John, This morning, I pinpointed the culprit. As expected, the output format is irrelevant. Ventricle filling is irrelevant (but notoriously less reliable on monkeys -- especially ones whose heads are tilted a tad chin up).
The real keys were peaks and using the hindbrain low threshold option. Just getting the peaks right wasn't enough; some stubborn hindbrain caused the high thresh hindbrain removal to threshold most of the white matter out of the segmentation. You'll need to edit out the cerebellum, unfortunately. Try running your hemisphere with these peaks and settings: * GMpeak=84; WMpeak=104 * eye disconnect off * hindbrain low threshold A capture of the result is attached. Donna On 06/05/2007 04:31 PM, Donna Dierker wrote:
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 offNormally, 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, JohnHi John, I think I've seen something like this once before, when the spec filethought 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 thesize of the normal fiducial surface. This doesn't seem to be related tothe image intensity because gray matter segements very well at 76(thevalue 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 .35mminstead 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 deselectthis 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'tseem to get anything other then this bad segmentation except for an errorabout in ability to find big mask. Any possible suggestions indicativeof these problems? Thanks for your help, John_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users_______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
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