--- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ - + # MRI Segmentation and Radiomics This repository contains example code from the paper in preparation on preclinical cancer imaging titled "MRI-based Deep Learning Segmentation and Radiomics of Sarcoma Tumors in Mice." @@ -20,12 +20,12 @@ ## Segmentation Segmentation was performed via a U-net CNN. The network functions on patches taken from image volumes. The general network structure is shown below. - + Training and perfomance anlysis is done using the [Segmentation.py](Segmentation/Segmentation.py) script. The results for a network trained on multi-contrast MR images with cross entropy loss is shown below. -  +  #### Requirements T2-weighted images are bias corrected using N4BiasFieldCorrection in [ANTs](http://stnava.github.io/ANTs/). @@ -48,7 +48,7 @@ Using this code, we achieved an AUC of 0.81 for predicting recurrence within these mice. - + #### Requirements Due to the high dimensionality of the data (321 features per tumor) feature selection is required