Hi, Martin Reiß-Zimmermann has kindly alerted me to the fact that "Sense 1 Coil Combine" was NOT checked in the protocols I have uploaded to share. This was an error, and "Sense 1" SHOULD be better checked under the "Sequence / Special" tab. I am actually using "Sense 1" (cf. Q2-Appendix recommendations of the HCP) - the error was due to exporting from a backup folder where I had not checked this.
I also want to mention that the protocol >should< be compatible to be processed by eddy, including a possible lsr restoration of future releases Jesper Andersson is working on. Cheers, Andreas Am 14.07.13 17:50 schrieb "Andreas Bartsch" unter <[email protected]>: >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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