推奨する書籍やWebページ

アイディアを形にする力（医療技術を生みだすために必要な思考プロセス）

• BIODESIGN

フリー教材

• Kaggle micro cources

• edX

• FutureLearn

• Khan academy

DICOM

• Digital Imaging and Communications in Medicine (DICOM): A Practical Introduction and Survival Guide 2nd ed. 2012 Edition

• JIRA：DICOMの世界（http://www.jira-net.or.jp/dicom/dicom_data_01.html）

医用画像処理/解析

• Pythonによる医用画像処理入門

• 新・医用放射線科学講座医用画像工学

• よくわかる医用画像工学

• 医用画像情報学 (診療放射線技術選書)：国家試験対策向け

• NEQ/DQE, MTF, ROC：新潟大学医学部保健学科

• Practical Imaging Informatics: Foundations and Applications for PACS Professionals

• Insight into Images: Principles and Practice for Segmentation, Registration, and Image Analysis

• 画像再構成法：篠原 広行先生のエクセルで学ぶシリーズ

• SlideShare：いろんなスライドが公開されているので検索してみて下さい

モダリティの基本

• Introducing MRI：youtube：https://www.youtube.com/watch?v=35gfOtjRcic

• MRI sequence and spin：youtube：https://www.youtube.com/channel/UCvO6D70am8_hVvMlIJNdPcQ

• edX：Biomedical Imaging Introduction

• X-ray physics：http://xrayphysics.com/index.html

ファントム解析

• RSNA QIBA：DRO

• PET標準化

• CT画像処理：JSRTで監修した教科書

• MRI画像処理：JSRTで監修した教科書

プレゼンテーションの参考

• TED

学会誌

• IEEE

• Radiology/RadioGraphics

• MII

• SIIM

• Journal of Digital Imaging

• SNM

• JSRTやRadiological Physics and Technology（JSRTの海外向け雑誌）

専門雑誌

• 画像診断

• インナービジョン

• Rad Fan

プログラミング

• ImageJプログラミング：http://wiki.cmci.info/documents/120206pyip_cooking/python_imagej_cookbook

• 東京大学・教養学部「情報」：プログラミング体験：http://hwb.ecc.u-tokyo.ac.jp/current/

• （Java）Javaプログラミング入門

• （Java）Eclipse完全攻略

• （Java）Javaコード入門：http://java-code.jp/

• Bio-medical Imaging in Java：http://bij.isi.uu.nl/index.htm

• 〜言語の絵本シリーズ

• （C/C++）ロベールのC++教室：http://www7b.biglobe.ne.jp/~robe/cpphtml/

• （Obj-C）Objective-C Tutorial：https://www.tutorialspoint.com/objective_c/

• （JavaScript）JavaScript tutorial ：https://www.w3schools.com/js/

• （JavaScript）初心者のためのJavaScriptプログラミング入門：http://libro.tuyano.com/index2?id=31001

• viエディタ：http://net-newbie.com/linux/commands/vi.html

• コマンドプロンプトの使い方：http://www5f.biglobe.ne.jp/ayum/command/command.html

Operating System

• Microsoft Windows：Windows

• Apple Mac：macOS

• Linux：Ubuntu, CentOS, Red Hat Enterprise Linux, Scientific Linux

• Google : Google Chrome OS

仮想OS用ソフトウェア

• Virtual box

GPU/CPU

• Intel

• Nvidia

• AMD

Sample Image Dataset

• ImageJ sample images：https://imagej.nih.gov/ij/images/

• OsiriX sample image set (takes long time for download...)

• Kobayashi's iPhone7

• JIRA DICOM data：http://www.jira-net.or.jp/dicom/dicom_data_01_02.html

• Angel Cruz-Roa Image Dataset：https://sites.google.com/site/aacruzr/image-datasets

• Mammo dataset for machine learning：https://archive.ics.uci.edu/ml/datasets/Breast+Cancer+Wisconsin+%28Diagnostic%29

• Lung CT(LIDC-IDRI) :https://wiki.cancerimagingarchive.net/display/Public/LIDC-IDRI

• MorphoSource(Bio sample model by Thematic Collections Network（TNC）:http://www.morphosource.org/

Excelで学ぶシリーズ

• はじめての人工知能：http://www.shoeisha.co.jp/book/download/1910/read

• エクセルで学ぶ画像再構成入門：http://www.iryokagaku.co.jp/frame/03-honwosagasu/373/373-dl.html

Open Source

• PyRadiomics

• MIPAV：https://mipav.cit.nih.gov/pubwiki/index.php/MIPAV:Current_events#MipavClassSchedule

• dcm4che

• dcmtk

• Open Source Physics

• OsiriX-OS(32-bit)：

• Horos: free DICOM viewer similar to OsiriX (macOS)

• GRAPHY for macOS(64-bit)：Visionary Imaging Services, Inc, free DICOM viewer similar to OsiriX (macOS)

• ITK：The ITK Software Guide Book 2: Design and Functionality（guide:https://itk.org/ItkSoftwareGuide.pdf）

• VTK：VTK User's Guide

• pydicom：http://pydicom.readthedocs.io/en/stable/getting_started.html

• MITK：http://docs.mitk.org/nightly/UserManualPortal.html

• OpenCL：

• WebGL：

• OpenGL：

• MIRT：https://web.eecs.umich.edu/~fessler/code/

• UCLA Computation Core:https://dragon.nuc.ucla.edu/

• さまざまなOpenSource.http://www.apfelkraut.org/freemedsw/

• deepmedic：https://github.com/Kamnitsask/deepmedic

• Exposure Render:https://code.google.com/p/exposure-render/

• ImageJ:http://imagej.nih.gov/ij/

• OsiriX:http://www.osirix-viewer.com/

• Fiji:http://fiji.sc/Fiji

• BoneJ:http://bonej.org/

• MeshLab:http://meshlab.sourceforge.net/

• ClearCanvas:https://www.clearcanvas.ca/

• K-PACS:http://www.k-pacs.net/

• 3D Slicer:http://www.slicer.org/

• VolView:http://www.kitware.com/opensource/volview.html

• ParaView:http://www.paraview.org/

• dicompyler:https://code.google.com/p/dicompyler/

• RT_image:http://rtimage.sourceforge.net/index.html

• Metavol:http://www.metavol.org/

• http://www.turkupetcentre.net/petanalysis/image_tools.html

• PET analysis tools:http://www.turkupetcentre.net/petanalysis/sw_pet.html

• http://www.dclunie.com/medical-image-faq/html/part8.html

• Xcode_java:https://www.youtube.com/watch?v=CmbdOfYNc3g

• phUSE:http://www.phusewiki.org/wiki/index.php?title=Standard_Script_Index

• http://www.pennstatehershey.org/web/nmrlab/resources/software

• MeVis：http://www.mevislab.de/

• SlicerRT：http://slicerrt.github.io/

• いろんな医用画像ソフト（harvard）：http://www.med.harvard.edu/JPNM/DisplayFreeware/

• PST：https://github.com/JalaliLabUCLA

• NAMIC（National Alliance for Medical Image Computing）：http://www.na-mic.org/

• Airway Inspector：http://airwayinspector.acil-bwh.org/download

• imageprocessingplace：http://www.imageprocessingplace.com/index.htm

• TensorFlow：https://www.tensorflow.org/

• OpenAI：https://gym.openai.com/

• LIBSVM：http://www.csie.ntu.edu.tw/~cjlin/libsvm/

• Weka：http://www.cs.waikato.ac.nz/ml/weka/

• STIR：http://stir.sourceforge.net/

MRIシーケンス

• 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.

• MRI Denoising: Very powerful package including various denoise methods for MRI (only for .nii (not .nii.gz) format). A DTI denoise tool is here.

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

• Quantitative ASL processing (MGH)

• ASL Why & How

• ASL Toolbox (U Penn)

• 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.

• BioImage Suite: very comprehensive package for functional and dynamic image analysis

• DPTools: fMRI, DTI, flow, permeability analysis & statistics package

• SPIN: process SWI, PWI, DCE, MRA

• 3DMed & MITK: extend ITK for medical image segmentation, registration, visualization

• VivoQuant: commercial package by INVICRO

• OsiriX plugins

• 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 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

• 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 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

  • SWIM

  • STI (Susceptibility Tensor Imaging)

  • QSM (Matlab)

  • Regularized susceptibility mapping (Matlab)

• 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

• 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

GPGPU

• • JCuda:http://www.jcuda.org/ImageJ/ImageJHowTo.html

Registration

• • http://elastix.isi.uu.nl/

Natural language processing

• • 自然言語処理100本ノック：http://www.cl.ecei.tohoku.ac.jp/nlp100/

Machine learning/Deep learning

• • scikit learn

  • Tensorflow

  • PyTorch

Genetic Algorithm

• • http://ipr20.cs.ehime-u.ac.jp/column/ga/chapter1.html