Repository containing the code of the paper `Deep Learning Approximation of Attenuation Maps for Myocardial Perfusion SPECT with an IQ·SPECT Collimator`.
Using this code, it is possible to train a deep neural network to predict attenuation maps from non-attenuation-corrected reconstructions.
Training is inspired by the description in [1] and is implemented with [PyTorch](https://pytorch.org/).
For the optimization of hyperparameters, a random search procedure [2] is implemented.
To compute attenuation-corrected reconstructions, the script TODO implements the post-reconstruction attenuation correction (PRAC) [3] algorithm.
The open-source tomographic reconstruction software [STIR](https://stir.sourceforge.net/) is used for this.
The training is inspired by the description in [1] and is implemented with [PyTorch](https://pytorch.org/).
A random search procedure [2] is implemented for the optimization of hyperparameters.
To compute attenuation-corrected reconstructions, the [script](/mu_map/scripts/compute_recons.py) implements the post-reconstruction attenuation correction (PRAC) algorithm [3].
It uses the open-source tomographic reconstruction software [STIR](https://stir.sourceforge.net/).
Reconstructions can be evaluated using the mean squared error or the normalized mean absolute error.
While there is also code to evaluate polar maps, they cannot be generated here.
For the purpose of the paper, grayscale polar maps were generated the Cedars-Sinai Cardiac Suite [4].
Polar maps cannot be generated with this code, but they can be evaluated.
For the purposes of this paper, grayscale polar maps were generated using the Cedars-Sinai Cardiac Suite [4].
## Results
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@@ -32,7 +32,7 @@ To install STIR run:
2.`cd libs && ./install.sh && cd ..`
### Tesseract OCR
Because we could not export perfusion scores from polar maps generated with the Cedars-Sinai Cardiac Suite, but only RGB images with scores written in a green font, we added a [script](/mu_map/polar_map/get_perfusion) to help extract these scores.
Because we could not export perfusion scores from polar maps generated with the Cedars-Sinai Cardiac Suite, but only RGB images with scores written in a green font, we added a [script](/mu_map/polar_map/get_perfusion.py) to help extract these scores.
This script uses [Tesseract](https://tesseract-ocr.github.io/) to automatically parse these numbers from the image.
