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.
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