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 Red for Class1 (=controls)< Class2 (=Patients) and BLue for Class1>Class2 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.