DeepSeA

ACKNOWLEDGEMENT

If you use this program in your research and/or publication(s), you must cite the paper below:

• Wei, D., Weinstein, S., Hsieh, M. K., Pantalone, L., & Kontos, D. (2018). Three-Dimensional Whole Breast Segmentation in Sagittal and Axial Breast MRI With Dense Depth Field Modeling and Localized Self-Adaptation for Chest-Wall Line Detection. IEEE Transactions on Biomedical Engineering, 66(6), 1567-1579.

FUNCTIONALITY

This package provides functionality for 3D whole breast segmentation in breast MRI. It supports both sagittal and axial breast MRI data. Currently it requires T1w nonfat-suppressed images for segmentation.

ENVIRONMENTS

This package has been tested under:

1. Windows 7 Ultimate with Service Pack1, using MATLAB R2014b.
2. Windows 7 Enterprise with Service Pack1, using MATLAB R2014b.
3. Windows 10 Home Edition 17134.165, using MATLAB R2017a.

USAGE

To start using the package inside a Matlab environment, call

MR_startup

which will add all modules into MATLAB paths so that user can call the pipeline and individual functions in the Matlab workspace.

EXAMPLES

This package includes two examples with anonymized real subject data --- one for sagittal breast MRI and the other for axial breast MRI --- to illustrate basic usage.

Example #1:

segdata = wholeBreastSegment('demoData\AX_T1_BILAT\', 'Results\', 'LateralBounds', true)

This example loads axial breast MRI data (T1w nonfat-suppressed) from DICOM files in the folder .\demoData\AX_T1_BILAT\, and writes the results to the folder .\Results\. In addition, it sets the optional input LateralBounds to true, dictating the program to define lateral bounding planes for the breasts on the outer sides of the body. The output segdata is a struct containing various segmentation results, e.g., 3D breast masks, breast size in cm^3, etc. Please refer to the help info of the function wholeBreastSegment for detailed description.

Example #2:

segdata = wholeBreastSegment('demoData\SAG_T1_3D_BILAT\', 'Results\', 'BottomBound', true)

This example loads sagittal breast MRI data (T1w nonfat-suppressed) from DICOM files in the folder .\demoData\SAG_T1_3D_BILAT\, and writes the results to the folder .\Results\. In addition, it sets the optional input BottomBound to true, dictating the program to define the inferior bounding planes for the breasts. The output segdata is a struct containing various segmentation results, e.g., 3D breast masks, breast size in cm^3, etc. Please refer to the help info of the function wholeBreastSegment for detailed description.

Example #2 takes much longer than Example #1 to finish due to the finer in-plane resolution of the sagittal demo data. However, you can also control the resolution used during processing by setting the VoxelSize optional input; please refer to the help info of the function wholeBreastSegment for detailed description.

CONTACT

For bug regporting, etc., please email: weidong111624@gmail.com / Dong.Wei@uphs.upenn.edu / Meng-Kang.Hsieh@uphs.upenn.edu