Software Open Access

neurodata/ndmg: Stable ndmg-DWI Pipeline Release

Greg Kiar; Eric Bridgeford; William Gray Roncal; Vikram Chandrashekhar; Disa Mhembere; Randal Burns; joshua vogelstein

Main Package Features

  • One-click pipeline for structural connectome estimation from DWI and T1w images
  • Leverages Dipy, Plotly, Nilearn, FSL, Networkx, and others
  • Supports several command-line APIs, including the BIDS app specification
  • Has session- and group-level analysis, performing connectome estimation and summary statistic computation, respectively
  • Session-level analysis generates 1mm resolution connectomes across 25 parcellations ranging in size from 48 to 72,000 nodes, all in MNI152 standard space.
  • Direct interfaces with Amazon Web Services for batch processing of data stored in the cloud.
  • Public repository of connectomes available at http://m2g.io

For more information, please see the README of this repository.

Install Instructions

pip install ndmg* * once FSL is installed

OR

Available through Docker, with: docker pull bids/ndmg:v0.1.0. Container is compatible with Singularity 2.4.1, though pulling from Singularity Hub is not currently available for this pipeline.

Usage Instructions

Through the BIDS app interface, ndmg can be used as follows:

ndmg_bids bids_directory output_directory {session, group} [--participant_level []] [--session_level []]

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