Software

MRI Sequence

• • Look-Locker T1 mapping sequence

  • Multiband EPI for preclinical MRI scanner

  • HARDI q-table

  • MP-RAGE simulator

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

• • 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

  • 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

• • Quantitative ASL processing (MGH)

    • ASL Why & How

  • ASL Toolbox (U Penn)

    • ASLtbx forum

      • 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

• • 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)

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)

• • 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

  • TORTOISE -- DTI processing pipeline by NIH, including various tools for artifact correction

Effective connectivity

• • Dr Seth's Granger toolbox (Matlab)

  • 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)

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)

  • Connectome Analyzer

  • GRETNA -- graph theory analysis for rsMRI data.

  • Cytoscape -- general purpose network visualization tool.

  • BRAPH -- Brain Analysis using Graph Theory

Visualization

• • BrainNet Viewer

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

• • Correct with cluster size threshold

  • Correct with False Discovery Rate

Machine Learning

• • Pattern Recognition for Neuroimaging Toolbox (PRoNTo)

  • 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.

  • jMRUI

  • 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.

  • FSL-MRS: easy to use tool integrated as part of FSL.

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 & 3D visualization

• • 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

  • BrainRender: display cellular data in Allen Brain.

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

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

  • COMKAT (compartment model kinetic analysis tool)

Electrophysiology

• FieldTrip

• 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

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