There's also the flag -mprage which can be used, intended for the mprage developed by Andre van de Kouwe, which I believe is the same as that now used by Siemens.
Nick On Wed, 2009-08-26 at 09:37 -0500, Michael Harms wrote: > No, our current "CAP" MPRAGE at WU on the 3T TimTrio is very similar to > the "ADNI" mprage, so that old flag shouldn't be used. > > -MH > > On Wed, 2009-08-26 at 09:24 -0500, Alexander Li Cohen wrote: > > Ah I see, > > this raises a question then, of whether the optimizations are still > > applicable to WU acquired MP-RAGE data, as we are currently collecting > > 3T Trio data, and I believe Randy's data is 1.5T Vision data, however > > the sequence (our CAP MP-RAGE) is quite similar... can anyone up there > > speak to this? > > > > -Alex > > ~)------------- > > > > ---------------------------------------------------------------------- > > Alexander Li Cohen > > al...@npg.wustl.edu (WORK Email) > > alexco...@gmail.com (Non-secure / rapid-response Email) > > Petersen/Schlaggar Lab > > Medical Scientist Training Program > > Washington University in St. Louis School of Medicine > > ---------------------------------------------------------------------- > > > > This message is intended only for the exclusive use of the intended > > recipient(s) named herein and may contain information that is > > PRIVILEGED and/or > > CONFIDENTIAL. If you are not the intended recipient, you are hereby > > notified > > that any use, dissemination, disclosure or copying of this > > communication is > > strictly prohibited. If you have received this communication in > > error, please > > destroy all copies of this message and its attachments and notify us > > immediately. > > > > The materials in this message are private and may contain Protected > > Healthcare Information or other information of a sensitive nature. If > > you are not the intended recipient, be advised that any unauthorized > > use, disclosure, copying or the taking of any action in reliance on > > the contents of this information is strictly prohibited. If you have > > received this email in error, please immediately notify the sender via > > telephone or return mail. > > > > On Aug 26, 2009, at 8:41 AM, Bruce Fischl wrote: > > > > > yes, it was optimized for the mp-rages that Randy B used to collect > > > there, not for example ADNI. > > > On Tue, 25 Aug 2009, Michael Harms wrote: > > > > > >> > > >> I assume that that flag (-washu_mprage) is somewhat antiquated, > > >> right? > > >> That is, it was included for an older set of scans (generated at > > >> WashU > > >> generated years ago before Siemens had its own MPRAGE sequence) that > > >> happened to have darker gray matter, and doesn't need to be applied > > >> for > > >> "modern" MPRAGE scans, correct? > > >> > > >> -MH > > >> > > >> On Tue, 2009-08-25 at 13:33 -0400, Nick Schmansky wrote: > > >>> Alex, > > >>> > > >>> The -washu_mprage flag affects mri_normalize and mri_segment. It > > >>> adjusts the parameters of those binaries to match the assumed > > >>> intensity > > >>> profile in mprage scans, eg. to account for darker grey matter. I've > > >>> updated the help text in recon-all. > > >>> > > >>> Nick > > >>> > > >>> > > >>>> As a side note, there appears to be a switch for recon-all: > > >>>> -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol > > >>>> yet there is no documentation as to what this determines, nor > > >>>> whether > > >>>> the raw, or locally atlas-aligned data should be provided. (Avi > > >>>> didn't > > >>>> know either...) > > >>>> > > >>>> Many Thanks! > > >>>> > > >>>> -Alex Li Cohen > > >>>> ~)----------------- > > >>>> > > >>>> ---------------------------------------------------------------------- > > >>>> Alexander Li Cohen > > >>>> al...@npg.wustl.edu (WORK Email) > > >>>> alexco...@gmail.com (Non-secure / rapid-response Email) > > >>>> Petersen/Schlaggar Lab > > >>>> Medical Scientist Training Program > > >>>> Washington University in St. Louis School of Medicine > > >>>> ---------------------------------------------------------------------- > > >>>> > > >>>> This message is intended only for the exclusive use of the intended > > >>>> recipient(s) named herein and may contain information that is > > >>>> PRIVILEGED and/or > > >>>> CONFIDENTIAL. If you are not the intended recipient, you are > > >>>> hereby > > >>>> notified > > >>>> that any use, dissemination, disclosure or copying of this > > >>>> communication is > > >>>> strictly prohibited. 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