Awesome Neuroimaging — Project Awesome

Acquisition

Management

DAX 28 updated 2d ago

Distributed Automation for XNAT: use containerization w/YAML defined input/output.

Quality Assurance and Checking

mrQA 14 updated 1y ago

Tools for quality assurance in medical imaging datasets, including protocol compliance.

bids-validator 35 updated 7d ago

Validator for the Brain Imaging Data Structure.

Pipelines

BOLD

HALFpipe 119 updated 2d ago

User-friendly software that facilitates reproducible analysis of fMRI data.

fmri_processing_scripts 4 updated 2mo ago

Legacy pipeline for maximal preprocessing.

Raw Data

dcm2niix 1.1k updated 4mo ago

DICOM to NIfTI converter.

heudiconv 276 updated 2mo ago

A flexible DICOM converter for organizing brain imaging data into structured directory layouts.

med2image

Python CLI tool for generating jpg or png images from DICOM or nifti files.

Imaging Tools

Modeling

tat2 1 updated 9d ago

Time-averaged T2* wrapper script using AFNI binaries from lncdtools.

lcmodel 14 updated 3mo ago

Implements linear-combination modeling of magnetic resonance spectroscopy data.

Osprey 92 updated 6d ago

An all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data.

hurst (archived)

Algorithm to assess intrinsic excitation-inhibition imbalance in MR (Trakoshis et al, eLife, 2020).

Provenance and Automation

datalad

Keep code, data, containers under control with git and git-annex. Esp datalad run --input=... --output=....

Libraries

R

oro.nifti 2 updated 1y ago

Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.

MATLAB

imtool3D_td 48 updated 1y ago

3D Image Viewer with ROI tools for Matlab (NIFTI viewer, Manual segmentation).

Neuroimaging

Contents