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NIH BRAIN CONNECTS - LINC UM1 Human Data

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This repository provides human brain imaging data from the NIH BRAIN CONNECTS - LINC UM1 project, released through the DANDI Archive. The dataset is part of the Center for Large-scale Imaging of Neural Circuits (LINC), a BRAIN CONNECTS effort focused on developing imaging technologies that link macroscopic diffusion MRI with microscopic anatomical measurements.

The dataset includes human diffusion MRI derivatives, tractography products, anatomical imaging, and large-scale microscopy / X-ray phase-contrast tomography data. It is intended for cross-scale studies of human brain connectivity, microstructure, and cortico-subcortical pathways relevant to neuromodulation and deep-brain stimulation.

  • Source: https://dandiarchive.org/dandiset/001278
  • DANDI ID: 001278
  • Dataset name: NIH BRAIN CONNECTS - LINC UM1 - Human Data
  • Status: Draft
  • Access: Open access
  • Data standards: BIDS and OME-NGFF
  • License: Creative Commons Attribution 4.0 International (CC BY 4.0)

Dataset Overview

  • Species: Human

  • Subjects: 3

  • Samples: 11

  • File count: 195

  • Dataset size: ~5.7 TB

  • Primary modalities:

    • Diffusion MRI
    • Anatomical MRI
    • Tractography derivatives
    • X-ray phase-contrast tomography / microscopy data

Keywords

  • Multimodal imaging
  • Diffusion MRI
  • Tractography

Subject Matter

  • Internal capsule
  • Hyperdirect pathway
  • Basal ganglia

Project Background

The LINC project is part of the NIH BRAIN Initiative Connectivity Across Scales (BRAIN CONNECTS) program. Its goal is to develop and deploy imaging methods that connect multiple spatial scales of brain organization, from whole-brain MRI to microscopic anatomical measurements.

This human dataset supports:

  • High-resolution diffusion MRI analysis
  • Cross-scale validation of tractography
  • Microstructural modeling
  • Cortico-subcortical pathway mapping
  • Deep-brain stimulation pathway research

Data Organization

The DANDI release includes both raw source data and derivatives.

Top-level structure includes:

sourcedata/
derivatives/
dataset_description.json
.bidsignore

sourcedata/

Contains raw or source imaging data, including anatomical MRI and large microscopy / X-ray phase-contrast tomography files.

Examples:

sourcedata/raw/sub-Hb1/anat/
sourcedata/raw/sub-Hb2/micr/

Large OME-Zarr assets are included for microscopy / XPCT data.

derivatives/

Contains processed diffusion MRI, tractography, microstructure maps, anatomical derivatives, and aligned data products.

Examples:

derivatives/sub-Ha1/dwi/
derivatives/sub-Hb1/anat/
derivatives/sub-Hb1/dwi/

Diffusion MRI Derivatives

The diffusion MRI derivatives include high-resolution diffusion products and model-derived maps.

Example derivative files include:

sub-Ha1_sample-RightHemi_acq-HighRes+MultiShell_desc-CSD+fodf+l0.nii.gz
sub-Ha1_sample-RightHemi_acq-HighRes+MultiShell_desc-CSD+dec+scalar.nii.gz
sub-Ha1_sample-RightHemi_acq-HighRes+MultiShell_desc-CSD+tdi+scalar.nii.gz
sub-Ha1_sample-RightHemi_acq-HighRes+MultiShell_desc-SANDIdot+fneurite.nii.gz
sub-Ha1_sample-RightHemi_acq-HighRes+MultiShell_desc-SANDIdot+fsoma.nii.gz

These derivatives support:

  • Fiber orientation distribution modeling
  • Constrained spherical deconvolution
  • Tract density imaging
  • Neurite / soma-related microstructure analysis

Tractography Products

The dataset includes tractography files for whole-brain and pathway-specific reconstructions.

Example tractography files include:

sub-Ha1_sample-RightHemi_space-orig_tract-wholebrain_track-ifod_tractogram.trk
sub-Ha1_sample-RightHemi_space-MNI152NLin2009bAsym_tract-AnteriorCommissure_track-ifod_tractogram.trk
sub-Ha1_sample-RightHemi_space-MNI152NLin2009bAsym_tract-Fornix_track-ifod_tractogram.trk
sub-Ha1_sample-RightHemi_space-MNI152NLin2009bAsym_tract-MedialForebrainBundle_track-ifod_tractogram.trk
sub-Ha1_sample-RightHemi_space-MNI152NLin2009bAsym_tract-DentatoThalamicTract_track-ifod_tractogram.trk

The release also includes a basal-ganglia pathway atlas label file:

sub-Ha1_sample-RightHemi_atlas-BGPathwaysMaffei2026_label-Tracts+SubcorticalNuclei_dseg.txt

Anatomical and Microscopy Data

The dataset includes high-resolution anatomical and microscopy-related data for human brain samples.

Example data types include:

FLASH T2*-weighted anatomical MRI
XPCT microscopy / tomography data
OME-Zarr microscopy volumes
SuperSynth segmentation derivatives
White-matter orientation maps

Example files include:

sub-Hb1_sample-lefthemi_acq-FLASH_T2starw.nii.gz
sub-Hb1_sample-lefthemi_acq-FLASH_res-500um_desc-SuperSynth_dseg.nii.gz
sub-Hb1_sample-lefthemi_space-XPCT_acq-FLASH_T2starw.nii.gz
sub-Hb1_sample-lefthemi_space-XPCT_acq-highres_desc-WMorientation.nii.gz
sub-Hb2_sample-leftHemi-overview_XPCT.ome.zarr

Scientific Applications

This dataset is useful for:

  • Human brain tractography validation
  • Cross-scale connectomics
  • Diffusion MRI microstructure modeling
  • High-resolution pathway reconstruction
  • Basal ganglia and hyperdirect pathway studies
  • DBS-relevant connectivity mapping
  • Registration between MRI and microscopy / XPCT data
  • Fiber Data Hub visualization and tractography distribution

Data Access

The dataset can be accessed from DANDI:

https://dandiarchive.org/dandiset/001278

Using the DANDI CLI:

dandi download DANDI:001278/draft

Because this Dandiset is currently listed as a draft, users should check the DANDI page for updates or future published versions before citation or redistribution.

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 permits sharing, reuse, and adaptation, 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 - Human Data.
DANDI Archive.
https://dandiarchive.org/dandiset/001278

Please also cite related LINC publications and preprints listed on the DANDI page, including work describing multi-dimensional diffusion MRI for mapping axonal architecture and microstructure in the primate brain.

Contact

DANDI contact:

Kabilar Gunalan

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

Note

This repository is currently marked by DANDI as under review by NIH for potential modification in compliance with U.S. federal Administration directives. Users should verify the current DANDI record before downloading, citing, or redistributing derived data.

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