Building the overview we wish existed when we started.
| Tool | Description | Added |
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|---|---|---|---|---|---|
| Data Conversion | |||||
| dcm2niix | Converts DICOM files to NIfTI format with BIDS-compatible JSON sidecar output. | C++ | Multi-modal | ||
| HeuDiConv | Flexible DICOM-to-BIDS converter using user-defined heuristic files to handle complex naming schemes. | Python | Multi-modal | ||
| BIDScoin | DICOM-to-BIDS conversion with a GUI-configurable mapping and a plugin system. | Python | Multi-modal | ||
| ReproIn | Scanner naming convention and setup for fully automatic BIDS-ready data organization at acquisition time. | Python | Multi-modal | ||
| BIDS Validator | Checks whether a dataset complies with the BIDS specification before sharing or pipeline submission. | JavaScript | Multi-modal | ||
| Quality Control | |||||
| MRIQC | Extracts image quality metrics from structural and functional MRI and produces visual reports. | Python | Multi-modal | ||
| mrQA | Checks MRI datasets for protocol compliance and flags deviations in acquisition parameters. | Python | Multi-modal | ||
| Preprocessing | |||||
| fMRIPrep | End-to-end fMRI preprocessing pipeline with minimal user input and detailed visual QC reports. | Python | fMRI | ||
| dMRIPrep | Preprocessing pipeline for diffusion MRI following the fMRIPrep design framework. | Python | Diffusion | ||
| sMRIPrep | Structural MRI preprocessing pipeline; used standalone or as the anatomical component of fMRIPrep. | Python | Structural | ||
| Nibabies | fMRIPrep adapted for infant brain MRI, with templates and workflows suited to developing brains. | Python | fMRI | ||
| HALFpipe | Containerized fMRI pipeline wrapping fMRIPrep with smoothing, filtering, confound regression, and interactive QA. | Python | fMRI | ||
| FreeSurfer | Cortical surface reconstruction, parcellation, and cortical thickness analysis from structural MRI. | C++ | Structural | ||
| CAT12 | SPM toolbox for voxel-based and surface-based morphometry of structural MRI data. | MATLAB | Structural | ||
| FSL | Comprehensive library for analysis of fMRI, structural, and diffusion MRI data. | C++ | Multi-modal | ||
| AFNI | Suite of programs for fMRI preprocessing, regression modelling, and statistical analysis. | C | fMRI | ||
| Tedana | Multi-echo fMRI denoising — separates BOLD signal from noise using T2* decay across echo times. | Python | fMRI | ||
| FastSurfer | Deep learning-based cortical surface reconstruction and parcellation; produces FreeSurfer-compatible output in minutes. | Python | Structural | ||
| SynthStrip | Skull-stripping tool using deep learning; works across contrasts and resolutions without retraining. | Python | Multi-modal | ||
| SynthSeg | Contrast-agnostic brain segmentation via deep learning; handles any MRI contrast without fine-tuning. | Python | Multi-modal | ||
| C-PAC | Configurable Pipeline for the Analysis of Connectomes — flexible fMRI preprocessing and connectivity analysis with GUI configuration. | Python | fMRI | ||
| ASLPrep | Arterial spin labeling preprocessing pipeline from the NiPreps family, producing CBF maps and QC reports. | Python | ASL | ||
| Mindboggle | Automated brain morphometry and cortical labeling; computes shape measures from FreeSurfer and ANTs surface outputs. | Python | Structural | ||
| Nighres | High-resolution brain MRI processing tools optimized for 7T data, including laminar and columnar analysis. | Python | Structural | ||
| fMRIDenoise | Automated pipeline for benchmarking fMRI denoising strategies across multiple confound models and QC metrics. | Python | fMRI | ||
| LayNii | Layer-fMRI analysis tools for cortical layerification, columnarization, layer-smoothing, and VASO analysis. | C++ | fMRI | ||
| Registration & Normalization | |||||
| ANTs | Toolkit for deformable image registration, segmentation, and normalization of brain images. | C++ | Multi-modal | ||
| FSL FLIRT/FNIRT | FSL tools for linear (FLIRT) and nonlinear (FNIRT) brain image registration. | C++ | |||
| Templateflow | Version-controlled archive of brain MRI templates and atlases with a Python API for programmatic access. | Python | Multi-modal | ||
| Statistical Analysis | |||||
| SPM | Statistical parametric mapping framework for fMRI, PET, and voxel-based morphometry analysis. | MATLAB | |||
| Nilearn | Machine learning and statistical tools for neuroimaging data, including GLMs and multivariate decoding. | Python | fMRI | ||
| Fitlins | Estimates first-level fMRI models specified in BIDS statistical model format. | Python | fMRI | ||
| NiMARE | Python library for coordinate- and image-based neuroimaging meta-analysis, implementing ALE, MKDA, and other methods. | Python | fMRI | ||
| FSL Randomise | Permutation-based nonparametric inference for neuroimaging group-level statistics. | C++ | |||
| ENIGMA VBM | Fully automated DARTEL VBM pipeline with QC and sensitivity analyses, standardized for multi-site mega-analysis. | MATLAB | |||
| ENIGMA Toolbox | Python/MATLAB ecosystem for accessing 80+ ENIGMA working group datasets and contextualizing findings with connectomic and transcriptomic data. | Python/MATLAB | |||
| IBMMA | Image-based meta- and mega-analysis framework for mass-univariate analysis across voxel, vertex, and connectome features from multi-site data. | Python | Structural | ||
| Neuromaps | Maps brain annotations onto standard surfaces and compares them against transcriptomic and receptor reference atlases. | Python | Multi-modal | ||
| BrainSMASH | Generates spatially autocorrelation-preserving surrogate brain maps for null hypothesis testing of brain-behavior correlations. | Python | Multi-modal | ||
| PALM | Permutation analysis of linear models for neuroimaging; supports complex designs, exchangeability blocks, sign-flipping, and TFCE. | MATLAB | Multi-modal | ||
| Neurosynth Compose | Web platform for reproducible neuroimaging meta-analysis with PRISMA-guided study curation, integrated with NeuroStore. | Web | fMRI | ||
| GingerALE | Coordinate-based meta-analysis using Activation Likelihood Estimation to identify consistent activation foci across studies. | Java | fMRI | ||
| SDM-PSI | Seed-based d Mapping with Permutation of Subject Images — hybrid CBMA tool that combines coordinate and image-based data. | MATLAB | fMRI | ||
| SnPM | Nonparametric permutation testing toolbox for SPM; controls for multiple comparisons without distributional assumptions. | MATLAB | fMRI | ||
| Connectivity | |||||
| XCP-D | Post-processing pipeline for functional connectivity from fMRIPrep outputs — denoising, parcellation, and network metrics. | Python | fMRI | ||
| CONN | MATLAB toolbox for functional connectivity with seed-based, ROI-to-ROI, and ICA analysis methods. | MATLAB | fMRI | ||
| BrainSpace | Toolbox for gradient decomposition and manifold learning of functional and structural connectivity matrices. | Python/MATLAB | fMRI | ||
| nibetaseries | Beta series estimation for task fMRI connectivity using least-squares separate or least-squares all approaches. | Python | fMRI | ||
| ENIGMA Tractometry Toolbox | Standardized white matter tract-based morphometry protocol for multi-site diffusion MRI mega-analysis across ENIGMA working groups. | Python | Diffusion | ||
| Visualization | |||||
| FSLeyes | Image viewer from the FSL team for overlaying brain images, statistical maps, and atlases. | Python | Multi-modal | ||
| wb_view | Connectome Workbench viewer for surface and volume neuroimaging data, designed for HCP-style CIFTI files. | C++ | Multi-modal | ||
| Nilearn plotting | Python functions for plotting brain maps, glass brains, and statistical overlays on MRI templates. | Python | fMRI | ||
| NiReports | Visual reporting library that generates the QC HTML pages used by fMRIPrep and MRIQC. | Python | Multi-modal | ||
| ITK-SNAP | Interactive tool for segmentation of 3D medical images with manual editing and automatic active contour methods. | C++ | Multi-modal | ||
| ggseg | R package for plotting brain atlas segmentations as ggplot2 geoms, supporting cortical and subcortical parcellations. | R | Structural | ||
| MRIcroGL | GPU-accelerated volume rendering and visualization of NIfTI brain images with MIP and raycasting modes. | Pascal | Multi-modal | ||
| Workflow Managers | |||||
| Nipoppy | Manages the full neuroimaging workflow from raw data through BIDS conversion, pipeline execution, and derivative extraction. | Python | Multi-modal | ||
| Nipype | Pipeline framework wrapping FSL, SPM, FreeSurfer, and others into reproducible Python workflows. | Python | Multi-modal | ||
| Brainlife.io | Free cloud platform for running containerized neuroimaging pipelines with provenance tracking. | Web | |||
| Neurodesk | Containerized neuroimaging desktop environment with 100+ analysis tools, accessible via browser. | Docker | Multi-modal | ||
| DataLad | Distributed data management system for version-controlled datasets and reproducible analyses. | Python | Multi-modal | ||
| Clinica | Software platform for clinical neuroimaging studies, with standardized pipelines for structural, diffusion, and PET data. | Python | Multi-modal | ||
| QuNex | Integrative platform for HCP-style processing of structural, functional, and diffusion MRI across large cohorts. | Python | Multi-modal | ||
| Pydra | Next-generation dataflow engine from the NiPype team for building reproducible, scalable neuroimaging workflows. | Python | Multi-modal | ||
| Libraries | |||||
| PyBIDS | Python library for querying, loading, and writing BIDS-formatted datasets. | Python | Multi-modal | ||
| Nibabel | Python library for reading and writing common neuroimaging file formats including NIfTI, GIFTI, and CIFTI. | Python | Multi-modal | ||
| Datasets | |||||
| OpenNeuro | Free platform for sharing and downloading BIDS-formatted neuroimaging datasets; over 1,000 public datasets. | ||||
| NeuroVault | Repository for sharing unthresholded statistical brain maps from published studies. | ||||
| Human Connectome Project | High-resolution structural, functional, and diffusion MRI from 1,200 healthy adults. | ||||
| ADNI | Longitudinal MRI and PET data from participants across the Alzheimer's disease spectrum. | ||||
| OASIS | Cross-sectional and longitudinal structural brain MRI datasets for aging and dementia research. | ||||
| IXI | Around 600 structural MRI scans from healthy subjects collected at three London hospitals. | ||||
| ABCD | Longitudinal brain imaging study tracking 10,000+ adolescents across the US. | ||||
| UK Biobank | Population-level brain imaging from 100,000+ UK participants; access requires application. | ||||
| HBCD | Longitudinal study of early brain and cognitive development tracking children from birth to age ten with structural and functional MRI. | ||||
| NeuroStore | Centralized database of 30,000+ neuroimaging studies with pre-extracted activation coordinates, powering Neurosynth Compose. | ||||
| BrainMap | Curated database of neuroimaging coordinates and metadata from peer-reviewed studies; powers GingerALE meta-analyses. | ||||
| Data Discovery | |||||
| NeuroBagel | Federated search across neuroimaging datasets using semantic annotations and a common data model. | ||||
| MR-Hub | Community directory of open-source MRI reconstruction and simulation software, maintained by the ISMRM. | ||||
| NeuroStars | Q&A forum for neuroinformatics, neuroimaging methods, and tool support. | ||||
| Consortia | |||||
| ENIGMA | Global consortium for large-scale neuroimaging genetics meta-analyses spanning 80+ working groups and countries. | ||||
| ReproNim | NIH center for reproducible neuroimaging computation — training, tools, and standards. | ||||
| INCF | International Neuroinformatics Coordinating Facility — standards, training, and infrastructure for neuroscience. | ||||
| CONP | Canadian Open Neuroscience Platform — data sharing and open science infrastructure for neuroimaging research. | ||||
| OHBM Open Science SIG | OHBM special interest group advancing open sharing of ideas, data, and tools in neuroimaging. | ||||
| Standards & Protocols | |||||
| ENIGMA Protocols | Standardized imaging protocols for cortical, subcortical, DTI, and VBM analysis used across ENIGMA working groups. | ||||
| protocols.io | Platform for sharing and discovering versioned, citable step-by-step research protocols. | ||||
| Preregistration & Publishing | |||||
| OSF | Open platform for preregistration, data and code sharing, and DOI-based archiving of study materials. | ||||
| AsPredicted | Lightweight preregistration platform — answer a short fixed questionnaire to lock hypotheses before data collection. | ||||
| bioRxiv | Preprint server for biology and neuroscience; shares findings publicly before peer review. | ||||
| NeuroLibre | Reproducible neuroscience preprints with live, executable code and data embedded in the publication. | ||||
| Zenodo | Archives code, data, and posters with citable DOIs; integrates directly with GitHub releases. | ||||
| PROSPERO | International registry for preregistering systematic reviews and meta-analyses before they begin. | ||||
| Training & Events | |||||
| Neurohackademy | Summer institute in neuroimaging and data science at the University of Washington. | ||||
| OHBM Brainhack | Annual hackathon for collaborative neuroimaging projects, co-located with the OHBM annual meeting. | ||||