awesome-neuroimaging

CLI focused, regular expression based, and iteration friendly BIDS conversion pipeline from

DICOM to NIfTI converter.

Grassroots DICOM is a C++ library and CLI tool for DICOM medical files.

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

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

Reads Siemens .dat 'twix' raw data files. Python port of Philipp Ehses' Matlab tool mapVBVD.

Voxel-by-voxel arithmetic on 1D to 4D datasets. From AFNI.

Program to calculate the deconvolution of a measurement 3D+time dataset with a specified input stimulus time series. This program can also perform multiple linear regression using multiple input stimulus time series.

OpenMP parallelized

Advanced Normalization Tools includes probabilistic tissue segmentation and machine learning methods based on expert labeled data to order to maximize reliability and consistency of multiple modality image segmentation.

GUI guided analysis of simple experiment based on general linear modeling. Part of

Warping software provided by

Long-term Adolescent Brain Cognitive Development study including 1000s of longitudinal MRI scans.

AFNI's

Tutorials and videos about neuroimaging analysis from start to finish in all the major software packages (AFNI, SPM, and FSL).

A mattermoust community of neuroimagers.

Start-to-end use cases of specific applications in neuroimaging using provenance tracking software

The Enhancing Neuro Imaging Genetics through Meta Analysis Consortium contains 50 working group's imaging and genomics data.

Analysis of Functional NeuroImages is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of multiple MRI modalities.

An image processing pipeline for fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data.

Uses fmriprep for preprocessing fMRI data and implements a variety of additional processing steps important for functional connectivity analyses such as nuisance regression and filtering.

A tractography software tool that maps brain connections and correlates findings with neuropsychological disorders.

Accessible preprocessing pipeline robust to variations in scan acquisition protocols with comprehensive error and output reporting. Input is BIDS dataset.

Legacy pipeline for maximal preprocessing.

Volumetric viewer from the AFNI suit. GUI's aesthetic defined by the '90s era Motif toolkit.

DSI viewer from the dsi-studio suit of tools.

Surface and volumetric image viewer in Freesurfer suit. Uses the QT toolkit.

Volumetric viewer from FSL.

Multi-image Analysis GUI is a viewer for medical research images for dcm, nii, surface, etc; version 4.1 released in 2019.

Volumetric viewer that works on windows.

Brain Imaging Data Structure - directory hierarchy and file naming specification.

Open-source, free and secure reproducible neuroscience analysis platform.

CBRAIN is web-based software that allows neuroimaging researchers to perform computationally intensive analyses on data by connecting them to High-Performance Computing (HPC).

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

Real-time motion monitoring for fMRI, diffusion, and navigated T1/T2 image acquisition.

A cloud-based imaging research data platform for data capture, curating, automation, and machine learning.

Validator for the Brain Imaging Data Structure.

Extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.

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

Keep code, data, containers under control with git and git-annex. Esp

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