AFNI

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

freeview

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

fsleyes

Volumetric viewer from FSL.

mricron

Volumetric viewer that works on windows.

dsistudio

DSI viewer from the dsi-studio suit of tools.

osirix

DICOM database organizer and viewer.

Mango

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

`wb_view`

Connectome workbench surface file viewer.

reproIn

Naming exam card sequences.

BIDS

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

PACS

Picture Archiving and Communication System standard used to store and transfer DICOM images from medical equipment and likely implemented by scanner manufacture. See [Siemens Healthineers Syngo Carbon](https://www.siemens-healthineers.com/en-us/digital-health-solutions/syngo-carbon), [Phillips Vue PACS](https://www.documents.philips.com/assets/20240227/5a788a79bbdd4e1986f1b12300b0e534.pdf), [GE HealthCare True PACS](https://www.gehealthcare.com/products/healthcare-it/true-pacs).

XNAT

An extensible open-source imaging informatics software platform dedicated to imaging-based research.

LORIS

LORIS (Longitudinal Online Research and Imaging System) is web-based data and project management software for neuroimaging research studies.

brainlife.io

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

cbrain

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

FIRMM

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

`Dimon`

Monitor real-time acquisition of DICOM image files with AFNI.

MRIQC

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

mrQA

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

bids-validator

Validator for the Brain Imaging Data Structure.

AFNI

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.

FSL

A comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.

SPM

Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.

Qu|Nex

The Quantitative Neuroimaging Environment & Toolbox (QuNex) is an open-source software suite that collectively supports an extensible framework for data organization, preprocessing, quality assurance, and analyses across neuroimaging modalities.

fmriprep

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

`afni_proc.py`

Best practice pipelines with pre-configured blocks using AFNI.

HALFpipe

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

XCP-D

Post-processing and noise regression pipeline picks up right where fMRIprep ends.

clpipe

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.

fmri_processing_scripts

Legacy pipeline for maximal preprocessing.

HCP Pipeline

Pipeline scripts implement the Minimal Preprocessing Pipeline (MPP) described in [Glasser et al. 2013](http://www.ncbi.nlm.nih.gov/pubmed/23668970).

dsi-studio

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

qsiprep

Configures pipelines for processing diffusion-weighted MRI (dMRI) data.

Freesurfer

An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.

CIVET

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

dcm2niix

DICOM to NIfTI converter.

heudiconv

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

gdcm

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

`pydicom`

Python package and cli tool for inspecting, modifying, and creating DICOM files.

`dcmdirtab`, `dcmtab_bids`

CLI focused, regular expression based, and iteration friendly BIDS conversion pipeline from [lncdtools](https://github.com/lncd/lncdtools/).

pymapVBVD

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

med2image

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

make

follow script recipes defined in `Makefile`.

datalad

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

`3dNotes`

A program to add, delete and show notes for AFNI datasets.

`niinote`

Add AFNI nifti XML history to header to run and record any command. Part of [lncdtools](https://github.com/lncd/lncdtools/).

optibet

Shell script to combine afni and fsl tools for more robust skull stripping in patient populations.

`3dSkullStrip`

[AFNI](https://afni.nimh.nih.gov/)'s skull stripping utility with many parameters.

`bet`

[FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)'s brain extraction tool.

`antsBrainExtraction.sh`

[ANTs](http://stnava.github.io/ANTs/) version.

`mri-watershed`

Part of the [Freesurfer](https://freesurfer.net/) pipeline.

ROBEX

Robust Brain Extraction without parameter tweaking.

ANTs

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.

3dQwarp

OpenMP parallelized [AFNI](https://afni.nimh.nih.gov/) tool to compute a nonlinearly warped version of source dataset to match a base dataset.

flirt, fnirt

Warping software provided by [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) tools.

templateflow

A modular, version-controlled resource that allows researchers to use templates "off-the-shelf" and share new ones.

MNI152

Unbiased standard magnetic resonance imaging template brain volume for normal population.

3dcalc

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

fslmaths

Simple but powerful program to allow mathematical manipulation of images. From FSL.

fscalc

Freesurfer wrapper of fslmaths.

3dDeconvolve

[AFNI](https://afni.nimh.nih.gov/) - 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.

FEAT

GUI guided analysis of simple experiment based on general linear modeling. Part of [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki).

lcmodel

Implements linear-combination modeling of magnetic resonance spectroscopy data.

FSL-MRS

A suite of tools for MR Spectroscopy, including single voxel (SVS), MRS imaging (MRSI), functional MRS (fMRS), diffusion MRS (dwMRS), edited spectroscopy, etc.

Osprey

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

`fooof`

Fast, efficient, and physiologically-informed tool to parameterize neural power spectra.

hurst

Algorithm to assess intrinsic excitation-inhibition imbalance in MR ([Trakoshis et al, eLife, 2020](http://doi.org/10.7554/eLife.55684)).

tat2

Time-averaged T2* wrapper script using AFNI binaries from [lncdtools](https://github.com/lncd/lncdtools/).

nipy

Includes `nibabel`, `nipype`, and `nilearn`.

oro.nifti

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

SPM

Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.

`imtool3D_td`

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

Andy's brain blog

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

DataLad handbook

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

Hitchhacker's guide to the brain

Notes from study planning to reporting and data sharing by way of acquisition, processing, analysis, and quality control.

Online Neuroimaging Resources

A laundry list of online resources for MRI, fMRI, EEG, MEG.

U of A: Neuroimaging Core Documentation

Documentation for approaches used and/or developed by the neuroimaging core at the University of Arizona.

neurostars

General neuroimaging `discuss` form. `fmriprep` suggested Q&A site.

afni discuss

AFNI's `discuss` instance.

brainhack

A mattermoust community of neuroimagers.

openneuro

A free and open platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG, and iEEG data.

NDA

National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains.

NITRC

NeuroImaging Tools & Resources Collaboratory library of neuroinformatics software and data.

ABCD

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

UK Biobank

A large-scale biomedical database and research resource with 500,000 research participants.

NCANDA

National Consortium on Alcohol and Neurodevelopment in Adolescence (4000+ MR visits).

PNC

A population-based sample of over 9500 individuals from the greater Philadelphia area, ages 8-21 years who received medical care at the CHOP network.

ENIGMA

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