You might try the low threshold hindbrain removal, but don't get your hopes too high.
How much did you shift the GMpeak? This is definitely what I would have tried, and if that failed, I'd try lowering the WMpeak (leaving the GMpeak constant). > Thank you, Donna! > > I have uploaded a bias-corrected version named > "freckles_bias_corrected.zip" (using BrainSuite's BFC algorithm). After > adjusting the peaks, the segmentation runs through, but the > posteriormost parts of the cortex are always missing. I have tried a > manual correction of the segmentation volume, but, while I am able to > remove unwanted parts from the fiducial surface, I am apparently unable > to add missing parts. Is this possible? If so, is there a special step > involved other than selecting "Segmentation Volume Post Processing" and > the manually corrected segmentation volume? > > In case it is not possible to add missing parts using a manual > correction of the segmentation volume, is there anything else I can do? > Shifting the grey matter peak in the appropriate direction for including > the missing voxels makes the segmentation process fail. > > Best, > > Jochen > > On 4/5/2010 8:12 AM, Donna Dierker wrote: >> Hi Jochen, >> >> I think your biggest problem was that your peaks were set too low. >> >> The MRI quality is not the best, and perhaps some nonuniformity >> correction (e.g., FSL's fast) might improve your result further. But >> your GM peak was set way too low. You histogram is somewhat misleading >> (capture attached). If you set it at the peaks, the way you did, the >> GMpeak will be way too low. See >> http://brainvis.wustl.edu/help/peak_tweaking for more help on peaks. >> >> Try GMpeak=190, WMpeak=230 and see how you do. My results looked >> reasonable (reasonable.jpg). In my case, though, the graph error >> correction method cut off a lateral slab. Turning it off should restore >> sanity (if not a few pesky handles). >> >> There were two issues with stereotactical_coord_AC_R.hdr: >> >> * The name suggests right hem, but the hem appeared to be a left hem >> (left-right flipped?). >> >> * It was not centered near the AC, so the origin would need to be re-set >> before you could hope to get any decent segmentation. >> >> Donna >> >> On 04/02/2010 01:20 PM, Jochen Ditterich wrote: >>> Hi Donna and John, >>> >>> I am trying to segment a macaque brain and to flatten the cortex, but >>> I haven't been able to make it through the segmentation process >>> without error messages. I am not sure whether this is due to quality >>> issues with the MRI or whether it has something to do with the >>> implanted recording chambers. I have uploaded a file named >>> "freckles.zip" that contains both the uncropped volume as well as the >>> cropped volumes for the two hemispheres. Any feedback would be >>> appreciated. Does anybody have experience segmenting MRIs taken from >>> animals with implants? >>> >>> Thanks a lot, >>> >>> Jochen >>> >>> ------------------------- >>> >>> Jochen Ditterich, Ph.D. >>> Assistant Professor >>> Center for Neuroscience >>> University of California >>> 1544 Newton Court >>> Davis, CA 95618 >>> USA >>> >>> office: +1 (530) 754-5084 >>> lab: +1 (530) 754-6987 >>> fax: +1 (530) 757-8827 >>> _______________________________________________ >>> 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 > > -- > > ------------------------- > > Jochen Ditterich, Ph.D. > Assistant Professor > Center for Neuroscience > University of California > 1544 Newton Court > Davis, CA 95618 > USA > > office: +1 (530) 754-5084 > lab: +1 (530) 754-6987 > fax: +1 (530) 757-8827 > _______________________________________________ > 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
