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.Watson@childrens.**harvard.edu<christopher.wat...@childrens.harvard.edu> >>>> >, >>>> "Winter, Warren" >>>> <Warren.Winter@childrens.**harvard.edu<warren.win...@childrens.harvard.edu> >>>> >, >>>> "freesur...@nmr.mgh.harvard.**edu <freesurfer@nmr.mgh.harvard.edu>" < >>>> freesur...@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.Watson@**childrens.harvard.edu<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> >>>> >>>> >>[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<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<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<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 >>>> >freesur...@nmr.mgh.harvard.**edu <Freesurfer@nmr.mgh.harvard.edu> >>>> >>>> >https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> >>>> >>>> >> >> >> >>
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