SoftwareMRI SequenceDICOM anonymize
- DICOM Cleaner: free web-based DICOM patient info remover with lots of customized options.
DICOM viewer
- Horos: free DICOM viewer similar to OsirisX (macOS)
Convert image format- MRI Convert: converting DICOM on Bruker ClinScan/Siemens Trio to Analyze (*.img) or Nifti (*.nii) format.
- Bru2Nii: convert Bruker 2dseq to Nifti format.
- dcm2nii: convert DICOM to Nifti.
- fdf2img.m: converting Varian FDF format to Analyze.
- readVarianInfo.m: read Varian data acquisition info from procpar file.
- c3d_affine_tool: convert transformation matrix from FSL to ITK format used by ANTs (part of Convert3D)
Data Pre-Processing- Brain extraction:3D PCNN for rodent brain
- RATS: rodent brain extraction by university of Iowa.
- BEaST (Brain Extraction based on nonlocal Segmentation Technique)
- PhsIO: toolbox for physiological artifact removal.
- MRI Denoising: Very powerful package including various denoise methods for MRI (only for .nii (not .nii.gz) format). A DTI denoise tool is here.
- SLOMOCO: slice-by-slice motion correction. Would be useful for multiband.
- HD-BET: Machine-learning-based human brain extract.
fMRI Analysis
- FACT: Functional MRI Analysis and Clustering Tools
- Other extension tools for FSL, including real-time fMRI, network analysis, etc.
- BrainVoyager: the best commercial package; support realtime feedback
- NeuroLens (Mac OS X only)
- Aedes: Matlab-based versatile GUI tool for fMRI, rsMRI, ASL, T1/T2 fitting, etc. Natively support Bruker 2dseq format.
- Physiological Artifact Removal Tool
Image Analysis/ProcessingMorphometry- MouseMorph: Mouse VBM tool developed by Centre for Advanced Biomedical Imaging in UCL.
- CAT (Computational Anatomy Toolbox): VBM, DBM and surface-based morphometry toolbox for SPM developed by U of Jena.
- CBS High Res Brain Processing Tools: MIPAV plugins for high-res 7T human data (by Max Plank Institute for Human Cognitive and Brain Sciences)
ASL- SCORE for outlier removal (need to download an example data with outlier clean up).
- ExploreASL: A pipeline used in several multi-site studies. Very detailed document online.
- Vandpire ASL: More suitable for individual analysis.
- Oxford ASL: Part of FSL Basil package, includes partial volume correction.
MRI-PET- VINCI: designed for PET neuroimage with MRI-PET coregistration
- Carimas: PET kinetic modeling & cardiac analysis developed by Turku PET Center, Finland
- JIP Toolkit: Designed for rodent & monkey fMRI-PET analysis, including PET modeling with drug challenging.
Multi-purpose package- BioImage Suite: very comprehensive package for functional and dynamic image analysis
- DPTools: fMRI, DTI, flow, permeability analysis & statistics package
- ImageJ: general purpose tool with lots of plugins
- MIPAV: general purpose loaded with lots of processing tools like registration
- SPIN: process SWI, PWI, DCE, MRA
- 3DMed & MITK: extend ITK for medical image segmentation, registration, visualization
- VivoQuant: commercial package by INVICRO
- OsiriX: DICOM viewer, 3D visualization, support PACS (but Mac only)
Visualization and ROI analysis- AMIDE: the best tool for multi-dataset and multi-modality image display and ROI analysis
- MRIcro: easy tool especially for DICOM and converting formats
- 3D slicer: the best free 3D rendering and visualization tool
- VolView: free version of a commerical 3D visualization software for medical imaging
DCE-MRIPlugins for ImageJ, OsiriX
- DCE-MRI analysis with T1w contrast: TOPPACT plugin (using simplified linear approximation of Kety model)
- DSC-MRI analysis with T2w contrast: DSCoMAN
- DCE-MRI: OsiriX plugin
- UMMPerfusion: OsiriX plugin by University Medical Centre Mannheim
DCE MRI analysis toolboxes for Matlab, R, IDL
- R Package for the Analysis of DCE-MRI (run under statistical package R); blog
- DATforDCEMRI: Deconvolution Analysis Tool for DCE (also needs R)
- COMKAT (COmpartment Model Kinetic Analysis Tool): a Matlab tool for PET kinetic analysis and potentially for DCE-MRI.
- DCE@urLAB: DCE & Pharmacokinetic Analysis Tool for Preclinical Data
- Perfusion Mismatch Analyzer (PMA): Brain DSC perfusion MRI and diffusion for stroke by ASIST-Japan.
- Dynamika: free academic license
- ImageJ plugins
- MRI Processor (provide T1 and T2 fitting using Levenberg–Marquardt or Simplex algorithm)
- MRI Analysis Calculator (T1, T2, perfusion, diffusion calculation)
- MRI t2 Calculations (only simple 2 points T2 fit)
- QuickVol II pluginMRI & fMRI analysis (including T1 mapping of IR data)
- Varian data
- T1 fit of FSE-IR-T1map
- T1 fit of Look-Locker-T1map
- T2 fit of MEMS-T2map
- ClinScan data
- T1 fit of multi-scan IR-SE
- T2 fit of multi-echo SE
Cardiac AnalysisQSM- QSM (Matlab)
- Regularized susceptibility mapping (Matlab)
- Quantiphyse: tool for CEST, DCE-MRI and ASL by Oxford.
Network & connectivity analysisMIBCA multimodality brain connectivity analysis toolbox and pipeline
Structural connectivity (DTI Analysis)- DTI Studio -- by Susumu Mori's lab at Johns Hopkins Univ.
- DSI Studio -- Includes DTI, DSI, Q-ball reconstruction and fiber tracking; by Isaac Tseng's lab at National Taiwan Univ
- ExploreDTI -- Include nice motion correction method.
- Camino -- comprehensive tools by UCL but no integrated GUI package.
- TrackVis -- cross-platform
- MRTrix -- includes tract density imaging and tract-based analysis
- TORTOISE -- DTI processing pipeline by NIH, including various tools for artifact correction
- Large-scale Granger causality toolbox for voxel-wise analysis
- Structural Equation Modeling (SEM) for fMRI (Matlab)
- Onyx: Java-based SEM analysis with easy to use GUI
- SmartPLS: path modeling using partial least squares (PLS) method
- LISREL: Commercial SEM analysis software (Student version is free)
- REST -- Resting-state fMRI analysis toolkit & pipeline
- DPABI -- SPM-based integrated toolkit. Include template for Rat and Rhesus Macaque. Doesn't have extensive tool for data cleanup.
- CONN -- artifact removal, correlation matrix, graph analysis
- Network ROI for seed-based analysis -- by Mike Greicius's lab in Stanford
- Functional parcellation -- by Thomas Yeo in NUS
- DynamicBC -- dynamic functional connectivity and effective connectivity analysis
- C-PAC -- Very comprehensive and highly configurable pipeline for the analysis of Connectomes
- Spatiotemporal pattern analysis -- by U Sydney.
- Brain connectivity toolbox -- network measure, visualization, etc.
- BrainCAT -- combine DTI and rsMRI (Mac OSX only)
- GRETNA -- graph theory analysis for rsMRI data.
- Cytoscape -- general purpose network visualization tool.
- BRAPH -- Brain Analysis using Graph Theory
Connectivity-based brain parcellation
- pyClusterROI -- tools by Craddock for his paper on HBM 2011
- SLIC whole brain parcellation toolbox -- include methods used in several papers
Statistical Mapping
- Correct with False Discovery Rate
Machine Learning
- U-Net: convolutional network for image segmentation and other processing.
Optical tomography- Molecular Optical Simulation Environment
MRS- Gannet: GABA 1H-MRS analysis and other useful tips, review.
- TARQUIN: 1H-MRS analysis for in vivo & ex vivo data. Come with simulator of metabolites.
- INSPECTOR: Matlab-based and quite user friendly. Supports Varian, Bruker, GE, Siemens, Philips format.
- SIVIC: Cross-platform MRS and CSI tool. Supports DICOM and native formats of Varian, GE, Siemens and Philips.
MRI simulation, reconstruction
- MRILab: simulate the signal formation, k-space acquisition and image reconstruction.
- Fast Imaging Library: C library and Matlab toolbox for reconstruction of parallel imaging, UNFOLD, EPI ghost correction, etc.
- Michigan Image Reconstruction Toolbox: iterative recon tool, NUFFT, spectral-spatial pulse design, etc, from Jeff Fessler's lab.
- Lead-DBS: simulate, analysis and visualization toolbox for Deep Brain Stimulation
- VirtualBrain: use structural connectivity to simulate the whole brain neural dynamics
PET- CapAIBL (Computational Analysis of PET from AIBL): Automated brain surface projection of amyloid PET scan
- COMKAT (compartment model kinetic analysis tool)
Misc- deploypcode: useful tool to create p-code together with help for Matlab codes
Repository of Medical Imaging Software- NITRC: source for neuroimaging tools and resources
- NA-MIC: National Alliance for Medical Image Computing funded by NIH
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