Hi Bruce, Can you get good FLAIRs at 0.7mm isotropic?
The fluid thing makes sense for surface reconstruction, but I think it would mess up myelin maps if someone also wanted to do that using the ratio method. If the CSF is now dark and you divide the dark CSF in the T1w with dark CSF in the T2w, you would get unpredictable results in the partial volume region along the edge. Thanks, Matt. On 11/20/12 6:27 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Satra > >the T1 maps accomplish much of what the ratio does - it gets rid of >receive bias effects. I'm not really sure which is better. They are about >the same amount of scan time. > >The advantage of including the flair inversion pulse in the T2 space is >that it nulls fluid and lets intensities by monotonically decreasing >moving >outwards from the gray/white boundary. This makes partial volume effects >less of a problem. Dura is also pretty much totally absent from the FLAIR >and in the prelim data that we've processed having the FLAIR images lets >the surface recover from pretty much all mistakes in which dura is >included >in the pial surface. > >cheers >Bruce > > > >On Tue, 20 Nov 2012, Matt Glasser wrote: > >> If you make a T1 map you can use that to look at differences in myelin >> content, but I don't know all of the ways to calculate T1 or if you >>could >> get that from only two flip angles. Two images with roughly the same >> contrast won't work for the ratio method. You need to have opposite >> contrast. >> >> Also I'm not sure how a FLAIR would be better than a T2-SPACE. >> >> Peace, >> >> Matt. >> >> From: Satrajit Ghosh <sa...@mit.edu> >> Date: Tuesday, November 20, 2012 5:51 PM >> To: Matt Glasser <m...@ma-tea.com> >> Cc: "Watson, Christopher" <christopher.wat...@childrens.harvard.edu>, >> "Winter, Warren" <warren.win...@childrens.harvard.edu>, >> "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial >> surface recons? >> >> hi >> matt: could you generate the myelin maps say from two flash scans at >> different flip angles? >> bruce: if one had a choice between an mprage + t2 flair and 2 flash >>scans at >> 5/20 flip angles, what would be your recommendation? >> >> cheers, >> >> satra >> >> On Tue, Nov 20, 2012 at 6:35 PM, Matt Glasser <m...@ma-tea.com> wrote: >> If you get an MPRAGE and T2-SPACE you can make myelin maps too. >> FreeSurfer's final surface placement benefits a lot from high >> resolution >> images (less than 1mm) and you can still get good SNR with when >> you use >> 32-channel coils. >> >> Peace, >> >> Matt. >> >> On 11/20/12 4:41 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> >> wrote: >> >> >Yes, definitely. The t2-space flair is a big help >> > >> > >> > >> >On Nov 20, 2012, at 5:40 PM, "Watson, Christopher" >> ><christopher.wat...@childrens.harvard.edu> wrote: >> > >> >> Hi Bruce, >> >> So would you recommend acquiring a T2 in addition to an >> >>(ME)MPRAGE/SPGR? i.e. is it worth squeezing another >> acquisition into a >> >>protocol? >> >> >> >> Chris >> >> ________________________________________ >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> >>[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce >> Fischl >> >>[fis...@nmr.mgh.harvard.edu] >> >> Sent: Tuesday, November 20, 2012 3:01 PM >> >> To: Winter, Warren >> >> Cc: freesurfer@nmr.mgh.harvard.edu >> >> Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE >> data in pial >> >>surface recons? >> >> >> >> Hi Warren >> >> >> >> yes, it will be part of the upcoming 5.2 release, hopefully >> in Dec. It >> >> will use either a FLAIR or T2 (ideally T2-SPACE for either >> one) >> >> >> >> cheers >> >> Bruce >> >> On Tue, 20 >> >> Nov 2012, Winter, Warren wrote: >> >> >> >>> Hi all, >> >>> >> >>> Back in January and October Bruce mentioned that he had >> under >> >>>development some scripts designed to utilize T2-SPACE images >> for better >> >>>pial surface reconstruction in the presence of dura -- I was >> just >> >>>wondering if any of that is ready for trial? >> >>> >> >>> Thanks! >> >>> >> >>> Warren >> >>> >> >>> -- >> >>> Warren Winter >> >>> Research Coordinator >> >>> Boston Children's Hospital >> >>> Sheridan Laboratory of Cognitive Neuroscience >> >>> Division of Developmental Medicine >> >>> 1 Autumn Street, AU 650 >> >>> Boston, MA 02215 >> >>> 857-218-5224 >> >>> >> >>> >> >>> _______________________________________________ >> >>> Freesurfer mailing list >> >>> Freesurfer@nmr.mgh.harvard.edu >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>> >> >>> >> >>> >> >> _______________________________________________ >> >> Freesurfer mailing list >> >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> >> 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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
