And it is all handled automatically for the dMRI data in the HCP Pipeline.
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] From: <[email protected]> on behalf of Keith Jamison <[email protected]> Date: Friday, September 29, 2017 at 3:38 PM To: Jeffrey Spielberg <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: [HCP-Users] DWI in CCF Prisma protocol That's right. -Keith On Fri, Sep 29, 2017 at 4:33 PM, Jeffrey Spielberg <[email protected]<mailto:[email protected]>> wrote: One further question: it looks like there no separate AP/PA fieldmaps for dMRI in the CCF protocol, whereas there are SE fieldmaps for resting - is that correct? If so, is this because the b0 images from the dMRI can be used for this purpose (e.g., in topup)? Best, Jeff -- Jeffrey M. Spielberg, Ph.D. Assistant Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware Newark, DE 19716 Office: 307 McKinly Laboratory Lab: Suite 405 Wolf Hall Phone: 302.831.7078<tel:302.831.7078> Email: [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> Website: http://sites.udel.edu/jmsp/ On Sep 27, 2017, at 3:37 PM, Keith Jamison <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: To clarify, hopefully: "Vector set 1" dMRI_dir98_AP = 46 b=1500, 46 b=3000, 6 b=0 dMRI_dir98_PA = exact same as dir98_AP, but phase encode=P>>A "Vector set 2" dMRI_dir99_AP = 47 b=1500, 46 b=3000, 6 b=0 dMRI_dir99_PA = exact same as dir99_AP, but phase encode=P>>A So in total, we have 93 unique directions the b=1500 shell, and 92 unique directions for the b=3000 shell, plus 12 interspersed b=0. Each direction is acquired with phase-encode A>>P and then again with P>>A. For some added info, see attached screenshot, which is page 22 of the dMRI screenshot PDF distributed with the CCF protocol. -Keith On Wed, Sep 27, 2017 at 3:06 PM, Keith Jamison <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: We essentially split the ~197 direction in half, and the two halves can't have the exact same number of directions due to how they are stored on the scanner, so "part 1" is 98 directions and "part 2 is 99. each is then collected both AP and PA. FYI, each scan is actually 92 diffusion volumes plus 6 or 7 non-diffusion "b=0" This is probably available elsewhere under the CCF documentation, but the DWI scans are adapted from here: https://www.humanconnectome.org/study-hcp-lifespan-pilot/phase1b-pilot-parameters The way the sequence runs on the scanner, we set a single "maximum" b-value (b=3000), by which each of the diffusion vectors in the table is scaled. The entries that norm to 1 are b=3000, and the vectors that norm to 0.707 are b=1500. Note: 0.707 = sqrt(0.5). For whatever reason, this is how the scanner handles vector magnitudes. -Keith On Wed, Sep 27, 2017 at 2:29 PM, Glasser, Matthew <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: In general one wants to get as many gradient directions as possible. Perhaps Mike knows the answer to your other question. Matt. On 9/28/17, 2:59 AM, "[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> on behalf of Jeffrey Spielberg" <[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> on behalf of [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> wrote: >Hi all, > >I¹m interested in setting up a diffusion protocol similar to the CCF >protocol and have two questions. First, what¹s the difference between >the dir98 and dir99 acquisitions (beyond having different vectors)? It >looks like both sample on 2 shells, use the same b-values, and have about >50:50 vectors on each shell, so I¹m not clear on why both are needed. > >Second, I was playing around with the Caruyer q-space sampling tool and >noticed that the output differs from the vectors provided as part of the >CCF protocol. Specifically, for dir98, they match for 1 shell, but the >vector magnitudes in the other shell have been shortened to .7071. My >guess is that this is necessary to tell the scanner to use the second >b-value (e.g., 1500). Is that correct? > >Best, >Jeff > > > >-- >Jeffrey M. Spielberg, Ph.D. >Assistant Professor, Clinical Science >Department of Psychological and Brain Sciences >University of Delaware >Newark, DE 19716 > >Office: 307 McKinly Laboratory >Lab: Suite 405 Wolf Hall >Phone: 302.831.7078<tel:302.831.7078><tel:(302)%20831-7078> >Email: >[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>><mailto:[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>>> >Website: http://sites.udel.edu/jmsp/ > > >_______________________________________________ >HCP-Users mailing list >[email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> >http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]><mailto:[email protected]<mailto:[email protected]>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users <CCF_Prisma_Screenshots_dMRI_2016.03.07_page22.png> _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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