IMPORTANT:
MGH Adult Diffusion Data is available under a separate set of open access data use terms. Please review the MGH-USC HCP Data Agreement, and follow the steps to accept the terms that apply to your research.
The MGH-USC HCP team has acquired and shared diffusion imaging data from 35 healthy adults scanned on the customized Siemens 3T Connectom scanner. The imaging data is available to those who register and agree to the Open Access Data Use Terms.
The data were collected on the customized Siemens 3T Connectom scanner, which is a modified 3T Skyra system (MAGNETOM Skyra Siemens Healthcare), housed at the MGH/HST Athinoula A. Martinos Center for Biomedical Imaging (see Setsompop et al., 2013 for details of the scanner design and implementation). A 64-channel, tight-fitting brain array coil (Keil et al., 2013) was used for data acquisition.
Data was acquired from healthy adults between the ages of 20 and 59. Demographic information available in ConnectomeDB includes gender and age range. The participants gave written consent, and the procedures were carried out in accordance with the institutional review board approval and procedures.
Each dataset (in nifti format) consists of an MPRAGE scan, a high resolution T2-SPACE scan and diffusion scans with 4 different b-values.
Structural scans
| Type | T1w | T2w |
|---|---|---|
| Description | 3D MPRAGE | 3D T2-SPACE |
| TR/TE (ms) | 2530/1.15 | 3200/561 |
| TI (ms) | 1100 |
|
| Flip Angle | 7.0 deg |
|
| FOV (mm) | 256x256 | 224x224 |
| Voxel Size | 1mm isotropic | 0.7mm isotropic |
| BW (Hz/Px) | 651 | 744 |
| iPAT | 2 | 2 |
| Acquisition Time (min:sec) | 6:02 | 6:48 |
Diffusion scans:
| Parameter | Value |
|---|---|
| Sequence | Spin-echo EPI |
| TR/TE (ms) | 8800/57 |
| δ/Δ (ms) | 12.9/21.8 |
| FOV (mm) | 210x210 |
| Matrix | 140x140 |
| Slices | 96 slices, 1.5mm thick, 1.5mm isotropic voxel size |
| iPAT | 3 |
| Multiband factor | 1 |
| Echo spacing (ms) | 0.63 |
| BW | 1984 Hz/Px |
| Phase Partial Forier | 6/8 |
| b-values | 1000, 3000, 5000, 10,000 s/mm2 |
| Total acquisition time | 89 mins |
Other details: Structural scans were reviewed by a radiologist to assure absence of brain abnormalities. Diffusion data were acquired in oblique axial slices. Diffusion gradients are mono-polar. The echo time and diffusion times (δ/Δ) were optimized for the b-value=10,000 (s/mm2) shell, and fixed for all the lower b-value shells. The diffusion scans are comprised of 5 runs:
| Run No. | b-value (s/mm2) | diffusion directions | Acqusition Time (min:sec) |
|---|---|---|---|
| 1 | 1,000 | 64 | 11:44 |
| 2 | 3,000 | 64 | 11:44 |
| 3 | 5,000 | 128 (set1) | 21:51 |
| 4 | 10,000 | 128 (set1) | 21:51 |
| 5 | 10,000 | 128 (set2) | 21:51 |
One non-diffusion weighted (b=0) image was collected every 14 image volumes, yielding 552 volumes in total. Phase encoding direction was anterior to posterior. MultiBand acquisition was not used in this dataset.
Complete scanning protocols can be found in Appendix I (updated).
The imaging data was processed with software tools in Freesurfer V5.3.0 ( http://freesurfer.net/fswiki/FreeSurferWiki/) and FSL V5.0 ( http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/).
Structural Scans
Diffusion Scans
Other details: Both diffusion and structural data are provided in native space. Since the gradient field nonlinearity coefficients were protected by Siemens as proprietary information, the data provided as 'raw' for diffusion and T1w/T2w were already corrected for gradient nonlinearity.
This section lists the filenames and directory structure provided in ConnectomeDB. mgh_1001.zip (in /data/intradb/ftp/MGH/NIFTI/zips/bvec_fixed/) unzips to:
mgh_1001/ file_description.txt mgh_1001/anat/T1/ T1.nii.gz mgh_1001/anat/T2/ T2.nii.gz mgh_1001/diff/preproc/ bvals.txt bvecs_fsl_moco_norm.txt bvecs_moco_norm.txt mgh_1001/diff/preproc/mri/ diff_preproc.nii.gz mgh_1001/diff/raw/mri/ diff.nii.gz bvecs.txt bvecs_fsl.txt bvals.txt --------- ------- 7322043912 13 files