brianmanderson/Teaching-Python-to-Matlab-Users

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brianmanderson/Teaching-Python-to-Matlab-Users

brianmanderson

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Files for teaching python to matlab users

Dicom_RT_and_Images_to_Mask

Tools to help with the conversion of DICOM images, RT Structures, and dose to useful Python objects. Essentially DICOM to NumPy and SimpleITK Images

Segmentation_Evaluation_Tools

Tools for quantitative evaluation of prediction segmentations (Dice, Jaccard, volume similarity, false_negative, false_positive, mean, median, max, and std surface distances)

Dicom_Data_to_Numpy_Arrays

For parallel creation of RT structures into numpy arrays for deep learning training purposes

RegisteringImages

Tools for registering images with Dicom Registration files

Create_RT_From_Dicom_and_Mask

This is for the creation of a Dicom_RT structure using a template RT structure, the dicom images, and a mask

Intro_to_Raystation

small intro teaching some useful things for raystation along with basic code

Cyclical_Learning_Rate

Code adapted from https://github.com/bckenstler/CLR

Jupyter Notebook

AAPM_Summer_School_Workshop

This is a deformable registration code, adapted from the voxelmorph code available here: https://github.com/voxelmorph/voxelmorph

Jupyter Notebook

Make_Single_Images

Converting 3D images into groups of 2D images for speed of loading

Nifti_To_Dicom

Functions for turning nifti files to dicom

Data_Generators

Data generators that I use

Finding_Optimization_Parameters

Tools to help find the best parameters for your network

Image_Processors_Module

Image processors for keras, predictive models, datasets, and example loaders

Anonymize_Dicom

A simple tool to anonymize DICOM files

PDF_To_JPG_CSharp

A program which runs through a provided list of file locations to convert pdfs to jpegs

WorkingWPythonAria

Some basic work w Python and Aria

Jupyter Notebook

AW_Liver_Lobes_To_Raystation

Code for taking segmentations created on the AW and transforming them into Raystation segmentations

Raystation_Roi_Comparison_Scripts

Resample_Class

AAPM_SummerSchool_Jinzhong_Workshop

Jupyter Notebook

Raystation_Export_Oblique_Images_to_mhd

Export obliquely acquired examinations and ROIs to a folder

AAPM_Summer_School_Court_Workshop

Jupyter Notebook

Copy_Folders

Function to copy folders from one location to another

Plot_And_Scroll_Images

ExtractPlanInfo

A C# script for pulling information from Aria regarding a list of MRNs

Callbacks

RCBV-Calculator

Prediction_Model_Class

My base class for letting the server predict from multiple models

Copy-Shared-Google-to-Colab

This will let you copy over a folder from a shared link to your own work station in google colab

Jupyter Notebook

Make_Raystation_Data_Structure

Go through all patients in a raystation database to create a structure of MRN, Cases, Exams, and rois

Easy_VGG16_UNet

This is code to create an easy to use VGG16 pre-training with UNet attached

Keras_Utils

Local_Recurrence_Work

Scripts to determine if local recurrence occurred within region of minimum ablation

Unzip_Tool

A small tool to unzip files

Base_Deeplearning_Code

The base code that all of my deep learning projects will reference from

icecream_images

TeachingGithubProcedures

A simple repository designed to explain the commands of GitHub

Jupyter Notebook

Liver_Lobe_Segments_Dicom_Curation_to_Niftii

Steps and code for processing dicom lobe segments to correct for overlapping/lacking segmentations to niftii arrays