Dear all:

I am doing an FA group study (controls vs. patients without any covariant so my C = +1.00000 -1.00000) and I want to see if there are any clusters that survives by multiple comparison so I ran:

mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\
      --fsgd DTI_group_analysis.fsgd --C contrast.mtx --glmdir group_analysis.glmdir


and then:

 mri_glmfit-sim \
 --glmdir group_analysis.glmdir \
 --grf 2 neg \
--cwpvalthresh .025 \
 --overwrite

One of the output files is group_analysis.glmdir /contrast/sig.mgh which by my understanding is the significant uncorrected map which I can visualize it using freeview:

freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \
           /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat

The significant and corrected map containing the surviving clusters by multiple comparison should be the grf.th2.neg.sig.cluster.mgh   file but unfortunately when I try to visualize this clusters with Freeview I cannot see anything.

Can you please give me an advise on how I can see this clusters over the group-fa-tal.nii?

This is what I was trying and the only thing I can see is a white mask:


freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \
           /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th2.neg.sig.cluster.mgh:colormap=heat

Am I doing something wrong?


Thank you for your time and help.

Antonella