The Computational Environment for Radiological Research (CERR)
作者來(lái)自紐約大學(xué)念逞、劍橋大學(xué)挠乳，發(fā)表在medical physics
目的：醫(yī)學(xué)圖像量化分析残吩，包含數(shù)據(jù)導(dǎo)入、transformation，management窿撬，feature calculation, image segmentation, and visualization. 所有的 radiomics 計(jì)算被向量化獲得加速蔗草。此外a test suite is provided for reconstruction and comparison with radiomics features computed using other software platforms such as the Insight Toolkit (ITK) and PyRadiomics咒彤。
一些用于影像組學(xué)的開(kāi)源軟件
- ITK
- PyRadiomics, extract radiomics with a plugin for 3D Slicer, 缺乏the calculation of radiomics maps and DICOM-RT input of anatomical structures.
這些都是radiomics library而不是integrated platform
CERR旨在克服上述工具的缺陷，它提供了tests for its radiomics features against other open-source software咒精，同時(shí)也compute higher-order texture features using vectorized implementations镶柱，產(chǎn)生了顯著的加速。用純matlab開(kāi)發(fā)模叙，making it agnostic to the operating system and MATLAB versions.
1. Architecture
CERR關(guān)鍵的六大功能
- import imaging data with standard formats using different modalities歇拆，支持RTOG, DICOM, MHA, NRRD, NIfTI and XML
- delineate and import segmentations for radiomics calculation
輪廓工具包含鉛筆，刷子范咨，橡皮和active contour-based refinement models 以及 Boolean arithmetic to derive new structures from existing ones（比如取并集/交集）故觅。The segment labeler tool可以很方便的讓用戶(hù)graphically score 自動(dòng)分割結(jié)果的不同部分。 - define important parameters for radiomics calculation
- visualize and compare the resulting radiomics maps
- derive and store radiomics values along with imaging data
把原圖跟基于原圖的分割結(jié)果湖蜕、影像學(xué)特征存儲(chǔ)在一起逻卖，simplify the bookkeeping. CERR’s radiomics can be called from other applications by just passing the matrices for the image and the labels. - export the resulting radiomics scalars or maps to any other analysis software
2. Radiomics maps and pre-processing filters
- 快速計(jì)算Haralick, Law's and first-order statistical radiomics
- 預(yù)處理濾波器：wavelet, sobel, gabor and Laplacian of Gaussian
- 圖像插值到用戶(hù)指定的分辨率
- MR偏移場(chǎng)矯正 （李純明老師MICO）
Moreover, CERR’s data structure provides convenient access to images and associated metadata, making it straightforward for users to define custom normalizations or use filters from libraries such as ITK and MATLAB image processing toolbox。
3. Scalar radiomics (6個(gè))
(i) First-order/histogram statistics, (ii) Intensity-volume histogram, (iii) Peak/Valley昭抒，(iv) Shape, (v) Size, and (vi) Texture评也。
位大形變
Scalar texture
- 灰度共生矩陣；
- Neighborhood grey tone difference
- Neighborhood grey level dependence
- Run length
- Size zone
可以2D/3D計(jì)算灭返，特征可以被存儲(chǔ)在matlab的數(shù)據(jù)結(jié)構(gòu)或者輸出到一個(gè)CSV文件中盗迟。
