Hi Julia, If using High hindbrain with save intermediate volumes turned on gives a better looking Hindbrain.nii segmentation, then you can run segmentation twice: Once with high, and once with low. Use low as your baseline, but subtract the high intermediate volume hindbrain.nii using Volume: Math Ops.
Donna On 07/01/2010 03:40 AM, Julia Bender wrote: > 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
