Hi Anastasia, I'm attaching the graphic I arrived at with the command: > freeview -tv <subjectID>/dlabel/diff/aparc+aseg.flt.nii.gz -v <subjectID>/dmri/dtifit_FA.nii.gz
Here, I used the subject I send you (Sa69845.5) for the subjectID. I could not detect spill over in these images, mostly because the frontal lobe is a little cut off. Did you perhaps use a different viewer? I'm hoping to be able to detect these mis-registrations better for myself in the future. Thanks for all your help! Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 1:32 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Susie - Everything under dlabel/diff is mapped to DWI space (either > with flirt or with bbregister, whichever you use). The one in my screenshot > was dlabel/diff/aparc+aseg.flt.**nii.gz. > > a.y > > > On Wed, 27 Mar 2013, Susan Kuo wrote: > > 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 >> >> -- 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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