Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay?
I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Susie - I'm attaching a snapshot from your subject, showing the > aparc+aseg overlaid on the FA map. The registration has failed. The frontal > lobe has spilled out of the brain, the white matter has spilled into the > ventricles. > > I strongly recommend using bbregister for the intra-subject registration, > which is the default in the latest version of trac-all. > > Hope this helps, > a.y > > > On Tue, 26 Mar 2013, Susan Kuo wrote: > > Hi Anastasia, I did as you recommended and checked the >> diffusion-to-anatomical >> registration, and the overlay of aparc+aseg_mask on FA, and these views >> seem to be >> good. Upon closer inspection, what I find is that there are incipient >> 'bits' of all >> the tracts, but they seem to not have 'grown', though they are in the >> proper space >> (comparing them to good brains that yielded the full complement of >> tracts). Is there a >> configuration in your TRACULA that controls the growing of the tracts >> specifically? >> Perhaps I should look into that. >> >> Thank you, btw, for your very prompt reply yesterday- it was much >> appreciated! >> >> >> Sincerely, >> Susie Kuo >> NIH >> >> On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> >> wrote: >> >> Hi Susan - Good to hear that you get good results for most of your >> subjects. Have you checked the aparc+aseg and the >> diffusion-to-anatomical >> registration for the subjects that are failing? I'd check the >> aparc+aseg_mask (in the dlabel/diff directory) over the FA map to >> see if >> there are any holes or misregistration. >> >> a.y >> >> On Mon, 25 Mar 2013, Susan Kuo wrote: >> >> Hi FreeSurfers and Anastasia, TRACULA is working great for >> me, generating tracts for a sample of 20 subject >> brains I'm working with. However, for 3 of the brains, I'm >> receiving incomplete and poorly formed tracts. >> I've re-run trac-all at least 2x on each subject in case there >> was a mistake in my original configuration. >> However, I am reproducing the same results. Does anybody have >> an idea why I would see these "spotty" tracts? >> >> >> Thank you for all your help! >> >> -- >> Susie Kuo >> NIH >> >> >> >> >> 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<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. >> >> >> >> >> -- >> Susie Kuo >> >> Mediocrity knows nothing higher than itself, but talent instantly >> recognizes genius. - >> Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear >> >> -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear*
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