[caret-users] Caret Segmentation

John Arsenault johna at nmr.mgh.harvard.edu
Tue Jun 5 15:14:10 CDT 2007


Hi Donna,
  Thanks so much for taking a look.  I checked it out and it doesn't
appear to think it is mistakingly the right hemisphere but maybe that is
hidden to me. I uploaded it as chip_leftHem.zip.  Thanks so much for
checking this out,
      John


> 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:
>
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> I'll have a look.
>
> Donna
>
> 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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