Software
MRI Sequence
Image format
DICOM
DICOM Cleaner: free web-based DICOM patient info remover with lots of customized options.
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)
BrkRaw: Python-based Bruker raw data viewer and converter
MINC Toolkit: convert .mnc format to Nifti.
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 trained by multi-contrast (T1w, FLAIR, T2w, etc) normal and disease brain.
Tips: After install, download the model directly from Zenodo and copy to ~/hd-bet_params
Elastix: Very powerful and accurate motion correction. Works well even with contrast enhanced signal change.
fMRI Analysis
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.
LayNII: Layer fMRI analysis tool
TAPAS (Translational Algorithms for Psychiatry-Advancing Science): classification, effective connectivity (parallel DCM, rDCM) tools.
Image Analysis/Processing
Morphometry
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.
High-resolution anatomical MRI
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.
Open Science Initiative for Perfusion Imaging: include collection of current software, library, standardization, etc.
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)
OsiriX plugins
Visualization and ROI analysis
DCE-MRI
Plugins 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
Standalone package
Perfusion Mismatch Analyzer (PMA): Brain DSC perfusion MRI and diffusion for stroke by ASIST-Japan.
Dynamika: free academic license
T1 and T2 fitting
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 plugin MRI & 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 Analysis
QSM
CEST
Quantiphyse: tool for CEST, DCE-MRI and ASL by Oxford.
Network & connectivity analysis
MIBCA 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
Effective connectivity
Large-scale Granger causality toolbox for voxel-wise analysis
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)
Functional connectivity (Resting-state)
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
rsHRF -- Blind deconvolution of resting-state HRF from BOLD
Network analysis
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
PyBASC -- Bootstrapped Analysis of Stable Clusters for functional parcellation
Statistical Mapping
Machine Learning
U-Net: convolutional network for image segmentation and other processing.
Optical tomography
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.
Histology co-registration
QuickNII: matching serial histology to Allen Brain Atlas.
HistoloZee: matching histology to MRI
Mapping Histological Slice Sequences to the Allen Mouse Brain Atlas without 3D Reconstruction
Brain simulator and stimulation
Lead-DBS: simulate, analysis and visualization toolbox for Deep Brain Stimulation
VirtualBrain: use structural connectivity to simulate the whole brain neural dynamics
PET
Electrophysiology
FASST (fMRI Artefact rejection and Sleep Scoring Toolbox): for EEG-fMRI analysis, including MRI artifact removal in EEG data
Misc
deploypcode: useful tool to create p-code together with help for Matlab codes