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https://github.com/pytomography/slicer_spect_recon
3d slicer extension for pytomography to enable easy reconstruction of SPECT images
https://github.com/pytomography/slicer_spect_recon
3d-slicer-extension image-reconstruction
Last synced: 27 days ago
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3d slicer extension for pytomography to enable easy reconstruction of SPECT images
- Host: GitHub
- URL: https://github.com/pytomography/slicer_spect_recon
- Owner: PyTomography
- License: mit
- Created: 2023-10-20T07:49:15.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-12-03T11:18:28.000Z (about 1 month ago)
- Last Synced: 2024-12-03T12:21:56.737Z (about 1 month ago)
- Topics: 3d-slicer-extension, image-reconstruction
- Language: Python
- Homepage:
- Size: 162 MB
- Stars: 17
- Watchers: 3
- Forks: 6
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
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README
# 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](https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py)
- [DICOM Introduction](https://www.slicer.org/wiki/Documentation/Nightly/FAQ/DICOM)
- [DICOM Structure](https://www.slicer.org/wiki/Documentation/4.0/Modules/CreateDICOMSeries)
- [DICOM Browser](https://dicom.innolitics.com/ciods)
- [Subject Hierarchy](https://www.slicer.org/wiki/Documentation/4.5/Modules/SubjectHierarchy)
## 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](https://www.slicer.org/wiki/Documentation/Nightly/Developers).
Please read first the `CONTRIBUTING.md` file for further information on how to contribute. You can also check the Pytomography [readthedocs](https://pytomography.readthedocs.io/en/latest/) 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](https://pytomography.discourse.group/).