Hi John,
No trouble at all replicating the problem. I got the same little blob
near the midline.
Your peaks were way off, so I cranked them up -- around 80 on the GM,
100 on the WM. These can probably be tweaked more optimally. But my
first try still gave the bad result, so I'm not sure it wasn't really
one of the other variables I changed:
* output format to AFNI
* eye disconnect off
* hindbrain low threshold
* ventricles and everything below basic segmentation off
Normally, I change one variable at a time, but I'm headed home in five
minutes.
My first try at cranking up the peaks (80 and 95, I think) still gave
the bad result. Debug showed it was failing somewhere between eye fat
disconnection and hindbrain removal. The above combo with peaks 80,100
looks like it will give a decent result, albeit with some tedious
cerebellum to remove. This is the drawback of the low thresh hindbrain
removal: Less thresholding out of cortex you want, but more
thresholding in of hindbrain you don't want. The segmentation is still
running, but looks more promising.
Donna
On 06/05/2007 03:14 PM, John Arsenault wrote:
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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