NeuroimagingConnectomicsWhite matterNetwork scienceTractography MatchingMachine learningWeb servicesopen sciencereproducibility
O3D
O3D (Open Diffusion Data and Derivative) is a reference repository for precision connectome mapping, white matter tracts analysis and algorithmic development.Open Diffusion Data Derivatives
Open Diffusion Data Derivatives (O3D). Reproducible Neuroimaging via open cloud services: Data upcycling to advance discovery in brain science
This Open Diffusion Data Derivatives (O3D) repository contains data and processing pipelines used to generate the data. The repository contains diffusion-weighted and T1 contrast weighted magnetic resonance imaging data and various data derivatives, such as voxels reconstruction models, whole-brain tractograms, segmented white matter tracts, and connectivity matrices (connectomes). In addition, the repository also contains the methods for data processing used to generate the data derivatives implemented as open cloud services used to generate the data derivatives are published associated with the data. Data and processing pipelines are published as both preserved files and also as open services embedded in the brainlife.io cloud computing platform.
Please cite the following articles when reusing these data and services
Avesani, P., Caiafa, C., McPherson, B. Saykin, A., Hayashi, S., Herschel, R., A., Garyfallidis, E., Kitchell, L.,
Bullock, D., Patterson, A., O’Riley, S., Olivetti, E., Sporns, O., Saykin, A., Wang, L., Dinov, I., and Pestilli, F. Reproducible Neuroimaging Via Open Cloud Services: Data Upcycling To Advance Discovery In Network Neuroscience. (Scientific Data 6:69 (2019))[https://doi.org/10.1038/s41597-019-0073-y]
Preservation.
Preserved files for open data and services can be accessed at the permanent address https://doi.org/10.25663/bl.p.3.
Reuse.
The open cloud services analysis Apps and data can be accessed for additional cloud computing at the O3D brainlife.io project page.
Download.
The O3D repository data can be downloaded organized into the most current version of the Brain Imaging Data Structure (BIDS) diffusion-weighted MRI derivatives specification using the command line interface
# filter the subset of data of interest by querying brainlife
for id in $(bl dataset query \
--limit 200 \
--pub 5a0f0fad2c214c9ba8624376 \
--subject 0001 \
--json | jq -r ".[]._id");
do
# download the data
bl dataset download $id
done
Changes
Release 2
The data have been recomputed using the latest version of the apps. Further changes on published data:
- added tractograms in trk format,
- replaced the white matter classification (wmc) structure with a single trk file encoding as fiber property the tract classification.
The following data objects are published as part of this release.
Diffusion-weighted magnetic resonance data (dMRI), saved in NIfTI-1 format.
Various .mat files generated from Network Neuro Application
Diffusion-weighted magnetic resonance data (dMRI), saved in NIfTI-1 format.
Folder structure generated by FreeSurfer recon-all process.
T1-weighted magnetic resonance data (MRI), saved in NIfTI-1 format.
LiFE Output (fe structure)
TrackVis (.trk). Track file is one single binary file, with the first 1000 bytes as the header and the rest as the body.
TrackVis (.trk). Track file is one single binary file, with the first 1000 bytes as the header and the rest as the body.
Various .mat files generated from Network Neuro Application
T1-weighted magnetic resonance data (MRI), saved in NIfTI-1 format.
TrackVis (.trk). Track file is one single binary file, with the first 1000 bytes as the header and the rest as the body.
LiFE Output (fe structure)
Diffusion-weighted magnetic resonance data (dMRI), saved in NIfTI-1 format.
Diffusion-weighted magnetic resonance data (dMRI), saved in NIfTI-1 format.
TrackVis (.trk). Track file is one single binary file, with the first 1000 bytes as the header and the rest as the body.
TrackVis (.trk). Track file is one single binary file, with the first 1000 bytes as the header and the rest as the body.
TrackVis (.trk). Track file is one single binary file, with the first 1000 bytes as the header and the rest as the body.
LiFE Output (fe structure)
Various .mat files generated from Network Neuro Application
MRtrix Track Data (.tck)
MRtrix Track Data (.tck)
Folder structure containing all files generated by the VISTASOFT dtiInit.m
MRtrix Track Data (.tck)
Diffusion Signal Voxel Reconstruction Model
The following Apps were used to generate the data in this release.
| lmax | null |
|---|---|
| fibers | 500000 |
| fibers_max | 1000000 |
| phaseEncodeDir | 2 |
|---|---|
| resolution | default |
| rotateBvecsWithCanXform | false |
| rotateBvecsWithRx | false |
| eddyCorrect | -1 |
| noDwiAlignment | true |
| life_discretization | 360 |
|---|---|
| num_iterations | 500 |
| bvals_round | 100 |
|---|---|
| shell | 2000 |
| b0_max | 200 |
The following data objects are published as part of this release.
T1-weighted magnetic resonance data (MRI), saved in NIfTI-1 format.
T1-weighted magnetic resonance data (MRI), saved in NIfTI-1 format.
Folder structure generated by FreeSurfer recon-all process.
Diffusion-weighted magnetic resonance data (dMRI), saved in NIfTI-1 format.
The following Apps were used to generate the data in this release.
| bvals_round | 100 |
|---|---|
| shell | 2000 |
| b0_max | 200 |
| phaseEncodeDir | 2 |
|---|---|
| resolution | default |
| rotateBvecsWithCanXform | false |
| rotateBvecsWithRx | false |
| eddyCorrect | -1 |
| noDwiAlignment | true |
Citation for this publiction. Please see citation section under each release for App specific citations.
Resolving 10.25663/bl.p.3..
This publication is hosted in the following brainlife.io project
O3D
O3D (Open Diffusion Data and Derivative) is a reference repository for precision connectome mapping, white matter tracts analysis and algorithmic development.
Published data is released under the following license.
CC BY 4.0 - Creative Commons / Attribution 4.0 International This license lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of licenses offered. Recommended for maximum dissemination and use of licensed materials. More ...
connectomic surgery diffusion tensor imaging dti tractography as a targeting modality for surgical modulation of neural networks
Frontiers in Integrative Neuroscience | 2012
Deep brain stimulation (DBS) is being used to treat a growing number of neurological disorders. Until recently, DBS has been thought to act mainly by suppressing local neuronal activity, essentially producing a functional lesion. Numerous studies are now demonstrating that DBS has widespread network effects mediated by white matter pathways. The new science of connectomics aims to map the connectivity between brain regions in health and disease. Targeting DBS specifically to pathways which exhibit pathological connectivity could greatly expand the possibilities for treating brain diseases. This brief review examines the current state of brain imaging for visualization of these networks Show More
Jaimie M. Henderson
tractographyconnectomicsdeep brain stimulationdiffusion mrineuroimagingdefault mode networkwhite matterneurosciencemodalitypsychology