Has anyone had a chance to take a further look at the output differences in using the -mprage option yet? (I'm still new at freesurfer and probably wouldn't know what to look for...)
-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 27, 2009, at 8:41 AM, Bruce Fischl wrote: > 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. 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