<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:12pt"><div class="" style="direction: ltr; unicode-bidi: embed;">Hi,</div><div class="" style="direction: ltr; unicode-bidi: embed;">I
have a few questions about creating connectivity matrix with Camino and Freesurfer
labels.</div><div class="" style="direction: ltr; unicode-bidi: embed;"><o:p class="" style=""> </o:p></div><div class="" style="direction: ltr; unicode-bidi: embed;">First,
I followed the tutorial instructions to create fa.nii and md.nii files.</div><div class="" style="direction: ltr; unicode-bidi: embed;">I
checked these files using SPM8 display command. The images didn't seem to be
aligned, also I got different "Origin" and "Dir Cos" values
for the images and a warning : "shears involved" message (This
problem doesn’t occur using the tutorial data).</div><div class="" style="direction: ltr; unicode-bidi: embed;"><o:p class="" style=""> </o:p></div><div class="" style="direction: ltr; unicode-bidi: embed;">Second,
I used Freesurfer for labeling different volumes and SPM to register the labels
file "aprac+aseg.nii" using "orig.nii" (the structural
file) as source and the B0 data as reference.</div><div class="" style="direction: ltr; unicode-bidi: embed;">I
viewed some of the streamlines created by Camino (following the tutorial using dtfit) and volumes
from the registered image of labels with Paraview. It seems that there is a registration problem
since the streamlines appear shifted from the place they should be. </div><div class="" style="direction: ltr; unicode-bidi: embed;">Thanks
a lot,</div><div class="" style="">
</div><div class="" style="direction: ltr; unicode-bidi: embed;"> Oren</div><div class="" style=""><br class="" style=""></div></div></body></html>