[caret-users] Caret Segmentation

Donna Dierker donna at brainvis.wustl.edu
Tue Jun 5 14:45:15 CDT 2007

Hi John,

I think I've seen something like this once before, when the spec file 
thought it was a right hem, but it was really a left hem (or vice versa).

Once you rule out that possibility, then zip up your directory, 
including cropped hem, params, and any other files you think may help 
and upload the zip file here:


I'll have a look.


On 06/05/2007 12:06 PM, John Arsenault wrote:
> Hello,
>   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,
>                                                               John

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