Hi Donna, Putting the threshold to low did it. There were large artefacts in both cerebellums as you expected.
Thanks for your help. Julia > Hi Julia, > > The volumes were named identically, so the second overwrote the first. > > I ran the second one, and saw the problem you described. Then I ran it > again turning off eye and skull, error correction, etc. BUT, also > changing hindbrain to LOW hindbrain. I got the result in the attached > capture. > > The problem there is that much of the cerebellum is still hanging on, so > it has to be edited out. > > There is a way to run it both ways -- low and high hindbrain -- and save > the hindbrain segmentation from the high version and use it to patch > edit out the hindbrain from the low. I'd have to dig out those > instructions. But I think it is what looks like cerebellar lesions or > something that is causing the hindbrain to misbehave in this case. > > Perhaps your other case has similar issues. Try the low hindbrain > option and see what happens. > > Donna > > On 06/29/2010 10:30 AM, Julia Bender wrote: >> Hi Donna, >> >> I've uploaded both volumes. >> Thanks for you help! >> >> Julia >> >>> I could speculate, but having a look at your volumes will be much more >>> fruitful. Please upload them here: >>> >>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi >>> >>> On 06/29/2010 05:48 AM, Julia Bender wrote: >>> >>>> Hi, >>>> >>>> I have a problem segmenting 2 hemispheres. Although gray and white >>>> matter >>>> peaks seem to distinguish everything nicely before I run segmentation, >>>> a >>>> substantial part of the cortex is cut off during segmentation. I've >>>> tried >>>> unchecking the Automatic error correction step and also changeing it >>>> to >>>> just SureFit. Neither of those steps changed the results. I've also >>>> played >>>> around with gray and white matter peaks but that also didn't improve >>>> the >>>> output much. Do you have any suggestions what else could be going >>>> wrong? >>>> I'm having trouble with two left hemispheres. The right hemispheres of >>>> the >>>> same subjects went through without a problem. >>>> >>>> Thanks for your help! >>>> >>>> Julia >>>> >>>> Dipl. Psych. Julia Bender >>>> Humboldt Universität zu Berlin >>>> Mathematisch - Naturwissenschaftliche Fakultät II >>>> Institut für Psychologie, Abt. Klinische Psychologie >>>> Unter den Linden 6 >>>> D-10099 Berlin >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >> >> >> Dipl. Psych. Julia Bender >> Humboldt Universität zu Berlin >> Mathematisch - Naturwissenschaftliche Fakultät II >> Institut für Psychologie, Abt. Klinische Psychologie >> Unter den Linden 6 >> D-10099 Berlin >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > Dipl. Psych. Julia Bender Humboldt Universität zu Berlin Mathematisch - Naturwissenschaftliche Fakultät II Institut für Psychologie, Abt. Klinische Psychologie Unter den Linden 6 D-10099 Berlin _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
