Hi Anastasia, I saved out some of the completed trac-all.cmds following each TRACULA 'step', and I see where aparc+aseg is mapped to diffusion space. Thank you again for all your help - my project is starting to look a lot better!
Sincerely, Susie Kuo NIH On Wed, Mar 27, 2013 at 12:02 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Actually the brain mask used on the diffusion data *is* the aparc+aseg > mapped to diffusion space, so the reason you see that extra non-brain stuff > in the FA map is because the aparc+aseg was not aligned well to it. > > So you just need to switch on bbregister and switch off flirt in your > configuration file, and then rerun trac-all. If the DWI-to-T1 registration > is good, then the masking issue will be solved too. > > Good luck! > > a.y > > On Wed, 27 Mar 2013, Susan Kuo wrote: > > Hi Anastasia, Thank you! I can see that the aparc+aseg spilled over >> badly. I am >> going to try bbregister, and then re-betting (Brain Extraction Tool-ing) >> the original >> image, since the dtifit_FA looks to include non-brain near the frontal >> lobe. I'll keep >> you and the FS community updated on the results, in case anybody is >> curious. >> >> >> Sincerely, >> Susie Kuo >> NIH >> >> >> On Wed, Mar 27, 2013 at 10:41 AM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> >> wrote: >> >> Hi Susie - The -tv (tract volume) option of freeview is designed >> specifically to display the merged*.mgz output files of tracula. >> For a >> regular volume, use -v or no option at all. For best displaying the >> aparc+aseg, select it in freeview and choose "Lookup Table" from >> the Color >> map menu. >> >> Hope this helps, >> a.y >> >> On Wed, 27 Mar 2013, Susan Kuo wrote: >> >> 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 >> >> >> >> >> -- >> 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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