NIH Blueprint: The Human Connectome Project

CCF Protocol Template

This downloadable package contains electronic protocols a “Connectomic/HCP style” set of acquisitions. The protocols are configured for import into a Siemens 3T Prisma, acquiring the following scan series: 0.8 mm T1w/T2w structurals, 2.0 mm fMRI, and 1.5 mm dMRI.

This protocol is substantially similar to the parameters used for scanning of the Phase 1b Lifespan Pilot protocol on the Prisma at the Center for Magnetic Resonance Research (CMRR) at the University of Minnesota, but does differ in some regards (see “Version Changes” below).

VE11 version note

This package contains protocols exported under both VD13D and VE11B: "CCF_Prisma_VD13D_2016.07.14.edx" and "CCF_Prisma_VE11B_2016.07.14.exar1". The VD13D and VE11B versions are identical in their imaging parameters. However, it is recommended that VE11 users import the VE11 specific version, because of a couple quirks during the import/conversion process from VD13.

The multi-band accelerated EPI sequences developed at CMRR that are necessary to run this protocol are available at:

If you have questions about this protocol, you can ask them in the HCP Users email list.

Version Changes

Release 2016.07.14

  • “LeakBlock” (i.e., Split-slice GRAPPA reconstruction; ref. Cauley et al., MRM, 2014; 72:93-102) turned On for BOLD and dMRI scans to reduce interslice correlations/cross-talk.

Release 2016.04.13

  • Replaces VE11 version of exar1 file with one that will actually import. (VE11 version in the 2016.03.07 release package was corrupted).
  • Updated the parameter listing on the following pages so that the “Geometry – AutoAlign” sections now reflect what was actually occurring at run time under VE11. N.B. The parameter printout is from a VE11 system, while the “Screenshots” in this package were captured under a VD13 system.

Release 2016.03.07 (VD13D and VE11B versions, created under multi-band release “R013”)

  • Changed the SpinEchoFieldMaps (SEFM) so that the Echo Spacing of the SEFM is matched to that of the BOLD scans (0.58 ms) via the “Free echo spacing” option on the Sequence tab. (Previously, the matching of ES between the SEFM and BOLD scans was achieved by setting a hidden parameter called “Fake MB factor for SB” in the SEFM scans. However, exposing that hidden parameter required creation of a custom configuration file. Also, that “Fake MB” parameter is considered deprecated and unsupported. Therefore, use “Free echo spacing” instead as the mechanism to match the ES).
  • Changed TE of SEFM from 66.6 to 66.0 ms.
  • Added diffusion vector tables to the package.

Release 2015.11.30 (VD13D, created under multi-band release “R012c”)

  • First version of a package under VD13D that included an EDX.

Relative to the parameters used in the “Phase 1b Lifespan Pilot” the main changes of interest are:

  • TR increased from 720 to 800 ms. (Note: Number of Measurements left at 420 frames, which results in each rfMRI run being 34 sec longer. Can set Measurements to 380 to return each run to 5 min of data).
  • PPF set to Off in the “SpinEchoFieldMap” scans as well to match.
  • TI (inversion time) for the T1w structural changed from 1060 to 1000 ms (achieved by changing the “Gradient mode” from ‘Fast’ to ‘Performance’).