Gordon Xu who helped us set up the protocol reminded me of the following: "The main benefit of the readout PF is to reduce echo spacing, hence less blurring in the slice direction. The side benefit is that it also reduces the minimum TE, hence less dropout. However, you do give up some SNR at the high spatial frequency as Souheil mentioned. There are two senarios of this, a) the SNR is adequate, you only lose some SNR due to less sampling, b) if the SNR is borderline or worse, in addition to losing SNR you also lose some spatial resolution in the readout direction as the other side of the high spatial frequency k-space is less reliable.
I remember we did pilot acquisition with and without "asymmetric echo" in two subjects. You looked at the images and you either liked the one with asymmetric echo because of less blurring or at least indifferent between the two. So I assume with the Siemens 32ch coil we are in senario a) above." If I had to guess, we probably went with the readout partial fourier to reduce the dropout regions in the gradient echo MPRAGE and didn't see an obvious loss in resolution. Peace, Matt. On 5/13/13 1:03 PM, "Inati, Souheil (NIH/NIMH) [E]" <souheil.in...@nih.gov> wrote: >Hi Matt, > >Thanks for the link. > >Reading on pages 29-31, I am struck by the complexity of the procedure. >Not to say that it doesn't work, or that the single T1w image free-surfer >stuff is simple :-), on the contrary, it's just that I was expecting to >see something about an optimization that used both images, rather than >something based on the T1w image followed by an exclusion criterion based >on the T2w image. Anyway, works better than without. > >Minor question on the acquisition of the anatomicals: >- Why are you using partial fourier in the read direction? You're >throwing away a lot of SNR at the high spatial frequencies, seems a shame >to go to 0.7mm and then do that. > >Cheers, >Souheil > >On May 12, 2013, at 10:54 PM, Matt Glasser <m...@ma-tea.com> wrote: > >> This is available online now: >> >> http://authors.elsevier.com/sd/article/S1053811913005053 >> >> >> On 5/7/13 3:10 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >> >>> actually Matt Glasser points out that a brief description is in his >>>paper >>> that is coming out soon, and there is also some description in Andre's >>> multi-echo mprage paper >>> Bruce >>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] >>> wrote: >>> >>>> thanks :-) >>>> >>>> On May 7, 2013, at 3:28 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>> wrote: >>>> >>>>> no, of course not :) >>>>> >>>>> On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] >>>>> wrote: >>>>> >>>>>> Hi Bruce, >>>>>> >>>>>> Out of curiosity and for reference for my users, do you have a paper >>>>>> on the T2 or FLAIR assisted segmentation? >>>>>> >>>>>> Cheers, >>>>>> Souheil >>>>>> >>>>>> ------------------------- >>>>>> >>>>>> Souheil Inati, PhD >>>>>> Staff Scientist >>>>>> FMRI Facility >>>>>> NIMH/NIH/DHHS >>>>>> souheil.in...@nih.gov<mailto:souheil.in...@nih.gov> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On May 7, 2013, at 2:24 PM, Bruce Fischl >>>>>> <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> >>>>>>wrote: >>>>>> >>>>>> Hi Katie >>>>>> >>>>>> I'm really not sure. These days I would recommend a highres (e.g. >>>>>>1mm >>>>>> isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, >>>>>> but >>>>>> it's pretty noisy in brain. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> On Tue, 7 May 2013, Katie Surrence wrote: >>>>>> >>>>>> Dear Freesurfer gurus, >>>>>> >>>>>> At the course, André van der Kouwe mentioned in his morphometry >>>>>> methods talk that T2* weighted contrast from >>>>>> MEMPRAGE could be used to further seperate dura from cortex, as also >>>>>> discussed in this paper: >>>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408694/. We have a GE >>>>>> scanner in our lab. The internet suggests >>>>>> that a Multi-echo FSPGR/FGRE exists. Would this be the analog? >>>>>> Would it work the same way? Could you also >>>>>> use these images with the mris_make_surfaces command? >>>>>> >>>>>> Thanks very much for your insight -- and I enjoyed the course! >>>>>> >>>>>> /Katie Surrence >>>>>> >>>>>> -- >>>>>> Research Coordinator >>>>>> Social Cognition Laboratory >>>>>> New York State Psychiatric Institute >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> >>>>>>Freesurfer@nmr.mgh.harvard.edu<mailto: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 >>> >>> >>> 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
