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Multicenter dataset of multishell diffusion MRI in healthy traveling adults with identical setting

dataset
posted on 13.03.2020, 13:34 by Qiqi TongQiqi Tong, Hongjian He, Ting Gong, Chen Li, Peipeng Liang, Tianyi Qian, Yi Sun, Qiuping Ding, Kuncheng Li, Jianhui Zhong

Introduction

A multishell diffusion MRI dataset collected from three traveling subjects with identical acquisition setting in ten imaging centers. Both of the scanner type and imaging protocol for anatomical and diffusion imaging were well controlled.

This dataset is expected to replenish the individual reproducible study via multicenter collaborations by providing an open resource for advanced and novel microstructure and tractography quantifications.


Primary acquisition parameters

• T1-weighted images

Sequence: MP2RAGE

Resolution = 1x1x1.2 mm3


• Diffusion-weighted images

Sequence: SMS EPI

Resolution = 1.5x1.5x1.5 mm3

b-value = 1000,2000,3000 mm2/s

directions = 30,30,30

non-diffusion images = 6


Data download and unarchive

1. The DWI data were archived by bandizip software into multi-parts zip files as: sub-1.zip(.z01), sub-2.zip(.z01), and sub-3.zip(.z01). One pair for each subject respectively. The *.zip files are around 2.4GB each and *.z01 files are 4GB each. Please use the MD5 checksum as follows to verify the integrity of your download if possible.

sub-1.zip 67a5b404c2d67e74c37dbdd7f5825538

sub-1.z01 727e4fbddb104138dad89ba6ea60cd0f

sub-2.zip a3bd923a00a2cd35a88c56356ea3f9df

sub-2.z01 b46845a3105a0694358bd57a60e4b68b

sub-3.zip 9388d9745f4dce403261e70ae5f5f9bc

sub-3.z01 86aa3607462c483a85a64f1503217ace

2. The pair of zip parts should share exactly the same filename by default. However, it happens the filenames may be changed during downloading for some reason. Please correct and rename the filenames properly before unarchive progress, otherwise there may occur an error.

3. Instructions to extract the multi-part zip files.

A) For Windows users:

Consider to use applications like WinRAR, 7Zip, etc. Select one set of multi-part zip files for one subject -> Right click on files -> Select ‘Extract’ option listed in the pop-out menu.

B) For Unix/Linux and Mac users:

In the terminal command line, first, cd to the path where multi-part zip files are, then run the following commands to extract sub-1 for example:

 cat sub-1.z* > sub-1-cat.zip

 unzip sub-1-cat.zip

Mac users may also try the free applications like The Unarchiver, Dr.Unarchiver, etc.


Data structure

This dataset was orgnaized in BIDS format. However, due to the limit size of 5 GB for single file in the FigShare, the folders "sub-1", "sub-2", and "sub-3" were compressed into multi-part archives. After file extraction, you can see the whole dataset structure as follows (other folders contain similar files with sub-3/ and sub-3/ses-c10r3/):

| README

| CHANGES

| dataset_description.json

| participants.tsv

|▿ code/

|  example.sh

|  Prep_diffusion.sh

|  Prep_face_removal.sh

|  Prep_gibbsring.m

|▸ sub-1/

|▸ sub-2/

|▿ sub-3/

|  sub-3_sessions.tsv

| ▸ ses-c01r1/

| ▸ ses-c02r1/

| ▸ ses-c03r1/

| ▸ ses-c04r1/

| ▸ ses-c05r1/

| ▸ ses-c06r1/

| ▸ ses-c07r1/

| ▸ ses-c08r1/

| ▸ ses-c09r1/

| ▸ ses-c10r1/

| ▸ ses-c10r2/

| ▿ ses-c10r3/

|  ▿ anat/

|       sub-3_ses-c10r3_T1w.json

|       sub-3_ses-c10r3_T1w.nii.gz

|  ▿ dwi/

|       sub-3_ses-c10r3_dwi.bval

|       sub-3_ses-c10r3_dwi.bvec

|       sub-3_ses-c10r3_dwi.json

|       sub-3_ses-c10r3_dwi.nii.gz

|       sub-3_ses-c10r3_dwi_mask.nii.gz

|▿ derivatives/

| ▿ movement/

|  ▸ sub-1/

|  ▸ sub-2/

|  ▿ sub-3/

|   ▸ ses-c01r1/

|   ▸ ses-c02r1/

|   ▸ ses-c03r1/

|   ▸ ses-c04r1/

|   ▸ ses-c05r1/

|   ▸ ses-c06r1/

|   ▸ ses-c07r1/

|   ▸ ses-c08r1/

|   ▸ ses-c09r1/

|   ▸ ses-c10r1/

|   ▸ ses-c10r2/

|   ▿ ses-c10r3/

|        sub-3_ses-c10r3.eddy_parameters


Data use agreement

To use this dataset, we would like to follow the license CC BY (https://creativecommons.org/licenses/by/4.0/).


Contact

For more information on the data collection and pre-processing procedure, you can contact Qiqi Tong (tongqq@zju.edu.cn).

For other information or further cooperation with us, you can contact Dr. Hongjian He (hhezju@zju.edu.cn).

Funding

National Key R&D Program of China (2017YFC0909200)

National Natural Science Foundation of China (81871428)

Shanghai Key Laboratory of Psychotic Disorders (13dz2260500,K18-515007-007)

Capacity Building for Sci-Tech Innovation - Fundamental Scientific Research Funds (19530050157, 19530050184)

Beijing Talents foundation (2016000021223TD07)

Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support (ZYLX201609)

Beijing Brain Initiative of Beijing Municipal Science & Technology Commission

Major Scientific Project of Zhejiang Lab (2018DG0ZX01)

Fundamental Research Funds for the Central Universities (2019QNA5026, 2019XZZX001-01-08)

Zhejiang University Education Foundation Global Partnership Fund

Zhejiang Province Laboratory Work Research Project (YB201730)

Beijing Municipal Science and Technology Project of Brain cognition and brain medicine (Z171100000117001)

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