Hi Doug,
Sorry I forgot to ask one more question: after I am getting my clusters for my FA group study should I use the fsaverage (which is not on the CVS space) or the concatenated file GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz (registered over the CVS space) or I should use the CVS space to visualize my results, I mean should I use:
tkmedit fsaverage orig.mgz \ -ov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh \ -seg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.anat.mgh \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th3.pos.sig.ocn.lut \ -fminmax 1.3 5
or
freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/Group_Analysis.glmdir/contrast/grf.th3.pos.sig.cluster.mgh:colormap=heat
Also do I need to use the average value GroupAnalysis.Average-fa-masked.ANAT+CVS-to-avg35.mgz when I run the mri_glmfit or just the concatenated file GroupAnalysis-fa-masked.ANAT+CVS-to-avg35.mgz?
THANKS SO MUCH! Antonella