Anastasia, Rerunning with the reinit = 1 option worked great. One last question. If I want to compare tracts across subjects, should I rerun every subject with the reinitialization, or is it ok to only rerun the subjects/tracts that need it? Thanks for all you help.
-Tyler > > Thanks, Tyler. It looks like the initial pathway is problematic in that it > goes off the white matter (look at the "Reject due to" lines in the log > for exact voxel coords where this happens). > > This could mean that the subject is not well aligned to the atlas in that > area, or that you just got unlucky. If it's the latter, you can try "set > reinit = 1" in your dmrirc and rerun that pathway and see if you get a > better result with the new initialiation. > > Let me know if this makes sense. > > a.y > > On Thu, 1 Dec 2011, bla...@artsci.wustl.edu wrote: > >> Hi Anastasia, >> >> Attached is the log.txt produced by dmri_paths for the failed tract. I >> also have included the output of the terminal command in case that >> helps. >> Thanks again for all of your help. >> >> - Tyler >> >> >>> >>> Hi Tyler - In general this means that for some reason the pathway >>> doesn't >>> move at all from the location where it's initialized when the algorithm >>> is >>> run. There are a few different reasons why that'd happen, the mask >>> being >>> only one of them. >>> >>> If you could find the dmri_paths command line in trac-all.log, add >>> "--debug" to it and run it again and send the log file, I can try to >>> track >>> down what's going on. The command line will probably contain all the >>> tracts, but you can run it only for one that fails. >>> >>> Thanks, >>> a.y >>> >>> On Wed, 30 Nov 2011, Tyler Blazey wrote: >>> >>>> 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 >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
