yes, I think it will probably help a bit for mprage scans. Essentially it changes the default assumptions about noise and contrast characteristics (it assumes more of both) and will help the intensity normalization get a bit further out the thin white matter strands. Try it and see what you think
On Thu, 27 Aug 2009, Michael Harms wrote: > > Is there any gain/benefit then by including this -mprage flag? In what > circumstance is that flag to be used? > I'm still confused what the purpose of that flag is. > > thanks, > Mike H. > > On Thu, 2009-08-27 at 08:54 -0400, Bruce Fischl wrote: >> no, it's more agnostic. Optimized for both spgr and mprage (or neither, >> depending on your perspective). You're probably right that mp-rage is more >> common these days, but I think spgrs are still fairly widespread on GE. >> >> On Thu, 27 Aug 2009, Michael Harms wrote: >> >>> >>> So, are you saying that the default recon-all stream is really optimized >>> for SPGR, and anyone running a MPRAGE should be including the -mprage >>> flag when they run recon-all? If so, this is news to me, and I suspect >>> many other FS users. >>> >>> The default recon-all setting is "set IsMPRAGE = 0", but I suspect (just >>> a hunch, no data) that MPRAGE is the most commonly used type of input to >>> FS. >>> >>> thanks for clarifying, >>> -Mike H. >>> >>> >>> On Wed, 2009-08-26 at 12:53 -0400, Bruce Fischl wrote: >>>> 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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