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 were 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 packagessee 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 (Sotiropoulos et al., 2013).

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.