aseg.mgz  and to get the cluster summary I was running:


mri_volcluster --in GroupAnalysis_abs.glmdir/contrast/sig.mgh --mask GroupAnalysis_abs.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.mgh --sum GroupAnalysis_abs.glmdir/contrast/permcsd.sig.cluster.summary --ocn GroupAnalysis_abs.glmdir/contrast/permcsd.sig.ocn.mgh --cwpvalthresh .05 --seg cvs_avg35 aseg.mgz --csdpdf GroupAnalysis_abs.glmdir/contrast/permcsd.pdf.dat --csd GroupAnalysis_abs.glmdir/csd/permcsd.j001-contrast.csd --vwsig GroupAnalysis_abs.glmdir/contrast/permcsd.sig.voxel.mgh


 but then I am getting the following error:

NOT Adjusting threshold for 1-tailed test
Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt
INFO: loading mask volume: GroupAnalysis_abs.glmdir/mask.mgh
INFO: MRIbinarize01(): nhits = 961260
Found 961260 voxels in mask
ERROR: Input volume voxel dimensions do not match those
in the registration file. If the input volume is in
bshort/bfloat format, check that there is an accompanying
bhdr file.

Can you please help me to solve this problem. I am not sure what to do.

Thank you very much!
Antonella

PS. Just to remember you that I registered my FA data over the CVS space but I have for each subject from dt_recom the register.dat file so I suppose I need to keeo the fsaverage in the --reg COMMAND-LINE ARGUMENTS.