Hi Anastasia, Thanks so much for your quick reply. As far as I can tell the masks seem fine. There was a small amount of erosion around the edge of the brain when the recon mask was used. However, the end points of the tract were still within the mask. Just in case I reran trac-all with the 'usemaskanat = 0' setting and a more generous bet threshold. Even with these changes I still saw the problem with the bbregister version of a tract. Is there anything else I should check/change?
Thanks again, -Tyler On Nov 30, 2011, at 4:00 PM, Anastasia Yendiki wrote: > > Hi Tyler - Sometimes this happens if the brain mask (which will come either > from the FS recon or from the DWIs themselves, depending on your settings) is > missing part of that tract (usually one of the end region). Have you checked > your brain masks? > > a.y > > On Wed, 30 Nov 2011, Tyler Blazey wrote: > >> Hi List, >> >> I recently ran a group of around 70 subjects through trac-all. I have >> started to check the results, and have noticed that Tracula will often >> produce a tract with a really small volume and a posterior distribution that >> consists of just 0s and 1000s. When this occurs, the end point images >> usually contain only one voxel greater than 0. I am not sure what, if >> anything, is going wrong. The original recons are all of good quality, and >> the registrations to MNI space look good (the end point images look fine in >> MNI space as well). I also noticed this same issue in the right SLFP >> (bbregister version) of the Tracula tutorial subject. >> >> Is this a fixable error, or is it actually expected behavior? Thanks for any >> help. >> >> - Tyler >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
