That's right. -Keith
On Fri, Sep 29, 2017 at 4:33 PM, Jeffrey Spielberg < [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 > Email: [email protected]<mailto:[email protected]> > Website: http://sites.udel.edu/jmsp/ > > On Sep 27, 2017, at 3:37 PM, Keith Jamison <[email protected]<mailto:kjami > [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]>> 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]>> 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:hcp > [email protected]> on behalf of > Jeffrey Spielberg" <[email protected]<mailto:hcp > [email protected]> on behalf of > [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)%20831-7078> > >Email: [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]> > >http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > _______________________________________________ > HCP-Users mailing list > [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
