This toolbox was developed at the Computer Vision Laboratory (Laboratório de Visão Computacional - LAVI), at the University of São Paulo, São Carlos. The proposed toolbox was developed on MATLAB and is intended for academic usage, please review the license file. This is the first version of this manual, so if you have any concern, suggestion, bug report, please send me an email.
This software was firstly presented at this paper, and further validated at this paper. If you use the toolbox, our group will be very grateful if you refer to any of these papers.
The toolbox was developed based on the cone-beam computed tomography (CBCT) code, and further extended to the digital breast tomosynthesis (DBT) geometry, as illustrated in this Figure:
Two commercial DBT systems were used as a reference for the geometry. The first one from General Electric (GE), model Senographe Essential, and the second from Hologic, model Selenia Dimensions. It is important to note that there is an angle movement on the latter system, while the former is stationary. Section 4 has some specific information for the implementation of detector rotation geometry.
Each code on this software has its own comments, input requirements and output variables. Also, each method has specific references. Make sure to read them as you go deep in the codes.
The main code is named Reconstruction.m, and each specific reconstruction method has its proper name, e.g., SART.m. All other functions are located at the Functions folder, and the geometry configuration files are located at the Parameters folder. Follow these specific steps in order to perform a simple reconstruction:
.
The first option is to use real DBT images (projections) with DICOM format. The second option creates a three dimensional (3D) virtual Shepp-Logan phantom, and its projections based on the specified geometry.
If you skipped step 1, you probably want to use this virtual phantom. In case you choose to use real images, select the folder that contains the image files. If the DBT projections are from the Hologic equipment, make sure to organize the image files name as follow: xxx\_0.dcm to xxx\_14.dcm, as illustrated in the figure above. For the GE equipment, the software takes the image number from the DICOM header.
In this step, you have to choose the reconstruction method that you want to use. There are actually five methods implemented:
They are all written in the main code, so you just have to uncomment the one that you want to use. Note that the default method is FBP
The whole geometry was designed to reconstruct the right breast. In our system, the X and Y coordinates refer to the Chest Wall-Nipple direction and Lateral profile respectively, as shown in the figure below. The slices are reconstructed parallel to the detector along the Z coordinate.
The global coordinate system origin (X=0, Y=0, Z=0) is located at the detector plane, next to the chest wall and along with the lateral profile, as shown in the figure below.
The detector coordinate system (x=0, y=0), and the image coordinate system (i=1,j=1) are also located at the detector plane, as demonstrates the figure below. The origin of the image coordinate system refers to the cell 1 of MATLAB.
Note that if you want to implement geometries, which the detector rotates, e.g. Hologic, you must use the projectionDD.m and backprojectionDD.m. These codes implement this rotation.
Please, report any bug on this manual or in the codes.
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