brianmanderson
Clinical Assistant Professor at University of North Carolina, Chapel Hill
UNC Radiation OncologyChapel Hill, NC
Pinned Repositories
AAPM_Summer_School_Workshop
This is a deformable registration code, adapted from the voxelmorph code available here: https://github.com/voxelmorph/voxelmorph
Anonymize_Dicom
A simple tool to anonymize DICOM 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
Cyclical_Learning_Rate
Code adapted from https://github.com/bckenstler/CLR
Dicom_Data_to_Numpy_Arrays
For parallel creation of RT structures into numpy arrays for deep learning training purposes
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
DicomTemplateMakerCSharp
Intro_to_Raystation
small intro teaching some useful things for raystation along with basic code
RegisteringImages
Tools for registering images with Dicom Registration files
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)
brianmanderson's Repositories
brianmanderson/Cyclical_Learning_Rate
Code adapted from https://github.com/bckenstler/CLR
brianmanderson/AW_Liver_Lobes_To_Raystation
Code for taking segmentations created on the AW and transforming them into Raystation segmentations
brianmanderson/Easy_VGG16_UNet
This is code to create an easy to use VGG16 pre-training with UNet attached
brianmanderson/Keras_Utils
brianmanderson/Raystation_Export_Oblique_Images_to_mhd
Export obliquely acquired examinations and ROIs to a folder
brianmanderson/RCBV-Calculator
brianmanderson/CAT_Isoshifts
Create text files for shifts and Raystation code to import it
brianmanderson/Chung_Lab_Code
Code for the chung lab
brianmanderson/Create_Island_Contour
brianmanderson/DeepLearningTemplate
brianmanderson/DGX-Commands
Basic commands that are useful while running the DGX
brianmanderson/Drew_Dose_Resampler
brianmanderson/Edit_Raystation_Roi_Names
Removing the colons from roi names as they don't work with IBEX
brianmanderson/Example_Repository
brianmanderson/Fixing_RT_Structures
Fixing RT structures ReferencedSOPInstanceUIDs
brianmanderson/Installing_Tensorflow
General notes for installing tensorflow
brianmanderson/keras_deeplab_v3_plus
Keras implementation of Deeplab v3+ with pretrained weights
brianmanderson/MD_Anderson_Intro_To_AI_Workshop
Workshop for summer AI retreat at MD Anderson
brianmanderson/Project_Template
brianmanderson/PyPiCommands
Common commands for using pypi
brianmanderson/Raystation9B_PACS_AutoDownloads
repo for automatically uploading patients where each plan is a new case
brianmanderson/Raystation_Export_Exams_As_CSV
script for exporting exams that are given as CSV file
brianmanderson/ResampledNiftiPrediction2Dicom
brianmanderson/Send_Email_To_Phone
Something to text me phone when code is done running
brianmanderson/Slicer_RT_Target_Issue
a jupyter notebook illustrating an issue with representing hollowed, or 'target' structures in 3D slicer
brianmanderson/tensorflow
An Open Source Machine Learning Framework for Everyone
brianmanderson/Test
brianmanderson/Updating_to_TF2
Simple jupyter notebook for updating from my keras work to TF2
brianmanderson/Virtual-Environment-Instructions
Instructions for creating virtual environments
brianmanderson/Workshop_Modules
A set of modules which might be useful for workshops