Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?

-- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu On 11/20/12 8:11 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: >Hi Matt >I doubt you could accurately correct the 0.25mm distortions that would be >widespread, not to mention the extra interpolation. Much better to >distortion match the acquisitions >Bruce > > > >On Nov 20, 2012, at 8:45 PM, Matt Glasser matt@ma-tea.com wrote: > >> 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" fischl@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 >>>> fischl@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" >>>> fischl@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 >>>> satra@mit.edu >>>> Date: Tuesday, November 20, >>>> 2012 5:51 PM >>>> To: Matt Glasser >>>> matt@ma-tea.com >>>> Cc: "Watson, Christopher" >>>> Christopher.Watson@childrens.harvard.edu, >>>> "Winter, Warren" >>>> Warren.Winter@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 >>>> matt@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" >>>> fischl@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 >>>> 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-bounces@nmr.mgh.harvard.edu >>>> >>>>>> [freesurfer-bounces@nmr.mgh.harvard.edu] >>>> on behalf of Bruce >>>> Fischl >>>> >>>>>> [fischl@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. 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