Useful Programs & Utilities🔗

Tabulated Data🔗

NBDCtools
NBDCtools is an R package for creating custom, analysis-ready datasets by simply specifying the variable and/or table names you need. The package automatically retrieves the specified columns from locally downloaded HBCD tabulated data and assembles them into a single in-memory data frame, minimizing storage and memory use. This provides a flexible alternative to building datasets through the Lasso or DEAP platforms, eliminating the need to manually parse files or resolve formatting issues. In addition to dataset assembly, NBDCtools includes functions for working with shadow matrices as well as applying transformations and filters.
Download page for NBDCtools

Brain Imaging Data🔗

Interactive Visualization of Volumetric NIfTI (.nii.gz) files (e.g. T1w, T2w, DTI, etc.)🔗

ITK-Snap
A free, open-source software application used to visualize and segment 3D and 4D medical images. See an overview of ITK-Snap on Andy's Brain Blog here for a primer.
Download page for ITK-Snap

FSLeyes
A free, open-source image viewer for medical images, particularly MRI data. Part of the FSL software suite.
Download page for FSLeyes

Interactive Visualization & Processing of Surface Data🔗

Connectome Workbench is a free, open-source software package particularly useful for visualizing connectivity data, surface-based analyses, and more. It is recommended for viewing and processing surface data (.gii files), volume data (.nii/.nii.gz files), and CIFTI data (dlabel, dscalar, dtseries, pconn, etc. files) - check out this blog post for a helpful primer on the difference between these various file formats. Useful Workbench tools include wb_view and wb_command.
Download page for Connectome Workbench

wb_view
Good for: interactive visualization
An interactive GUI used for inspecting images, particularly useful for visualizing surface-based data. It allows users to view and manipulate 3D brain images, including the ability to rotate, zoom, and pan the images. It also provides tools for overlaying different types of data, such as functional and structural images, and for visualizing connectivity data.

wb_command
Good for: processing & analysis
A command-line tool that provides a variety of functions for processing and analyzing neuroimaging data. It can be used to perform a wide range of tasks, including image registration, surface generation, and statistical analysis. The command-line interface allows for batch processing of data and can be integrated into scripts for automated analysis.

Programming Languages🔗

MATLAB
MATLAB has a variety of built-in functions and toolboxes for neuroimaging data. Note that it is proprietary, but may be provided at no-cost through your institution or department. See Andy's Brain Blog Matlab for Neuroimagers for a primer.

Python
Python is also commonly used in the field of neuroimaging: useful Python modules for neuroimaging include NiBabel, Nilearn, Nipype, PyNIfTI, PySurfer, PyTorch, and others. See Andy's Brain Blog Python for Neuroimagers for a primer.

R/RStudio
Especially strong for statistical plots, often used in conjunction with analysis results.
Download page for R/RStudio

Electroencephalography Data🔗

The EEG Core of the HBCD Data Coordinating Center (HDCC) has developed some helpful tools for extracting summary statistics and trial measures from HBCD EEG release data. We encourage all users to explore these resources at the HBCD EEG Utilities website.