SPECT Tomographic Reconstruction 3D Slicer Extension

This is the official repository for the Slicer extension SlicerSPECTRecon.

This module enables the reconstruction of raw SPECT projection data, providing customizable options for image modeling and image reconstruction. The module has a SIMIND to DICOM converter to permit reconstruction of SIMIND Monte Carlo data.

The module is divided into the following sections:

• Data Converters: Provides tools for converting data from various sources into the DICOM format.
• Input Data: Users can select data from multiple bed positions after loading the projection data into the 3D Slicer DICOM database.
• System Modeling: Allows users to define transforms that are used to build the system matrix.
• Likelihood: Allows users to choose their preferred likelihood function.
• Reconstruction Algorithm: Provides the option of selecting a preferred reconstruction algorithm and their associated parameters

Please refer to the User_Manual.md file for further information

User interface

• Inputs
  • Input volume: input SPECT/CT dicom files, simind file (convert to dicom using the data converter)
• Outputs
  • Reconstructed volume: The volume will be saved under the specified name (or as the dataset name appended with _reconstructed) and will be located within the Subject Hierarchy in the Data Module.

Resources

The following link collection should facilitate understanding the code in this extension:

• Slicer Utils
• DICOM Introduction
• DICOM Structure
• DICOM Browser
• Subject Hierarchy

Sample Data

The links to the example data (sample patient and simind files) are in the sample_data.txt file in the Resources folder.

Contribute

If you'd like to contribute, you can find an orientation on the Slicer documentation for developers.

Please read first the CONTRIBUTING.md file for further information on how to contribute. You can also check the Pytomography readthedocs for an orientation on Pytomography.

License

SlicerSPECTRecon is subject to the MIT License, which is in the project's root.

Contact

Please post any questions to the Pytomography Discourse Forum.