[caret-users] Caret Segmentation

John Arsenault johna at nmr.mgh.harvard.edu
Tue Jun 5 12:06:56 CDT 2007

  I am attempting to segment a macaque left hemisphere to create surfaces
for data representation using caret.  I am using a very nice .35mm
isotropic anatomical with intensity normalization but for some reason the
resultant segmentation of surefit is a small blob of medial frontal white
matter that really has no anatomical correlate and is about 1/4 of the
size of the normal fiducial surface.  This doesn't seem to be related to
the image intensity because gray matter segements very well at 76(the
value prescribed by surefit) and white matter as well segments very well
at 100.  Also it doesn't seem to be the fact that the image is of .35mm
instead of the 1mm suggested since I was able to nicely segment the right
hemisphere.  Another possible problem is the fact that the image has been
skull stripped and the eyes have been disconnected but even if I deselect
this option in surefit I get no difference. I have tried various changes
to the surefit process to get the image to segment properly and I can't
seem to get anything other then this bad segmentation except for an error
about in ability to find big mask.  Any possible suggestions indicative of
these problems?  Thanks for your help,

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