# SIRF training course @ PSMR/TBPET Isola d'Elba 2024

## Supporting Material

Below is a set of links towards recorded lectures or reading material which we hope will be useful for course participants. Please note that we will not cover this material ourselves (except very briefly).

### Software and programming
- If you are new to Python and the Unix terminal, please check the excellent material on https://software-carpentry.org/lessons/. There are some additional links in the [Appendix of our starting guide for participants](https://github.com/SyneRBI/SIRF-Exercises/blob/master/DocForParticipants.md#appendix).
- Ben Thomas gave a lecture on Object Oriented Programming for the CCP in 2017. The associated [notebook](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/Introductory/object_oriented_programming.ipynb) has links for the video recording etc.
- [SIRF/CIL Docker on Mac video](https://mediacentral.ucl.ac.uk/Player/C1eAhHAi) and [PowerPoint](https://mediacentral.ucl.ac.uk/assoc_files/C1eAhHAi_0.pptx?token=16abhFB8)
- The SIRF paper:
Ovtchinnikov, Evgueni, Richard Brown, Christoph Kolbitsch, Edoardo Pasca, Casper da Costa-Luis, Ashley G. Gillman, Benjamin A. Thomas, et al. ‘SIRF: Synergistic Image Reconstruction Framework’. Computer Physics Communications 249 (1 April 2020): 107087. https://doi.org/10.1016/j.cpc.2019.107087. Link for the [accepted version](https://discovery.ucl.ac.uk/id/eprint/10087933/)
- The "SIRF and motion correction" paper:
Brown, Richard, Christoph Kolbitsch, Claire Delplancke, Evangelos Papoutsellis, Johannes Mayer, Evgueni Ovtchinnikov, Edoardo Pasca, et al. ‘Motion Estimation and Correction for Simultaneous PET/MR Using SIRF and CIL’. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379, no. 2204 (23 August 2021): 20200208. https://doi.org/10.1098/rsta.2020.0208.
- [CIL paper 1](https://arxiv.org/abs/2102.04560)
- [CIL paper 2](https://arxiv.org/abs/2102.06126)

### MR
- [Basics of MRI and MR image reconstruction](https://www.youtube.com/watch?v=xCv38thzljw)
**Gastao Cruz**. Overview of the basics of MRI, from nuclear spins and magnetic fields to the sampling requirements for k-space. Also advanced topics such as reconstruction from undersampled data (GRAPPA, SENSE) are discussed.
- [MR image reconstruction using SIRF](https://www.youtube.com/watch?v=vC66LgPfRNM)
**Christoph Kolbitsch**. MR image reconstruction (k-space sampling, coil sensitivity maps, GRAPPA) and how it can be done in SIRF.

### CT
- [CT basics](https://youtu.be/PI6vgzg5l7E)
Elizabeth Edney
- [Physics of Computed Tomography](https://youtu.be/-AfF3O1_duw)
Daniel Wessell

### PET
- [PET acquisition, backprojection, sinograms](https://youtu.be/3BC0bnWobLs)
Andrew Reader
- [Time of Flight PET](https://kuleuven.mediaspace.kaltura.com/media/Lecture+on+time-of-flight+in+positron+emission+tomography+%28Prof.+Johan+Nuyts%29/1_zqpnc5gw)
Johan Nuyts
- [PET acquisition modelling](https://liveuclac-my.sharepoint.com/:v:/g/personal/rmhathi_ucl_ac_uk/ERyfdeFKaptFiVv2hbJt89ABXSU2847gnOTgIGYFVEMATA?e=RedTba), including normalisation, scatter etc
Kris Thielemans

## Notebooks

These are listed in recommended order. Please do check the `README.md` in each folder as well for more information.

### General

* [object_oriented_programming.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/Introductory/object_oriented_programming.ipynb) (optional)
* [introduction.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/Introductory/introduction.ipynb)
* [acquisition_model_mr_pet_ct.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb)
* [image geometry notebooks](https://github.com/SyneRBI/SIRF-Exercises/tree/master/notebooks/Geometry#readme) (optional but recommended for SIRF and medical imaging)
* [registration notebook](https://github.com/SyneRBI/SIRF-Exercises/tree/master/notebooks/Reg) (optional, if you are interested only)

### MR
* [a_fully_sampled.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/MR/a_fully_sampled.ipynb)
* [b_kspace_filter.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/MR/b_kspace_filter.ipynb)
* [c_coil_combination.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/MR/c_coil_combination.ipynb)

### CT
* [00_CIL_geometry.ipynb](https://github.com/TomographicImaging/CIL-Demos/blob/main/training/2021_Fully3D/Week1/00_CIL_geometry.ipynb) (optional - for reference)
* [01_intro_walnut_conebeam.ipynb](https://github.com/TomographicImaging/CIL-Demos/blob/main/training/2021_Fully3D/Week1/01_intro_walnut_conebeam.ipynb)
* [02_intro_sandstone_parallel_roi.ipynb](https://github.com/TomographicImaging/CIL-Demos/blob/main/training/2021_Fully3D/Week1/02_intro_sandstone_parallel_roi.ipynb)
* [03_preprocessing.ipynb](https://github.com/TomographicImaging/CIL-Demos/blob/main/training/2021_Fully3D/Week1/03_preprocessing.ipynb)
* [04_FBP_CGLS_SIRT.ipynb](https://github.com/TomographicImaging/CIL-Demos/blob/main/training/2021_Fully3D/Week1/04_FBP_CGLS_SIRT.ipynb)
* [additional_exercises_data_resources.ipynb](https://github.com/TomographicImaging/CIL-Demos/blob/main/training/2021_Fully3D/Week1/additional_exercises_data_resources.ipynb)

Additional datasets have been pre-downloaded and are available on the STFC cloud at `/mnt/materials/SIRF/Fully3D/CIL`

If **not** running on the STFC cloud you will need to download the data see [CIL README](https://github.com/TomographicImaging/CIL-Demos/blob/c2bae4649b51ecc3f3d0bb77eacc9faeeb5f7503/training/2021_Fully3D/Week1/README.md)

### PET
See also the [PET README](https://github.com/SyneRBI/SIRF-Exercises/tree/master/notebooks/PET#week-1)
* [display_and_projection.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/PET/display_and_projection.ipynb)
* [image_creation_and_simulation.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/PET/image_creation_and_simulation.ipynb)
* [OSEM_reconstruction.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/PET/OSEM_reconstruction.ipynb)
* [reconstruct_measured_data.ipynb](https://github.com/SyneRBI/SIRF-Exercises/blob/master/notebooks/PET/reconstruct_measured_data.ipynb)