To be able to run this you will need to have a GPU card available and have tensorflow and keras libraries installed in python.
In order to train the model on CT head images
- clone the repository to your local drive.
- Put your images under 'image_folder' and masks under 'mask_folder'
- run unet_CT_SS.py
In order to extract brain from a CT head image.
- clone the repository to your local drive.
- put your images under image_folder
- set predict flag to be true in unet_CT_SS.py file
- make sure you set "testLabelFlag" to be False, in the unet_CT_SS.py
- run unet_CT_SS.py
1)If you want to run the model on a new data without mask, you should set "testLabelFlag=False", which computes the DICE metric if you have masks in the mask_data folder. If you run metrics "testLabelFlag=True" on your new data with mask, make sure that you have them both with the same name in their folders.
2)You should also download the model weights into the weights_folder as instructed in text file within the weights_folder.
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Please contact me if you have any difficulty in running this code.
Email: akkus.zeynettin@mayo.edu
Zeynettin Akkus
Please cite the paper below if you use the tool in your study:
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Zeynettin Akkus, Petro M. Kostandy, Kenneth A. Philbrick, Bradley J. Erickson. Proceedings Volume 10574, Medical Imaging 2018: Image Processing; 1057420 (2018) https://doi.org/10.1117/12.2293423
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Zeynettin Akkus, Petro M. Kostandy, Kenneth A. Philbrick, Bradley J. Erickson. Robust Brain Extraction Tool for CT Head Images. In Press. Neurocomputing.