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
