Hi Skyler - When you say it's been working fine, have you checked that the orientations are correct by viewing dtifit_V1.nii.gz and dtifit_FA.nii.gz, like in the snapshot that I sent you? If those orientations aren't correct, the gradient table isn't correct either.
a.y On Tue, 21 May 2013, Skyler Gabriel Shollenbarger wrote: > Hi Anastasia, > > Thank you for all of your help! 'trac-all' has been working fine with > the other subjects, so it doesn't appear to be the gradient vector file. > Yes, unfortunately the resolution is not the best. > > Would you consider this subject a loss or are there other fixes you suggest? > > Thanks again! > Skyler > > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: sholl...@uwm.edu > Cc: freesurfer@nmr.mgh.harvard.edu > Sent: Tuesday, May 21, 2013 10:40:59 AM > Subject: Re: [Freesurfer] tracula error > > > Hi Skyler - A couple of things. I'm attaching a screenshot of the FA map > and primary tensor eigenvectors of your subject. First, it looks like your > gradient directions are incorrect, given how the eigenvectors are oriented > in the corpus callosum (yellow arrows in the coronal and axial slice). The > eigenvectors follow the shape of the corpus callosum in the axial view but > not in the coronal view. My guess is your gradient vectors need to be > flipped in the z-direction. > > Second, your resolution is 4mm. There's going to be a lot of partial > voluming. You'll have to give up on the thinner tracts, like ccg/cab (see > purple arrow in sagittal view pointing to cingulum, you can barely resolve > it from the corpus callosum). > > Third, you have 14 gradient directions, so fitting the ball-and-stick > model to this data, which is done by bedpostx and which you need for the > tract reconstruction step, is going to be challening. > > I don't want to discourage you, but tractography may be a bit more than > this data can support. > > Please let me know if you have more questions, > a.y > > On Mon, 20 May 2013, sholl...@uwm.edu wrote: > >> Hi Anastasia, >> >> They were uploaded. Thanks for your help! >> >> Skyler >> >> Sent from my iPhone >> >> On May 20, 2013, at 10:20 AM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Skyler - If you upload the dmri/dmri.bedpostX/dlabel/scripts directories >>> of your subject for me, I'll take a look. >>> >>> http://gate.nmr.mgh.harvard.edu/filedrop2/ >>> >>> a.y >>> >>> On Fri, 17 May 2013, sholl...@uwm.edu wrote: >>> >>>> Hi Anastasia, >>>> >>>> The brain mask looks fine. Any other suggestions? >>>> >>>> Thanks for your help, >>>> Skyler >>>> Sent from my iPhone >>>> >>>> On May 17, 2013, at 12:24 PM, Anastasia Yendiki >>>> <ayend...@nmr.mgh.harvard.edu> wrote: >>>> >>>>> >>>>> Hi Skyler - How does the brain mask look like? Any major chunks of brain >>>>> missing in the area of the left uncinate? That's the tract where the >>>>> error occurs, and based on this info in the log file, I'm guessing it's a >>>>> masking issue: >>>>> >>>>> [...] >>>>> INFO: Rejected 4221 streamlines for straying off mask >>>>> INFO: Rejected 2 streamlines for reversing direction >>>>> INFO: Rejected 9 streamlines as length outliers >>>>> INFO: Have 56 total streamlines (min/mean/max length: 1/13/33) >>>>> [...] >>>>> >>>>> Hope this helps, >>>>> a.y >>>>> >>>>> On Wed, 15 May 2013, Skyler Gabriel Shollenbarger wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> We ran tracula prep stage and it exited with errors: 'Selected >>>>>> streamline has fewer than 5 points'. We have attached the log and error >>>>>> files if needed. >>>>>> >>>>>> Thank you in advance! >>>>>> Skyler >>>>> >>>>> >>>>> 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
