yes, that's true. The difference is between the SPGR and the MP-RAGE. If we don't know which it is we have to try to figure out the contrast and noise characteristics (spgr has worse contrast and less noise)
On Wed, 26 Aug 2009, Michael Harms wrote: > > Ok, now I'm confused again, because my understanding is that the Andre > van de Kouwe mprage, Siemen's default mprage, and the ADNI mprage really > are not very different in terms of their contrast. Is that not correct? > > Assuming they are indeed all similar, are you saying that a modern > "ADNI-like" mprage benefits from the inclusion of this -mprage flag? > > thanks, > Mike H. > > > On Wed, 2009-08-26 at 12:18 -0400, Nick Schmansky wrote: >> 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. 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. 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