You can correct the readout distortion with a field map. The main residual is just signal loss in the gradient echo image.
Peace, Matt. On 11/20/12 7:22 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >sure. Note that whichever you do it's absolutely critical to bandwidth >and readout match them so there is no differential distortion between the >contrast types >Bruce >On Tue, 20 Nov 2012, Satrajit Ghosh wrote: > >> thanks matt and bruce. this is very helpful. >> cheers, >> >> satra >> >> On Tue, Nov 20, 2012 at 7:53 PM, Bruce Fischl >><fis...@nmr.mgh.harvard.edu> >> wrote: >> yes, that's probably true. The FLAIR we use is just a T2-SPACE >> scan with an inversion pulse to put CSF at the null point, so if >> you can get T2-space at .7 you should be able to get FLAIR >> (although you do burn some SNR with the inversion) >> >> On Tue, 20 Nov 2012, Matt Glasser wrote: >> >> 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 >> . 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