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