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Automatic labeling of vascular structures with topological constraints via HMM [Research data]

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dc.contributor.author Wang, Xingce
dc.contributor.author Liu, Yue
dc.contributor.author Wu, Zhongke
dc.contributor.author Mou, Xiao
dc.contributor.author Zhou, Mingquan
dc.contributor.author González Ballester, Miguel Ángel, 1973-
dc.date.accessioned 2017-10-05T09:44:07Z
dc.date.available 2017-10-05T09:44:07Z
dc.date.issued 2017-06-15
dc.identifier.uri http://hdl.handle.net/10230/32858
dc.description ##Compile environment Windows 7(64-bit) Intel(R) Core(TM) i7-4790 CPU @ 3.6GHz RAM: 8.00GB Microsoft Visual Studio 2012 Python 2.7 Anaconda 4.1.0 (64-bit) XGBoost Library 0.4 (https://github.com/dmlc/xgboost/tree/master/windows) Scikit-Learn Library 0.18.1 hmmlearn 0.2.0 NURBS open-source library ## Running the code This file contains a summary of what you will find in each of the files that make up our experiments.. Step0: PreprocessingData Our proposed approach has been evaluated on the public dataset distributed by the MIDAS Data Server at Kitware Inc.. It contains 50 MRA images of the cerebral vasculature from healthy volunteers together with theirs segmentations and centerlines. (Bogunović et al. "Anatomical Labeling of the Circle of Willis Using Maximum A Posteriori Probability Estimation." IEEE Transactions on Medical Imaging 32(9) (2013):1587) We first prune the centerline model to a region around the CoW. “FeatureGenerating/data/skeleton”. Step1: FeatureGenerating(C/C++): To generate a feature matrix “FeatureGenerating/feature” from the skeleton data “FeatureGenerating/data/skeleton” that has been marked with Ground Truth“FeatureGenerating/data/cood.txt”. We employed the NURBS curve with features calculate available in NURBS open-source library. To compile the code, you also need to include the library. Step2: Pre_ML (C/C++): To Separate feature matrix “FeatureGenerating/feature” into the training set “data/ML/XXX/train.txt” and corresponding test set “data/ML/XXX/test.txt”. Step3: XGBoost(Python): To train model based on the training set in “data/ML”, and predict the results ”data/res_XGBoost” of corresponding test set. To compile the code, you also need to include the XGBoost library. Step4: Chain(C/C++): To “sort” the bifurcation and construct observation sequences “data/obs_list” and status sequences “data/GT_list” based on the results of XGBoost. Step5: Pre_HMM(C/C++): To generates 50 sets of observation matrices “data/obs” and transfer matrices “data/trans” based on observation sequences and state sequences. Row 1 in “seg/XXX” is the sequence of state, and Row 2 in “data/seg/XXX” is its corresponding sequence of observations. Step6: HMM(Python): Hidden Markov Process. Input:”data/seg/XXX”, “data/obs”, “data/trans” In the file “data/res_topo”, Row 1 is the results, and Row 2 is its corresponding Ground Truth. To compile the code, you also need to include the hmmlearn library. Step7: Result analysis: Metrics. In the file”data/matrix_XGBoost”and ”data/matrix_topo”, the first part is TP, FN, FP, TN value, the second part is A, P, R, S value, the last part is the confusion matrix.
dc.description.abstract The project contains the implementation of the method described in: Wang et al., "Automatic labeling of vascular structures with topological constraints via HMM", MICCAI 2017. We propose a novel graph labeling approach to anatomically label vascular structures of interest. Our algorithm can handle different topologies, like circle, chain and tree. By using coordinate independent geometrical features, it does not require prior global alignment.
dc.description.sponsorship This research was partially supported by the Chinese High-Technical Research Development Foundation (863) Program (No.2015AA020506), Beijing Natural Science Foundation of China(No.4172033), the Spanish Ministry of Economy and Competitiveness, through the Maria de Maeztu Programme for Centres/Units of Excellence in R&D (MDM-2015-0502), and the Spanish Ministry of Economy and Competitiveness (DEFENSE project, TIN2013-47913-C3-1-R).
dc.language.iso eng
dc.publisher Universitat Pompeu Fabra
dc.relation Publicació relacionada: Wang X, Liu Y, Wu Z, Mou X, Zhou M, González Ballester MA, Zhang C. Automatic labeling of vascular structures with topological constraints via HMM. Paper presented at: 20th International Conference on Medical Image Computing and Computer Assisted Intervention 2017 (MICCAI 2017); 2017 Sept 10-14; Quebec, Canada. [8 p.]. http://dx.doi.org/10.5281/zenodo.809931 http://hdl.handle.net/10230/32858
dc.relation.isreferencedby http://hdl.handle.net/10230/32744
dc.rights Aquest material està subjecte a una llicència de Creative Commons (Attribution-NonCommercial 4.0)
dc.rights.uri https://creativecommons.org/licenses/by-nc/4.0/
dc.title Automatic labeling of vascular structures with topological constraints via HMM [Research data]
dc.type info:eu-repo/semantics/other
dc.type Dataset
dc.identifier.doi http://dx.doi.org/10.5281/zenodo.809931
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/TIN2013-47913-C3-1-R
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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