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/Dicom_Data_to_Numpy_Arrays
For parallel creation of RT structures into numpy arrays for deep learning training purposes
brianmanderson/AAPM_Summer_School_Workshop
This is a deformable registration code, adapted from the voxelmorph code available here: https://github.com/voxelmorph/voxelmorph
brianmanderson/Intro_to_Raystation
small intro teaching some useful things for raystation along with basic code
brianmanderson/Make_Raystation_Data_Structure
Go through all patients in a raystation database to create a structure of MRN, Cases, Exams, and rois
brianmanderson/Nifti_To_Dicom
Functions for turning nifti files to dicom
brianmanderson/AAPM_Summer_School_Court_Workshop
brianmanderson/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
brianmanderson/Copy_Folders
Function to copy folders from one location to another
brianmanderson/icecream_images
brianmanderson/Liver_Lobe_Segments_Dicom_Curation_to_Niftii
Steps and code for processing dicom lobe segments to correct for overlapping/lacking segmentations to niftii arrays
brianmanderson/Raystation_Roi_Comparison_Scripts
brianmanderson/Teaching-Python-to-Matlab-Users
Files for teaching python to matlab users
brianmanderson/Easy_Make_UNet
A perfunctory UNet architecture that should be relatively easy to get yourself started
brianmanderson/Evaluate_Model_Repo
brianmanderson/H-DenseUNet
TMI 2018. H-DenseUNet: Hybrid Densely Connected UNet for Liver and Tumor Segmentation from CT Volumes
brianmanderson/Imaging_Physics_Workshop_1_28_20
workshop for imaging physics
brianmanderson/Labs
Container Orchestration Labs
brianmanderson/Liver_Lobe_Segmentation_Preparation_Steps
This includes steps to take segmentations created on the AW to RT structures in Raystation, and an iterative approach to then improve the segmentations of the liver lobes
brianmanderson/NCC_AAPM_Presentation_Workshop
brianmanderson/WIMP_Workshop_2020
Workshop for WIMP