Hi, I have put my 1.8mm isotropic Trio diffusion protocol for download here: Archiv.zip <http://www.logicalenemy.net/data/wue/hcp/Archiv.zip>
This is without GRAPPA but using the latest MB-GRAPPA reco refinements (cf. Steen Moeller's ISMRM poster this year) you may be able to use GRAPPA at an acceleration of 2, preferably with 72 reference lines, and cut down the TE to something like 73ms. I had observed a predominance of V1 RL/LR orientations (a "reddish bleeding" on the ColFA or dtifit V1/FA overlays) when using GRAPPA on our system. That does not seem to be completely resolved even though it has improved. It does not seem to affect probabilistic tractography with Xing fibers but it is the reason why I am still staying away from GRAPPA. Feedback and improvements are welcome, as is a notice and acknowledgement if you should use this for your studies. Cheers, Andreas Am 10.07.13 19:00 schrieb "[email protected]" unter <[email protected]>: >Send HCP-Users mailing list submissions to > [email protected] > >To subscribe or unsubscribe via the World Wide Web, visit > http://lists.humanconnectome.org/mailman/listinfo/hcp-users >or, via email, send a message with subject or body 'help' to > [email protected] > >You can reach the person managing the list at > [email protected] > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of HCP-Users digest..." > > >Today's Topics: > > 1. Re: HCP-Users Digest, Vol 8, Issue 6 (Rei?-Zimmermann) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Tue, 9 Jul 2013 17:25:33 +0000 >From: Rei?-Zimmermann, Martin > <[email protected]> >Subject: Re: [HCP-Users] HCP-Users Digest, Vol 8, Issue 6 >To: Andreas Bartsch <[email protected]>, > "[email protected]" <[email protected]> >Message-ID: > > <41e41d2635df1d4fb3430e087ba6f49328738...@s050003233.medizin.uni-leipzig. >de> > >Content-Type: text/plain; charset="iso-8859-1" > >Great news! Thank you very much Andreas. > >Best, >Martin >________________________________________ >Von: Andreas Bartsch [[email protected]] >Gesendet: Montag, 8. Juli 2013 22:16 >An: [email protected] >Betreff: Re: [HCP-Users] HCP-Users Digest, Vol 8, Issue 6 > >Hi, > >I can share a 1.8 mm isotropic mb-diffusion EPI from a 'standard' Trio. >Cheers, >Andreas Bartsch > >Am 08.07.13 19:00 schrieb "[email protected]" unter ><[email protected]>: > >>Send HCP-Users mailing list submissions to >> [email protected] >> >>To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>or, via email, send a message with subject or body 'help' to >> [email protected] >> >>You can reach the person managing the list at >> [email protected] >> >>When replying, please edit your Subject line so it is more specific >>than "Re: Contents of HCP-Users digest..." >> >> >>Today's Topics: >> >> 1. Re: HCP-dMRI gradient table on a TRIO - any experience? >> (Harms, Michael) >> >> >>---------------------------------------------------------------------- >> >>Message: 1 >>Date: Mon, 8 Jul 2013 14:44:26 +0000 >>From: "Harms, Michael" <[email protected]> >>Subject: Re: [HCP-Users] HCP-dMRI gradient table on a TRIO - any >> experience? >>To: Rei?-Zimmermann, Martin >> <[email protected]>, "Xu, Junqian" >> <[email protected]> >>Cc: "[email protected]" <[email protected]> >>Message-ID: <ce003573.1b7fe%[email protected]> >>Content-Type: text/plain; charset="iso-8859-1" >> >> >>Hi Martin and Satra, >>The HCP itself has not extensively evaluated a 1.5 mm multiband DWI >>acquisition on the Trio platform, so we don't have anything concrete to >>share at this time. Perhaps we should rephrase that sentence in the >>Appendix I release guide, but it was included primarily to encourage >>individuals on other platforms to pilot beyond the "standard" 2 mm >>resolution. >> >>I'd encourage you to start by piloting ~1.8 mm isotropic on Trio/Verio >>scanners with a multiband factor of 3-4. >> >>cheers, >>-MH >> >>-- >>Michael Harms, Ph.D. >> >>----------------------------------------------------------- >>Conte Center for the Neuroscience of Mental Disorders >>Washington University School of Medicine >>Department of Psychiatry, Box 8134 >>660 South Euclid Ave. Tel: 314-747-6173 >>St. Louis, MO 63110 Email: [email protected] >> >> >> >> >>On 7/7/13 10:46 AM, "Rei?-Zimmermann, Martin" >><[email protected]> wrote: >> >>>Hello Gordon, >>> >>>thank you very much for your answers. Due to our resolution limited to 2 >>>mm isotropic we have a substantial lower TR (3270 vs. HCP 5520 ms) and a >>>TE of 110.4 ms (HCP 89.50 ms). I wasn't sure if it is the one gradient >>>direction that needs to be changed (since it always stopped at the same >>>point) or something else (in this case using a longer TR/TE). >>>Thanks to your answer, I will now gradually increase TR in a >>>trial-and-error-fashion. >>> >>>Any chance, the mentioned 1.5mm-DTI-TRIO-sequence can be posted here? (I >>>guess, there are a couple more TRIO users in the mailing list) >>> >>>Best regards, >>>Martin >>> >>> >>>________________________________________ >>>Von: Xu, Junqian [[email protected]] >>>Gesendet: Samstag, 6. Juli 2013 16:57 >>>An: Rei?-Zimmermann, Martin >>>Cc: [email protected] >>>Betreff: Re: [HCP-Users] HCP-dMRI gradient table on a TRIO - any >>>experience? >>> >>>Martin, >>> >>>Sorry that I misunderstood your problem. However It is still gradient >>>duty cycle related. The Siemens VB software version doesn't estimate >>>gradient heating as accurately/conservatively as the Siemens VD software >>>version. Hence the minimum TE/TR allowed by the sequence can still trip >>>the gradient duty cycle limit in real time, causing scan crash. >>> >>>The solution is to relax the TE/TR little by little with try-and-error >>>until you find a stable combination that passes your test. >>> >>>Gordon >>> >>>On Jul 5, 2013, at 9:12 PM, "Xu, Junqian" <[email protected]> wrote: >>> >>>> Martin, >>>> >>>> The culprit is the gradient power amplifier (GPA) duty cycle too high >>>>on the Y axis (i.e. the consecutive high value of 0.992 and -0.975). We >>>>have encountered similar problem in HCP and have implemented a solution >>>>to solve the gradient duty cycle issue. >>>> >>>> You can find the solution to this problem in Sotiropoulos et al. >>>>NeuroImage special issue >>>> >>>> http://www.ncbi.nlm.nih.gov/pubmed/23702418 >>>> >>>> Section: Q-space sampling >>>> >>>> "However, even when realistic sequences of diffusion gradient >>>>orientations were used (even with interleaved shells), the gradient >>>>duty >>>>cycle, due to accumulated heating, could still limit the achievable >>>>minimal TR. The order of the diffusion gradient orientations in the >>>>final HCP dMRI protocol was therefore optimised by swapping adjacent >>>>orientations to reduce the auto-correlation (lag = 1) of absolute >>>>gradient amplitude (~ < 0.5) for each physical gradient axis." >>>> >>>> Please let me know if this is clear enough for you to solve your >>>>specific case. >>>> >>>> Regards >>>> Gordon >>>> >>>> On Jul 5, 2013, at 11:06 AM, "Rei?-Zimmermann, Martin" >>>><[email protected]> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I tried implementing and converting the HCP dMRI-sequences for our >>>>>TRIO. I followed the suggestions in the Appendix I and with minor >>>>>modifications (2 mm isotropic) it works well with MB3 and the >>>>>MDDW-gradient table (60 directions). >>>>> >>>>> However, when I use the HCP gradient table the measurement stops at >>>>>reproducable stops within the sequence (see following) and always with >>>>>the same error (hope I can translate that somehow from German into >>>>>English): >>>>> Error in gradient amplifier, GPA not ready. duty cycle is to high. >>>>>Please check sequence parameters. >>>>> >>>>> The sequences always stop at these points: >>>>> >>>>> 95dir-dMRI: direction number 47 (-1.000 , -0.001 , -0.011) >>>>> 96dir-dMRI: direction number 75 (-0.094 , 0.992 , -0.082) >>>>> 97dir-dMRI: direction number 55 (-0.134 , -0.975 , 0.180) >>>>> >>>>> The images before look great! >>>>> >>>>> I took a look at the page of Emmanuel Caruyer - but if I create a >>>>>gradient table of 90 dir (the HCP 96dir-table seems to have 6 b0 and >>>>>the rest b1000-3000, the E.C.-table seems to encode b>0 values, >>>>>right?) >>>>>it is totally different from the HCP one. >>>>> >>>>> I also read the note in the HCP gradient table that these gradients >>>>>are customized for the Connectome-Scanner. >>>>> >>>>> So my question is: Shall I just use one created on Emmanuel's page or >>>>>can I (or better: someone else) change the one from HCP? >>>>> >>>>> The Appendix I also mentions that the dMRI-sequence has been >>>>>successfully tested on a TRIO and Verio with 1.5 mm isotropic >>>>>resolution (and b2000). Is it possible that you could post the >>>>>protocol >>>>>(including the gradient table). >>>>> >>>>> Thank you very much. Best regards, >>>>> Martin >>>>> ____________________________________________________ >>>>> Dr. med. Martin Reiss-Zimmermann >>>>> Abteilung f?r Neuroradiologie >>>>> Universit?tsklinikum Leipzig A?R >>>>> Liebigstr. 20 >>>>> 04103 Leipzig >>>>> >>>>> Mail: [email protected] >>>>> Fon: +49 - 341 - 97 17 585 >>>>> Fax: +49 - 341 - 97 17 490 >>>>> Net: http://www.neuroradiologie-leipzig.de >>>>> >>>>>...................................................................... >>>>>. >>>>>. >>>>>...................................................................... >>>>>. >>>>>. >>>>>........................................................ >>>>> Universit?tsklinikum Leipzig - Anstalt ?ffentlichen Rechts | >>>>>Aufsichtsratsvorsitzender: Prof. Dr. Wolfram Knapp >>>>> Medizinischer Vorstand und Sprecher: Prof. Dr. med. Wolfgang E. Fleig >>>>>| Kaufm?nnischer Vorstand: Dipl.-Kfm. Ekkehard Zimmer >>>>> Sitz: Liebigstra?e 18, 04103 Leipzig | Telefon +49-341-971709 | >>>>>St.Nr.: 23114904074 | IK: 261401052 >>>>> Bankverbindung: Deutsche Bank | BLZ: 86070000 | Kto.: 1247998 | >>>>>Swift-Code: DEUTDE8L | IBAN: DE27860700000124799800 >>>>> Internet: www.uniklinikum-leipzig.de >>>>> >>>>> Universit?t Leipzig | Ritterstr. 26, 04109 Leipzig | K?rperschaft des >>>>>?ffentlichen Rechts | Vertreten durch die Rektorin Prof. Dr. Beate >>>>>Sch?cking >>>>> Zust?ndige Aufsichtsbeh?rde: SMWK, Wigardstr. 17, 01097 Dresden, >>>>>www.smwk.de >>>>> Umsatzsteuer-Identifikationsnummer gem?? ?27a Umsatzsteuergesetz DE >>>>>141510383 >>>>> >>>>> Diese E-Mail enth?lt vertrauliche und/oder rechtlich gesch?tzte >>>>>Informationen. Sollten Sie nicht der richtige Empf?nger sein oder Sie >>>>>haben diese E-Mail irrt?mlich erhalten, informieren Sie uns bitte >>>>>sofort und vernichten diese E-Mail. 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