├── .gitignore ├── Binary ├── dcm2nii.exe ├── reg_aladin.exe └── reg_f3d.exe ├── Core ├── BFCDis.py ├── BatchDis.py ├── BetDis.py ├── BrainSegDis.py ├── DataDis.py ├── Dicom2niiDis.py ├── Feature.py ├── FeatureDis.py ├── N4Correct │ ├── N4BiasFieldCorrection.exe │ ├── N4Correct.py │ └── __init__.py ├── PostSegProcess.py ├── Readme.md ├── RegistrationDis.py ├── Report.docx ├── Report.py ├── SegmentDis.py ├── __init__.py ├── batch │ ├── __init__.py │ └── batch.py ├── bet │ ├── Bet.py │ ├── __init__.py │ ├── bet2.exe │ ├── config.py │ ├── data_loading.py │ ├── hd-bet │ ├── network_architecture.py │ ├── paths.py │ ├── predict_case.py │ ├── run.py │ └── utils.py ├── brainSeg │ ├── __init__.py │ ├── brainSeg.py │ ├── cross_train.py │ ├── model.py │ ├── models │ │ └── model9900.vrn │ ├── runSeg.py │ └── utils.py ├── dicom2nii │ ├── Dicom2nii.py │ └── __init__.py ├── hippoSeg │ ├── LiviaNet │ │ ├── .vscode │ │ │ └── settings.json │ │ ├── LiviaNet.py │ │ ├── LiviaNet3DConvLayer.py │ │ ├── LiviaSoftmax.py │ │ ├── Modules │ │ │ ├── General │ │ │ │ ├── Evaluation.py │ │ │ │ ├── GT_Img87.nii │ │ │ │ ├── Utils.py │ │ │ │ ├── __init__.py │ │ │ │ ├── label087.nii │ │ │ │ └── read.txt │ │ │ ├── IO │ │ │ │ ├── ImgOperations │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── imgOp.py │ │ │ │ ├── loadData.py │ │ │ │ ├── sampling.py │ │ │ │ └── saveData.py │ │ │ ├── NeuralNetwork │ │ │ │ ├── ActivationFunctions.py │ │ │ │ ├── __init__.py │ │ │ │ └── layerOperations.py │ │ │ ├── Parsers │ │ │ │ ├── __init__.py │ │ │ │ └── parsersUtils.py │ │ │ └── __init__.py │ │ ├── __init__.py │ │ ├── generateNetwork.py │ │ └── startTraining.py │ ├── Segmentation.ini │ ├── __init__.py │ ├── imgOp.py │ ├── liviaTest_Epoch16 │ ├── loadData.py │ ├── networkSegmentation.py │ ├── roi │ │ └── mask.nii │ ├── sampling.py │ ├── savedata.py │ ├── segment.py │ ├── startTesting.py │ └── writeini.py ├── hippoSegMedic │ ├── .gitignore │ ├── COPYRIGHT.md │ ├── LICENSE.txt │ ├── MANIFEST.in │ ├── README.md │ ├── __init__.py │ ├── config │ │ ├── deepMedic.model.ckpt.data-00000-of-00001 │ │ ├── deepMedic.model.ckpt.index │ │ ├── mask.nii │ │ ├── masks.cfg │ │ ├── modelConfig.cfg │ │ ├── output.cfg │ │ ├── test.cfg │ │ └── testConfig.cfg │ ├── deepMedicRun.py │ ├── deepmedic │ │ ├── __init__.py │ │ ├── dataManagement │ │ │ ├── __init__.py │ │ │ ├── augmentation.py │ │ │ ├── io.py │ │ │ ├── preprocessing.py │ │ │ ├── sampling.py │ │ │ └── samplingType.py │ │ ├── frontEnd │ │ │ ├── __init__.py │ │ │ ├── configParsing │ │ │ │ ├── __init__.py │ │ │ │ ├── config.py │ │ │ │ ├── modelConfig.py │ │ │ │ ├── modelParams.py │ │ │ │ ├── testConfig.py │ │ │ │ ├── testSessionParams.py │ │ │ │ ├── trainConfig.py │ │ │ │ ├── trainSessionParams.py │ │ │ │ └── utils.py │ │ │ ├── sessHelpers.py │ │ │ ├── session.py │ │ │ ├── testSession.py │ │ │ └── trainSession.py │ │ ├── logging │ │ │ ├── __init__.py │ │ │ ├── accuracyMonitor.py │ │ │ ├── loggers.py │ │ │ └── utils.py │ │ ├── neuralnet │ │ │ ├── __init__.py │ │ │ ├── cnn3d.py │ │ │ ├── cost_functions.py │ │ │ ├── layers.py │ │ │ ├── ops.py │ │ │ ├── optimizers.py │ │ │ ├── pathwayTypes.py │ │ │ ├── pathways.py │ │ │ ├── trainer.py │ │ │ ├── utils.py │ │ │ └── wrappers.py │ │ └── routines │ │ │ ├── __init__.py │ │ │ ├── testing.py │ │ │ └── training.py │ ├── documentation │ │ ├── README.md │ │ ├── deepMedic.png │ │ └── dmRes.png │ ├── plotTrainingProgress.py │ ├── setup.cfg │ └── setup.py ├── mask.nii ├── output │ ├── logs │ │ └── testSessionDm.txt │ └── predictions │ │ └── testSessionDm │ │ └── predictions │ │ └── NSN_r_TR_MR_02._Segm.nii.gz ├── pre.py ├── registration │ ├── __init__.py │ └── registration.py ├── render.html ├── resource_rc.py ├── setting.py ├── test.png └── utils.py ├── LICENSE ├── Main.py ├── Modules ├── General │ ├── Evaluation.py │ ├── Utils.py │ ├── __init__.py │ └── read.txt ├── IO │ ├── ImgOperations │ │ ├── __init__.py │ │ └── imgOp.py │ ├── loadData.py │ ├── sampling.py │ └── saveData.py ├── NeuralNetwork │ ├── ActivationFunctions.py │ ├── __init__.py │ └── layerOperations.py ├── Parsers │ ├── __init__.py │ └── parsersUtils.py ├── __init__.py └── savedata.py ├── Readme.md ├── Report ├── Report.doc ├── Report.docx ├── liviaTest_Epoch16 └── test.png ├── UI ├── __init__.py ├── batchUI.py ├── betUI.py ├── bfcUI.py ├── dataUI.py ├── dicomUI.py ├── display.py ├── featureUI.py ├── icon.png ├── mainUI.py ├── mainUI2.py ├── regUI.py ├── res.py ├── resource_rc.py ├── tca_pyqt.py └── ui_segment.py ├── data ├── Ref.nii ├── __init__.py └── hard_classif.nii ├── environment.yaml ├── images ├── batch.png ├── bet.png ├── betRes.png ├── bfc.png ├── bfcRes.png ├── brainTissue.png ├── bs.png ├── dicom.png ├── dicomRes.png ├── feature.png ├── hs.png ├── hsRes.png ├── main.png ├── reg.png └── regRes.png ├── licence ├── FSL_LICENSE ├── NifiyReg_LICENCE └── pyradiomics_LICENCE └── requirement.txt /.gitignore: -------------------------------------------------------------------------------- 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