QIICR (Quantitative Image Informatics for Cancer Research)

QIICR: open source imaging informatics tools based on 3D Slicer to support research workflows of the NCI Quantitative Imaging Network.QIICR is supported by the NIH National Cancer Institute ITCR program, award U24 CA180918. – QIICR About Page

dcmqi: DICOM for Quantitative Imaging is a free, open source library that can help with the conversion between imaging research formats and the standard DICOM representation for image analysis results – dcmqi User’s Guide, Reference Paper

QuantitativeReporting: Segmentation-based measurements with DICOM import and export of the results. – Quantitative Reporting User’s Guide

TCIABrowser: 3D Slicer module for browsing and downloading medical imaging collections from The Cancer Imaging Archive (TCIA). – TCIA Bowser’s Wiki

PETTumorSegmentation: A 3D Slicer Extension for for tumor and lymph node segmentation in PET scans: – PETTumorSegmentation Documentation

PETLiverUptakeMeasurement: An extension of 3D Slicer that allows automated measurement of liver uptake in SUV normalized whole-body FDG-18 PET scans and export to DICOM. The extension provides the automated algorithm, a GUI module for providing additonal input, and functionality to export quantification results to DICOM SEG and SR files. – PETLiverUptakeMeasurement Documentation, References (Paper 1 & Paper 2)

PETPhantomAnalysis: 3D Slicer Extension for Analysis of Uniform Cylinder Phantom PET scans – Documentation, Sample Data Set (zipped files)

atom-dicom-dump: Atom editor package for examining the content of DICOM files – ATOM DICOM Viewer

Iowa2DICOM: Scripts used for conversion of the data for the PET/CT quantitative imaging biomarker development project by the Iowa site of NCI QIN. – Reference Paper

DICOM4QI: an open demonstration and connectathon with the purpose of promoting and improving the use of DICOM for exchanging the quantitative image analysis results. – Reference, Instructions

PETDICOM: an extension of 3D Slicer that implements calculation of the Standard Uptake Value (SUV) correction for Positron Emission Tomography (PET) images. The SUV approaches implemented include: SUV body weight, SUV lean body mass, SUV body surface area and SUV ideal body weight. The extension contains three modules:

SUVFactorCalculatorCLI: a command line interface module that generates SUV factors and stores the result as a DICOM Real World Value Mapping (RWVM) object
DICOMPETSUVPlugin and DICOMRWVMPlugin: DICOM plugins that implement loading and automatic calculation of SUV for PET DICOM series, and loading of the DICOM RWVM objects, respectively.

– Wiki Documentation, Reference Paper

PET-IndiC: a 3D Slicer extension for quantifying uptake in PET. PET-IndiC is an extension of 3D Slicer that implements calculation of the various quantitative measures given the SUV-corrected PET image series, and a segmented region of interest. The measures calculated by this module include the generic summary statistics measures, such as volume and mean SUV, but also the PET-specific items such as SUV Peak, Total Lesion Glycolysis (TLG) and Standardized Added Metabolic activity (SAM). – Documentation, Reference Paper

DCMTK: DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. In particular, DCMTK includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. DCMTK is is written in a mixture of ANSI C and C++. It comes in complete source code and is made available as “open source” software. DCMTK is developed and maintained by a team located in Oldenburg, Germany, consisting of OFFIS e.V., Open Connections GmbH and J. Riesmeier.QIICR supported implementation of the new functionality into DCMTK, specifically, development of the following components:

dcmiod: a library for working with information objects and modules
dcmseg: a library for working with segmentation objects
dcmpmap: a library for working with parametric map objects
support of the DICOM TID 1500 family of templates to support structured reporting of image measurements within dcmsr: a structured reporting library and utility apps

– DCMTK Documentation, References (Paper 1 & Paper 2)

DICOM4MICCAI: Tutorial online GitHub material at the MICCAI Conference: MICCAI tutorial webpage