Dear Doug,

Can I run the mri_volcluter without --reg ?

I am asking this because when I run:

mri_glmfit-sim \
    --glmdir GroupAnalysis_ADC.glmdir \
    --grf 3 neg \
    --cwpvalthresh .05 \
    --overwrite

gives me the following error (I also attached the log file):

Also, does neg means now that Class1 (=controls)< Class2 (=Patients) for my MD values?

Many thanks.

Antonella

$Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $
Tue Feb 14 14:28:11 EST 2012
Linux EW-LNX3 2.6.32.26-175.fc12.x86_64 #1 SMP Wed Dec 1 21:39:34 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
elysa
setenv SUBJECTS_DIR /media/2Tra/Antonella_2011/DTI_FS/GLM_CVS
FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y GroupAnalysis-ADC-MASKED.ANAT+CVS-to-avg35.mgz --fsgd GroupAnalysis.fsgd dods --C contrast.mtx --glmdir GroupAnalysis_ADC.glmdir

DoSim = 0
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 2.252995
mri_volcluster --in GroupAnalysis_ADC.glmdir/contrast/sig.mgh --mask GroupAnalysis_ADC.glmdir/mask.mgh --reg /usr/local/freesurfer/subjects/fsaverage/mri.2mm/reg.2mm.dat --no-fixmni --cwsig GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.cluster.mgh --sum GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.cluster.summary --ocn GroupAnalysis_ADC.glmdir/contrast/grf.th3.neg.sig.ocn.mgh --cwpvalthresh .05 --seg fsaverage aparc+aseg.mgz --fwhmdat GroupAnalysis_ADC.glmdir/fwhm.dat --sign neg --thmin 3
Adjusting threshold for 1-tailed test.
If the input is not a -log10(p) volume, re-run with --no-adjust.
Using defalt ctab /usr/local/freesurfer/FreeSurferColorLUT.txt
INFO: loading mask volume: GroupAnalysis_ADC.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.