Resource

MRI Sequence

• Look-Locker T1 mapping sequence
• HARDI q-table
• MP-RAGE simulator

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.

Data Pre-Processing

• Brain extraction: 3D PCNN for rodent brain
• RATS: rodent brain extraction by university of Iowa.
• PhsIO: toolbox for physiological artifact removal

fMRI Analysis

• FACT: Functional MRI Analysis and Clustering Tools
• FSL
  • Other extension tools for FSL, including real-time fMRI, network analysis, etc.
• SPM
• 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/Processing

ASL

• Quantitative ASL processing (MGH)
  • ASL Why & How
• ASL Toolbox (U Penn)

MRI-PET

• NEUROSTAT/3D-SSP
• 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
• 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-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
• Segment
  • QSM
• SWIM
• STI (Susceptibility Tensor Imaging)
• QSM (Matlab)
• Regularized susceptibility mapping (Matlab)
  • Network & connectivity analysis
  • MIBCA multimodality brain connectivity analysis toolbox and pipeline
  • Structural connectivity (DTI Analysis)
• MedINRIA
• 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
  • Effective connectivity
• Dr Seth's Granger toolbox (Matlab)
• 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)

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
• ROI for seed-based analysis -- by Mike Greicius's lab in Stanford
• Network 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

Network analysis

• Brain connectivity toolbox -- network measure, visualization, etc.
• BrainCAT -- combine DTI and rsMRI (Mac OSX only)
• Connectome Analyzer
• GRETNA -- graph theory analysis for rsMRI data.
• Cytoscape -- general purpose network visualization tool.

Statistical Mapping

• Correct with cluster size threshold
• Correct with False Discovery Rate

Machine Learning

• Pattern Recognition for Neuroimaging Toolbox (PRoNTo)

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.
• jMRUI

MRI simulator

• MRILab: simulate the signal formation, k-space acquisition and image reconstruction.

PET

• CapAIBL (Computational Analysis of PET from AIBL): Automated brain surface projection of amyloid PET scan

Misc

• deploypcode: useful tool to create p-code together with help for Matlab codes

Repository of Medical Imaging Software

• I Do Imaging
• NITRC: source for neuroimaging tools and resources
• NA-MIC: National Alliance for Medical Image Computing funded by NIH

Neuroimaging software is used to study the brain function.

• 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.
• 3D Slicer Extensible, free open source multi-purpose software for visualization and analysis.
• Amira 3D visualization and analysis software
• Analysis of Functional NeuroImages (AFNI)
• Analyze developed by the Biomedical Imaging Resource (BIR) at Mayo Clinic.
• Brain Image Analysis Package
• BrainSuite,[1] a collection of tools for extraction of cerebral cortex, segmentation and labeling brain volumes and surfaces, and distortion correction and coregistration of diffusion data with structural MRIs.
• CamBA
• Caret Van Essen Lab, Washington University in St. Louis
• CONN (functional connectivity toolbox)
• EEGLAB
• ExploreDTI [2] is a graphical toolbox, for exploratory diffusion (tensor) MRI and fiber tractography.
• FMRIB Software Library (FSL)
• FreeSurfer
• ISAS (Ictal-Interictal SPECT Analysis by SPM)
• LONI Pipeline, Laboratory of Neuro Imaging, USC
• Mango,[3] developed at the Research Imaging Center, University of Texas Health Science Center at San Antonio
• Neurophysiological Biomarker Toolbox
• nilearn,[4] Machine learning for Neuro-Imaging in Python
• NITRC The Neuroimaging Informatics Tools and Resources Clearinghouse. An NIH funded database of neuroimaging tools
• nordicICE
• Olea Medical: Olea Sphere 3.0, a CE - marked and FDA cleared product to automatize image processing for Neuroimaging and others fields and pathologies.
• Signed differential mapping (SDM)
• The Spinal Cord Toolbox (SCT) is the first comprehensive and open-source software for processing MR images of the spinal cord.[5]
• Statistical parametric mapping (SPM)
• Brain connectivity toolbox -- network measure, visualization, etc.
• BrainCAT -- combine DTI and rsMRI (Mac OSX only)
• Connectome Analyzer
• GRETNA -- graph theory analysis for rsMRI data.
• Cytoscape -- general purpose network visualization tool.
• Dr Seth's Granger toolbox (Matlab)
  • 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
  • ROI for seed-based analysis -- by Mike Greicius's lab in Stanford
  • Network 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
  • Quantitative ASL processing (MGH)
    • ASL Why & How
    • ASL Toolbox (U Penn)
• 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
• 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
• Pattern Recognition for Neuroimaging Toolbox (PRoNTo)
• Tortoise[6] Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble. A software package is for processing diffusion MRI data
• MedINRIA
• MIBCA multimodality brain connectivity analysis toolbox and pipeline
• 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
• SWIM
• STI (Susceptibility Tensor Imaging)
• QSM (Matlab)
• Regularized susceptibility mapping (Matlab)
• 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.
• jMRUI
• MRILab: simulate the signal formation, k-space acquisition and image reconstruction.
• 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)