NIH Blueprint: The Human Connectome Project

HCP 3T Imaging Protocol Overview

Structural, fMRI, and dMRI acquisitions were collected over 4 total imaging sessions, each approximately 1 hour in duration.  Resting-state and task-fMRI data was collected in two sessions. Each session consisted of two resting-state acquisitions of approximately 15 minutes each, followed by task-fMRI acquisitions of varying durations (see below).

Vitamin E capsule on right side. 

A capsule of vitamin E was taped to the subject’s right temple in every scan session, to enable definitive determination of the right side in the image data. 

The following provides basic parameters for the main scan types in each session, and pertinent details about each session.  A more complete set of imaging parameters can be found in the protocol exports from the scanner, available in Appendix 1. FOV positioning in all runs was handled in an automated manner using Siemens AutoAlign feature.

Structural session

Type

Series
Description

Description

TR
(ms)

TE
(ms)

TI
(ms)

Flip
Angle

FOV
(mm)

Voxel Size

BW
(Hz/Px)

iPAT

Acquisition Time (min:sec)

T1w

T1w_MPR1

3D MPRAGE

2400

2.14

1000

8 deg

224x224

0.7 mm isotropic

210

2

7:40

 

T2w

T2w_SPC1

3D T2-SPACE

3200

565

 

variable

224x224

0.7 mm isotropic

744

2

8:24

 

Resting-state fMRI (rfMRI)

rfMRI data were acquired in four runs of approximately 15 minutes each, two runs in one session and two in another session, with eyes open with relaxed fixation on a projected bright cross-hair on a dark background (and presented in a darkened room). Within each session, oblique axial acquisitions alternated between phase encoding in a right-to-left (RL) direction in one run and phase encoding in a left-to-right (LR) direction in the other run.
Resting state images were collected with the following parameters:

Parameter

Value

Sequence

Gradient-echo EPI

TR

720 ms

TE

33.1 ms

flip angle

52 deg

FOV

208x180 mm (RO x PE)

Matrix

104x90 (RO x PE)

Slice thickness

2.0 mm; 72 slices; 2.0 mm isotropic voxels

Multiband factor

8

Echo spacing

0.58 ms

BW

2290 Hz/Px

Condition

Runs

Frames per run

Run Duration (min:sec)

REST (Resting-state)

4

1200

14:33

Task-evoked fMRI (tfMRI)

Following completion of rfMRI in each of the two fMRI scanning sessions, subjects were asked to complete tasks that were designed to activate a variety of cortical and subcortical networks.  The following table provides a listing of the fMRI scans collected.  For each scan type, one run was acquired with right-to-left phase encoding, and a second run with left-to-right phase encoding (in-plane FOV [field of view] rotation obtained by inverting both the RO (readout) and PE [phase encoding] gradient polarity).

T-fMRI data were acquired with the same EPI pulse sequence parameters as R-fMRI, except for the run duration information listed below.  There are seven tasks (14 tfMRI runs) totaling one hour of total tfMRI scan time, with 3 tasks collected in one session and the remaining 4 tasks collected in another session. 

Task

Runs

Frames per run

Run Duration (min:sec)

Working Memory

2

405

5:01

Gambling

2

253

3:12

Motor

2

284

3:34

Language

2

316

3:57

Social Cognition

2

274

3:27

Relational Processing

2

232

2:56

Emotion Processing

2

176

2:16

Scans necessary for field mapping correction were also acquired in each of the fMRI scan sessions.

EV (Explanatory Variable) files included in the dataset provide a set of conditions (and their associated timing) that can be used in the analysis of each task.  An EPRIME_TAB.txt (tab-delimited text spreadsheet) describes task parameters that can be used in various tfMRI analysis packages; see Task-fMRI files and protocol details.

Diffusion imaging (dMRI)

Parameter

Value

Sequence

Spin-echo EPI

TR

5520 ms

TE

89.5 ms

flip angle

78 deg

refocusing flip angle

160 deg

FOV

210x180 (RO x PE)

matrix

168x144 (RO x PE)

slice thickness

1.25 mm, 111 slices, 1.25 mm isotropic voxels

Multiband factor

3

Echo spacing

0.78 ms

BW

1488 Hz/Px

Phase partial Fourier

6/8

b-values

1000, 2000, and 3000 s/mm2


Other details:

Diffusion gradients are monopolar. Oblique axial acquisitions alternate between right-to-left and left-to-right phase encoding directions in consecutive runs.  Image reconstruction uses SENSE1 multi-channel.

A full dMRI session includes 6 runs (each approximately 9 minutes and 50 seconds), representing 3 different gradient tables, with each table acquired once with right-to-left and left-to-right phase encoding polarities, respectively.  Each gradient table includes approximately 90 diffusion weighting directions plus 6 b=0 acquisitions interspersed throughout each run.  Diffusion weighting consisted of 3 shells of b=1000, 2000, and 3000 s/mm2 interspersed with an approximately equal number of acquisitions on each shell within each run.  The diffusion directions were obtained using a toolbox available from INRIA that returns uniformly distributed directions in multiple q-space shells. The directions are optimized so that every subset of the first M directions is also isotropic.

References and the INRIA toolbox can be found at:
http://www-sop.inria.fr/members/Emmanuel.Caruyer/q-space-sampling.php.

Full scanning protocols (PDF)

Complete scanning protocols for each imaging modality can be found in Appendix 1.