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NIH BRAIN CONNECTS - LINC UM1 Macaque Data

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This repository provides macaque diffusion MRI data from the NIH BRAIN CONNECTS - LINC UM1 project, released through the DANDI Archive. The dataset is part of the Large-scale Imaging of Neural Circuits (LINC) effort, which aims to develop multimodal imaging resources for studying brain connections across scales.

The dataset focuses on high-resolution macaque diffusion MRI and derived tractography/microstructure products relevant to cortico-subcortical circuitry, including the internal capsule, hyperdirect pathway, and basal ganglia.

  • Source: https://dandiarchive.org/dandiset/001372
  • DANDI ID: 001372
  • Status: Draft
  • Data standard: Brain Imaging Data Structure (BIDS)
  • Access: Open access
  • License: Creative Commons Attribution 4.0 International (CC BY 4.0)

Dataset Overview

  • Dataset name: NIH BRAIN CONNECTS - LINC UM1 - Macaque Data
  • Species: Macaque
  • Subjects: 4
  • File count: 192
  • Dataset size: ~67.1 GB
  • Primary modality: Diffusion MRI
  • Data type: Derived BIDS-compatible diffusion imaging data

Keywords

  • Multimodal imaging
  • Diffusion MRI
  • Tractography

Subject Matter

  • Internal capsule
  • Hyperdirect pathway
  • Basal ganglia

Project Background

The Center for Large-scale Imaging of Neural Circuits (LINC) is part of the NIH BRAIN Initiative CONNECTS program. The project aims to develop imaging technologies that bridge microscopic and macroscopic scales of brain connectivity.

This macaque dataset supports research on:

  • Whole-brain diffusion MRI tractography
  • Cortico-subcortical projection mapping
  • Microstructural modeling
  • Cross-scale validation of brain connectivity
  • Deep-brain stimulation-related pathways

Data Contents

The current DANDI draft release contains diffusion MRI derivatives for:

sub-M1
sub-M2
sub-M3
sub-M4

The data are organized primarily under:

derivatives/<subject>/dwi/

Acquisition / Derivative Types

The asset list includes several diffusion MRI acquisition and derivative categories.

High-resolution multishell diffusion MRI

Example files:

sub-M*_acq-HighRes+MultiShell_dwi.nii.gz
sub-M*_acq-HighRes+MultiShell_dwi.bvals
sub-M*_acq-HighRes+MultiShell_dwi.bvecs

These files provide high-resolution multishell diffusion data and associated gradient tables.

High-resolution undersampled grid diffusion MRI

Example files:

sub-M*_acq-HighRes+UndersampledGrid_dwi.nii.gz
sub-M*_acq-HighRes+UndersampledGrid_dwi.bvals
sub-M*_acq-HighRes+UndersampledGrid_dwi.bvecs

These files provide an additional high-resolution diffusion sampling scheme.

Multi-dimensional diffusion MRI

Example files:

sub-M*_acq-MultiDim_run-*_dwi.nii.gz
sub-M*_acq-MultiDim_run-*_dwi.bval
sub-M*_acq-MultiDim_run-*_dwi.bvec

The multidimensional diffusion data include multiple runs and support modeling across diffusion weighting and acquisition dimensions.

Derived Maps

The repository includes several diffusion-derived scalar and vector maps.

Examples include:

desc-MultiTE+diravg.nii.gz
desc-SingleTE+diravg.nii.gz
desc-MultiTE+Rsoma.nii.gz
desc-MultiTE+fsoma.nii.gz
desc-MultiTE+T2soma.nii.gz
desc-MultiTE+fneurite.nii.gz
desc-MultiTE+T2neurite.nii.gz

These files may support microstructural modeling of soma- and neurite-related signal components.

Tractography / CSD Products

The dataset also includes constrained spherical deconvolution (CSD) and tractography-related derivatives.

Example files:

desc-CSD+fodf+l0.nii.gz
desc-CSD+dec+scalar.nii.gz
desc-CSD+dec+univec.nii.gz
desc-CSD+tdi+scalar.nii.gz
desc-CSD+tdi+univec.nii.gz

These derivatives can support:

  • Fiber orientation analysis
  • Tract density imaging
  • Tractography visualization
  • White matter pathway reconstruction

Suggested Applications

This dataset is useful for:

  • Macaque tractography benchmarking
  • Microstructure model development
  • High-resolution diffusion MRI reconstruction
  • Cortico-subcortical pathway mapping
  • Internal capsule and hyperdirect pathway analysis
  • Cross-scale connectomics research
  • Fiber Data Hub tractography visualization and distribution

Data Access

The dataset can be accessed from DANDI:

https://dandiarchive.org/dandiset/001372

Using the DANDI CLI:

dandi download DANDI:001372/draft

Because this Dandiset is currently in draft status, users should check the DANDI page for updates or future published versions before citing or redistributing derived products.

License

This dataset is released under:

Creative Commons Attribution 4.0 International (CC BY 4.0)

License text:

https://creativecommons.org/licenses/by/4.0/

This license allows sharing and adaptation of the data, including redistribution and derived works, provided that appropriate attribution is given.

Funding

This dataset is associated with the NIH BRAIN Initiative Connectivity Across Scales program.

  • Funding source: National Institutes of Health (NIH)
  • Award number: 1 UM1 NS132358

Citation

Please cite the DANDI dataset when using this repository:

NIH BRAIN CONNECTS - LINC UM1 - Macaque Data.
DANDI Archive.
https://dandiarchive.org/dandiset/001372

Please also cite any related publications or preprints listed on the DANDI page, including the LINC diffusion MRI work associated with this dataset.

Contact

DANDI contact:

Kabilar Gunalan

Listed contributors include members of the LINC / BRAIN CONNECTS team, including Ting Gong, Chiara Maffei, Kabilar Gunalan, Satrajit Ghosh, Suzanne Haber, and Anastasia Yendiki.

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