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*
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