Computational Collaborative Project in Synergistic PET-MR Reconstruction

Lead Research Organisation: University College London
Department Name: Medicine

Abstract

Magnetic Resonance (MR) and radionuclide imaging using Positron Emission Tomography (PET) have established roles in medical diagnosis, clinical research and drug development. In recognition of the complementary nature of these two modalities, which have historically been used separately, integrated PET-MR scanners have been designed and marketed by manufacturers. These devices open-up exciting avenues to exploit the synergy between these two modalities in many areas, including dementia, cardiology, and investigation of dynamic processes such as the uptake of contrast agents by tumours.

Both modalities are tomographic: from the measured data, (stacks of) slices or volumes representing anatomical and functional properties of the patient can be reconstructed using sophisticated algorithms. Image quality is critically dependent on image reconstruction methods. Development and testing of novel algorithms on patient data requires considerable expertise and effort in software implementation. We will establish a new Collaborative Computational Project (CCP) to connect researchers working at different sites and on the different modalities of PET and/or MR in the area of image reconstruction, concentrating on the logistical and computational aspects of integrated PET-MR.

The platform to be provided by this CCP will be an enabling technology which removes the frequent obstacles encountered when working with the raw medical imaging datasets acquired by PET and MR scanners. It will be straightforward to work with data in a standardized format, massively aiding and accelerating innovative developments in image reconstruction and processing for PET-MR, and ultimately enabling the possibility of synergistic image reconstruction.

Planned Impact

Medical imaging has had a phenomenal impact upon healthcare over the last 30 years, with inestimable socioeconomic benefits for the UK. Multi-modality imaging has been of particular benefit, as witnessed by the impact of PET-CT on the treatment of cancer due to its combination of functional and anatomical information. We are now on the threshold of another revolution: PET and MR have recently been combined into a single system, combining the remarkable molecular sensitivity of PET with the enormous flexibility and diverse imaging capabilities of MR. It is expected that the UK government will announce a major investment in PET-MR as part of its strategy to tackle dementia, a disease of which around 800,000 people in the UK suffer. PET-MR is uniquely suitable to study dementia and provide early diagnosis. However, there are significant challenges to be solved, many of them computational, before the full potential of PET-MR will be realised.
This is the crucial clinical context of this proposed CCP, which concerns the way medical imaging data from both the PET and MR imaging modalities is actually used to produce the end point images which are of such utility to clinical researchers, clinicians and ultimately of benefit to patients.
The following are expected beneficiaries beyond the academic community:
1) Patients
The CCP will accelerate research into novel algorithms for improved reconstructed image quality. Furthermore, researchers will be able to use our software platform to evaluate new algorithms on a much larger number of patient data sets than currently possible. This will lead to faster translation of successful algorithms into clinical research and practice. This ultimately delivers benefit to patients, such as those suffering from cancer, heart conditions, or brain disorders. In addition, the lower dose associated with PET-MR over PET-CT, especially when combined with synergistic algorithms to optimise image quality, has the benefit of reduced radiation risk to all patients and in particular paediatrics and those undergoing repeat examinations.
2) Pharmaceutical industry and advanced imaging centres
PET and MR are increasingly used in trials for new therapeutic agents. Synergistic reconstruction promises enhanced image quality and more accurate quantification on PET-MR devices. By providing early access to these new methods, such as sophisticated motion correction techniques, the CCP will enable advanced imaging centres to assist pharmaceutical companies in exploratory drug trials by detecting smaller effects. In the long term, the platform will enable pooling of data from multiple centres / scanners, increasing statistical power in later-stage drug trials, and hence reduce the huge costs associated with testing new therapies.
3) Imaging industry
PET-MR has not yet demonstrated a clear diagnostic benefit over conventional PET-CT or MR only, restricting the market size for PET-MR systems. However, the synergistic PET-MR developments of this CCP could well showcase PET-MR capabilities in a diagnostic context, which could be highly profitable to the manufacturers of the new generation of PET-MR scanners. The publically accessible knowledge and Open Source software will benefit SMEs by reducing the cost of creating new products, for instance for pre-clinical imaging or for dedicated reconstruction hardware. Finally, the training provided to young UK researchers will enlarge the skill base for future recruitment into the imaging industry.
4) Developing researchers
The training of use in standardised UK-wide software and its exploitation for modelling and algorithms to respond to the needs of clinical researchers will help the development of interdisciplinary researchers. The seminars and training from leading experts will enhance the research skills of participants in the network, providing ample opportunity to pursue careers in, for example, advanced imaging sciences, including fields beyond the medical arena.
 
Description This grant provides funding for networking and software development for image reconstruction in PET/MR, an example of dual-modality imaging.

An important output of this work is the experience with jointly developing a large open source project with contributions from several universities, relying on other existing open source projects. The associated training of about 20 PhD students, postdocs and staff members in active software development is substantial. In addition, the software itself is open source and therefore accessible to the whole community. Our training events using the software have now reached about 400 people.

We have established a UK-wide network with several international partners (currently most active international partners are in Germany, Australia and USA). Cross-fertilisation of ideas and methods is still growing. the open source software is a considerably help and motivator.

We have successfully lobbied with 2 major scanner manufacturers to disclose file format and some processing methods, allowing us (and others) to make open source software available.
Exploitation Route The software itself will remain open of course. This capabilities of the software provides a major enhancement in the way researchers can validate their new methods on clinical data, with hopefully major impact on accelerating translation towards clinical practice, and therefore patient benefit.

We will continue to present our experience at conferences to help other collaborative software projects.

We have secured follow-up funding to expand our network to other medical imaging modalities.
Sectors Digital/Communication/Information Technologies (including Software),Education,Healthcare

URL http://www.ccppetmr.ac.uk/
 
Description The software is now being used by at least one startup company for development of a PET head scanner. It is expected that the first device will be released with image reconstruction software based on our open source software. The software is also being used by the UK National Physical Laboratory to investigate and characterise uncertainty in images obtained from nuclear medicine scanners (SPECT). The aim is to establish a secondary standard for quantification that can be used by all hospitals for quantitative imaging in many applications. This is a long term project.
First Year Of Impact 2021
Sector Healthcare
Impact Types Societal,Economic

 
Description Alan Turing Institute Fellowship
Amount £10,000 (GBP)
Organisation Alan Turing Institute 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 09/2020
 
Description CCP on Synergistic Reconstruction for Biomedical Imaging
Amount £464,610 (GBP)
Funding ID EP/T026693/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 04/2020 
End 03/2025
 
Description Computational Science and Engineering: Software Flagship Project Call
Amount £523,639 (GBP)
Funding ID EP/P022200/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2017 
End 02/2020
 
Description EPSRC Industrial CASE
Amount £88,885 (GBP)
Funding ID voucher 210023 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 10/2021 
End 09/2025
 
Description Health And Bioscience IDEAS - Imaging, Data Structures, GEnetics And Analytical Strategies
Amount £799,401 (GBP)
Funding ID MR/V03863X/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 05/2021 
End 04/2023
 
Description Industrial PhD funding
Amount £150,000 (GBP)
Organisation Siemens Healthcare 
Sector Private
Country Germany
Start 10/2016 
End 09/2020
 
Description Open Source Software for quantitative reconstruction of SPECT data
Amount £90,043 (GBP)
Organisation National Physical Laboratory 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 03/2019
 
Description PET++: Improving Localisation, Diagnosis and Quantification in Clinical and Medical PET Imaging with Randomised Optimisation
Amount £821,421 (GBP)
Funding ID EP/S026045/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2019 
End 08/2022
 
Title NEMA image quality phantom acquisition on the Siemens mMR scanner 
Description NEMA image quality (IQ) phantom data acquired on the Siemens Biograph mMR PET/MR scanner. 60 minutes of PET data were acquired. The list mode acquisition and associated files required for reconstruction are provided. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact This dataset allows researchers to test PET image reconstruction software, in particular performance with quantification of PET data. It was acquired on a Siemens mMR PET/MR scanner. In particular, it can be used with our own STIR and SIRF open source reconstruction software. 
URL https://zenodo.org/record/1304453
 
Title Volumetric Quality Control Phantom Acquisition on the GE SIGNA PET/MR 
Description This is a Volumetric quality control (VQC) phantom dataset acquired on the GE SIGNA PET/MR Scanner at Invicro, London. This dataset comprises of : 1. LST : Uncompressed PET listmode file 2. MR: Reconstructed MRI images of the acquisition over 146 slices 3. MRRAW: Raw MR '.p' files 4. PT: Reconstructed PET images over 89 slices 5. PTRAW: Uncompressed raw emission and normalisation sinograms README.txt contains additional information of the dataset. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact This dataset allows researchers to test PET image reconstruction software, in particular performance with point sources and alignment between PET and MR images. t was acquired on GE Signa PET/MR scanner. In particular, it can be used with our own STIR and SIRF open source reconstruction software. 
URL https://zenodo.org/record/3887516
 
Description Data-driven methods for head motion correction in PET/MR 
Organisation Commonwealth Scientific and Industrial Research Organisation
Country Australia 
Sector Public 
PI Contribution Open source software for PET/MR image reconstruction (SIRF and STIR).Training in use and development of the software. Expertise in PET data-driven motion detection techniques. Financial assistance with travel and subsistence of PhD student.
Collaborator Contribution Contributions to the STIR open source software for handling data of the Siemens PET/MR scanner, with specific attention on co-registration between PET reconstructed by STIR and the scanner software. Methods for continuous head position estimation based on the PET data only.
Impact Several pull request to STIR open source software. Oral presentation at IEEE Medical Imaging Conference 2019.
Start Year 2018
 
Description Interaction on standards for file formats for PET and MR (ISMRMRD) 
Organisation National Institutes of Health (NIH)
Department National Heart, Lung, and Blood Institute (NHLBI)
Country United States 
Sector Public 
PI Contribution The International Society for Magnetic Resonance in Medicine has developed a standard for Raw Data for MR (ISRMRMRD 1.0). We are now joining discussions on an update of this standard which might include PET data.
Collaborator Contribution David Atkinson has contributed to version 1.0 of this standard.
Impact No outcome yet
Start Year 2016
 
Description Maastricht University Medical Center Cardiac PET-MR 
Organisation Maastricht University Medical Center+
Country Netherlands 
Sector Academic/University 
PI Contribution We have developed a framework for efficient free-breathing simultaneous whole-heart coronary magnetic resonance angiography (CMRA) and cardiac positron emission tomography (PET) on a 3T PET-MR system. The acquisition and reconstruction methods are implemented inline in the scanner software. Validation of the proposed framework in patients with cardiovascular disease is being performed in collaboration with Dr. Eline Kooi at the Maastricht University Medical Center .
Collaborator Contribution Dr Eline Kooi and Dr Rik Moonen will be acquiring clinical data to validate the proposed framework.
Impact No outcomes yet. The collaboration involves Physicists experts in Magnetic Resonance Imaging and Nuclear Medicine and clinicians, both cardiologists and radiologists.
Start Year 2017
 
Description Motion correction for cardiac PET/MR 
Organisation Physikalisch-Technische Bundesanstalt
Country Germany 
Sector Academic/University 
PI Contribution Our main contribution is via the open source software SIRF and associated software for PET reconstruction STIR, enabling reconstruction of data from the Siemens mMR PET/MR scanner in an independent and open framework, allowing offline processing, non-standard gating etc. We have provided financial support for visits by a PhD student and training in the software and development tools. In addition, we bring expertise on respiratory motion correction in PET/MR.
Collaborator Contribution MR expertise and test-data. In addition, Dr Kolbitsch and his PhD student have made substantial contributions to the training material for the software, as well as actively participating in training events. They are in the process of contributing an addition to our SIRF software allowing simulation of dynamic PET/MR with motion, which will be a major step towards giving researchers easy-to-use tools for developing and validating advanced motion correction strategies. Recent contributions include software for non-Cartesian MR sequences what are crucial for good cardiac imaging.
Impact jupyter notebooks for MR reconstruction via SIRF, see https://github.com/CCPPETMR/SIRF-Exercises. Paper published in Phys Med Biol on the simulation framework. Extra capabilities for SIRF are in development and will be contributed in the near future.
Start Year 2018
 
Description Phantoms for validation of synergistic image reconstruction methods 
Organisation Leeds Test Objects Ltd
Country United Kingdom 
Sector Private 
PI Contribution This initiative is a first step towards validation our open source software STIR and SIRF, and potentially others, for imaging in PET, SPECT, MR and CT. We provide the softwrare, support and advise on acquisition protocols.
Collaborator Contribution Leeds Test Object is a manufacturer of "phantoms" for imaging with different modalities. They have contributed with ideas on scans and phantoms. In the future, they will loan out phantoms to diffferent partners in the SyneRBI network. Univ of Manchester has a lot of expertise on this subject via harmonisation grants for PET/MR. They lead this project. University of Leeds has good relations with LTO and provided initial contact. They will also work on pre-clinical systems as part of this initiative.
Impact This initiative has just started. We are currently in planning stage of organising larger meetings etc, followed by scanning etc.
Start Year 2021
 
Description Phantoms for validation of synergistic image reconstruction methods 
Organisation University of Leeds
Country United Kingdom 
Sector Academic/University 
PI Contribution This initiative is a first step towards validation our open source software STIR and SIRF, and potentially others, for imaging in PET, SPECT, MR and CT. We provide the softwrare, support and advise on acquisition protocols.
Collaborator Contribution Leeds Test Object is a manufacturer of "phantoms" for imaging with different modalities. They have contributed with ideas on scans and phantoms. In the future, they will loan out phantoms to diffferent partners in the SyneRBI network. Univ of Manchester has a lot of expertise on this subject via harmonisation grants for PET/MR. They lead this project. University of Leeds has good relations with LTO and provided initial contact. They will also work on pre-clinical systems as part of this initiative.
Impact This initiative has just started. We are currently in planning stage of organising larger meetings etc, followed by scanning etc.
Start Year 2021
 
Description Phantoms for validation of synergistic image reconstruction methods 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution This initiative is a first step towards validation our open source software STIR and SIRF, and potentially others, for imaging in PET, SPECT, MR and CT. We provide the softwrare, support and advise on acquisition protocols.
Collaborator Contribution Leeds Test Object is a manufacturer of "phantoms" for imaging with different modalities. They have contributed with ideas on scans and phantoms. In the future, they will loan out phantoms to diffferent partners in the SyneRBI network. Univ of Manchester has a lot of expertise on this subject via harmonisation grants for PET/MR. They lead this project. University of Leeds has good relations with LTO and provided initial contact. They will also work on pre-clinical systems as part of this initiative.
Impact This initiative has just started. We are currently in planning stage of organising larger meetings etc, followed by scanning etc.
Start Year 2021
 
Description Quantitative synergistic image reconstruction to enhance positron emission tomography for imaging patients with Alzheimer's disease 
Organisation Positrigo
Country Switzerland 
Sector Private 
PI Contribution Software, know how
Collaborator Contribution Hardware, data, and know how
Impact No outputs yet but our software is expected to be used in the commercial clinical product
Start Year 2020
 
Description Reconstructing PET data of the GE Signa PET/MR scanner 
Organisation GE Healthcare Limited
Department Molecular Imaging/CT
Country United Kingdom 
Sector Private 
PI Contribution Open source software STIR (integrated into SIRF) for PET image reconstruction, test data to validate the software, and expertise on how to handle data from GE scanners.
Collaborator Contribution Leeds has contributed time from a PhD student to extend STIR to data from the GE PET/MR scanner. Imanova (now part of Invicro) and Newcastle University contributed scanning time, data and expertise. GE Healthcare waved confidentiality rights on data formats and some processing methods, and allowed us and Leeds to convert our knowledge into open source software. In addition, they have provided technical assistance and support. Estimating the value of this support is virtually impossible, but it has potentially tremendous impact in opening raw PET data to the research community, especially in Big Data/AI projects.
Impact several pull requests to open source software STIR several contributions in international conferences and a recently accepted paper in Methods. extension of methodology to other GE PET/CT scanners, benefitting other grants.
Start Year 2017
 
Description Reconstructing PET data of the GE Signa PET/MR scanner 
Organisation Imanova
Country United Kingdom 
Sector Private 
PI Contribution Open source software STIR (integrated into SIRF) for PET image reconstruction, test data to validate the software, and expertise on how to handle data from GE scanners.
Collaborator Contribution Leeds has contributed time from a PhD student to extend STIR to data from the GE PET/MR scanner. Imanova (now part of Invicro) and Newcastle University contributed scanning time, data and expertise. GE Healthcare waved confidentiality rights on data formats and some processing methods, and allowed us and Leeds to convert our knowledge into open source software. In addition, they have provided technical assistance and support. Estimating the value of this support is virtually impossible, but it has potentially tremendous impact in opening raw PET data to the research community, especially in Big Data/AI projects.
Impact several pull requests to open source software STIR several contributions in international conferences and a recently accepted paper in Methods. extension of methodology to other GE PET/CT scanners, benefitting other grants.
Start Year 2017
 
Description Reconstructing PET data of the GE Signa PET/MR scanner 
Organisation Newcastle University
Country United Kingdom 
Sector Academic/University 
PI Contribution Open source software STIR (integrated into SIRF) for PET image reconstruction, test data to validate the software, and expertise on how to handle data from GE scanners.
Collaborator Contribution Leeds has contributed time from a PhD student to extend STIR to data from the GE PET/MR scanner. Imanova (now part of Invicro) and Newcastle University contributed scanning time, data and expertise. GE Healthcare waved confidentiality rights on data formats and some processing methods, and allowed us and Leeds to convert our knowledge into open source software. In addition, they have provided technical assistance and support. Estimating the value of this support is virtually impossible, but it has potentially tremendous impact in opening raw PET data to the research community, especially in Big Data/AI projects.
Impact several pull requests to open source software STIR several contributions in international conferences and a recently accepted paper in Methods. extension of methodology to other GE PET/CT scanners, benefitting other grants.
Start Year 2017
 
Description Reconstructing PET data of the GE Signa PET/MR scanner 
Organisation University of Leeds
Country United Kingdom 
Sector Academic/University 
PI Contribution Open source software STIR (integrated into SIRF) for PET image reconstruction, test data to validate the software, and expertise on how to handle data from GE scanners.
Collaborator Contribution Leeds has contributed time from a PhD student to extend STIR to data from the GE PET/MR scanner. Imanova (now part of Invicro) and Newcastle University contributed scanning time, data and expertise. GE Healthcare waved confidentiality rights on data formats and some processing methods, and allowed us and Leeds to convert our knowledge into open source software. In addition, they have provided technical assistance and support. Estimating the value of this support is virtually impossible, but it has potentially tremendous impact in opening raw PET data to the research community, especially in Big Data/AI projects.
Impact several pull requests to open source software STIR several contributions in international conferences and a recently accepted paper in Methods. extension of methodology to other GE PET/CT scanners, benefitting other grants.
Start Year 2017
 
Description Secondary Standard for Quantitative Imaging in Nuclear Medicine 
Organisation National Physical Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution Our open source software STIR forms the basis for this collaboration with the UK National Physical Laboratory to investigate and characterise uncertainty in images obtained from nuclear medicine scanners (SPECT). We provide advise on the software, help with further developments. In addition, we provide scientific and technical advice on SPECT and PET imaging and factors affecting image quality and quantification.
Collaborator Contribution Mediso provides complete information on their trimodality PET/SPECT/CT scanner (the Mediso Anyscan), installed at NPL. This information is under NDA. NPL provides many measurements of phantom data, and has one staff member fully dedicated to this project, who has contributed many components to the open source software, as well as wrote the (closed) software specific for the Mediso AnyScan. In addition, NPL provides statistical analysis of the data, with a publication forthcoming. They also are in contact with other national standardisation institutions about this project.
Impact The aim is to establish a secondary standard for quantification that can be used by all hospitals for quantitative imaging in many applications.This is a long term project, but with potentially large impact on hospital practices.
Start Year 2019
 
Description Software collaboration with the Gadgetron project for Open Source software for MR image reconstruction 
Organisation National Institutes of Health (NIH)
Department National Heart, Lung, and Blood Institute (NHLBI)
Country United States 
Sector Public 
PI Contribution Our contributions have been small at present. We have contributed a few bug fixes and documentation enhancements. We are also suggesting alternative ways for building the interface between the Gadgetron and Python and MATLAB, based on our own work.
Collaborator Contribution The Gadgetron is one of the best-established open source projects for MR image reconstruction. It is able to reconstruct data from many clinical systems. Moreover, we have had discussions on software architecture that help us in building a computationally efficient tool for the research community.
Impact As our CCP will develop synergistic PET-MR reconstruction, being able to use the Gadgetron is a large time and money saver in terms of man-years, but also in terms of available expertise.
Start Year 2015
 
Description TUM (Technische Universität München) Cardiac PET-MR 
Organisation Technical University of Munich
Department Department of Nuclear Medicine
Country Germany 
Sector Academic/University 
PI Contribution We have developed a framework for efficient free-breathing simultaneous whole-heart coronary magnetic resonance angiography (CMRA) and cardiac positron emission tomography (PET) on a 3T PET-MR system. The acquisition and reconstruction methods are implemented inline in the scanner software. Validation of the proposed framework in patients with cardiovascular disease is being performed in collaboration with Dr. Stephan Nekolla Head of Multimodal Cardiac Imaging at the Department of Nuclear Medicine in Munich.
Collaborator Contribution Karl Kunze, PhD student from TUM Munich, spent two weeks at KCL to learn how to use the framework and acquire the data. Currently he is acquiring data on patients in TUM.
Impact The collaboration involves Physicists experts in Magnetic Resonance Imaging and Nuclear Medicine and clinicians, both cardiologists and radiologists. From this collaboration two abstracts were accepted for the international conference ISMRM in 2017. The journal article "Motion-corrected whole-heart PET-MR for the simultaneous visualisation of coronary artery integrity and myocardial viability: an initial clinical validation" is currently under revision in EJNMMI.
Start Year 2016
 
Description University of Edinburgh Cardiac PET-MR 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution We have developed a framework for efficient free-breathing simultaneous whole-heart coronary magnetic resonance angiography (CMRA) and cardiac positron emission tomography (PET) on a 3T PET-MR system. The acquisition and reconstruction methods are implemented inline in the scanner software. Validation of the proposed framework in patients with cardiovascular disease is being performed in collaboration with Dr Mark Dweck and Dr Scott Semple at the University of Edinburgh.
Collaborator Contribution Dr Mark Dweck and Dr Scott Semple will be acquiring clinical data to validate the proposed framework.
Impact No outcomes yet. The collaboration is multidisciplinary as involves Physicists experts in Magnetic Resonance Imaging and Nuclear Medicine and clinicians, both cardiologists and radiologists.
Start Year 2017
 
Description testing motion correction for neuro PET-MR 
Organisation University Hospital Leipzig
Country Germany 
Sector Academic/University 
PI Contribution We provide open source software for image reconstruction and motion estimate, as well as know-how. We also hosted and trained an MSc student.
Collaborator Contribution The PET centre at Leipzig has developed a head-phantom suitable for PET-MR acquisitions, as well as a robot to move the phantom in reproducible ways. This is an excellent tools for testing robustness of different motion correction methods, including the manufacturer's, but also our own.
Impact Currently one oral presentation at the IEEE Medical Imaging Conference and a paper in preparation. Ultimately, this will give researchers way a comparison between different methods.
Start Year 2020
 
Title CCP 
Description Open Source software for reconstruction of PET and MR raw data. Developed under an EPSRC Collaborative Computing Project. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Further funding for a 'flagship' application. 
URL http://www.ccppetmr.ac.uk
 
Title CCP PETMR reconstruction software 
Description Prototype release of research software for image reconstruction for Positron Emission Tomography and Magnetic Resonance Imaging (PET-MR). The software is intended to allow synergistic reconstruction, i.e. data from both modalities is used together. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact This software has been created based on discussions within the research community, bringing together experts from many universities and institutions. This process has engaged researchers in our network, but also has made many to think for the first time on how to design software that will be used by many and will be co-developed by a team. As this is a prototype, further impact will be for the future. 
URL https://github.com/CCPPETMR
 
Title PET Raw data tools v2.0 
Description pet-rd-tools provides a set of tools for handling raw data from PET scanners. It enables researchers to use the data from their own scanners, unpack them etc, and then use as input for their own image reconstruction software, including our own STIR and SIRF packages. This second release adds support for data from GE PET/CT scanners. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact This software has enabled various researchers to handle data from their scanner with greater easy, leading to several publications on validation of the software and novel methods. It is now part of the suite of packages provided by our CCP PETMR/SyneRBI. 
URL https://github.com/UCL/pet-rd-tools/
 
Title PETPVC: Software for Partial Volume Correction 
Description First public release of software for Partial Volume Correction (correcting for quantification problems due to a blurring effect) in Positron Emission Tomography. The software implements a wide variety of image-based PVC methods. Many of these are capable to use an image with anatomical "labels" corresponding to different structures in the body. This is commonly derived from MRI images using "parcellation" software (for which we rely on existing open source projects). PETPVC was mostly developed at University College London, with additional input from the Clinical Imaging Research Centre, A*STAR-NUS. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact This software has only just been released and a publication is currently under review. 
URL https://github.com/UCL/PETPVC
 
Title SIRF v2.0 
Description SIRF (Synergistic Image Reconstruction Framework) wraps various open source projects in one consistent C++/Python/MATLAB framework. v2.0 adds image registration and resampling as a basis for motion correction. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact This software is still in relatively early stage but is already enabling researchers in UK, Germany and Australia to perform research on novel methods for processing of PET/MR data. 
URL http://www.ccppetmr.ac.uk/
 
Title SIRF v2.1 
Description SIRF (Synergistic Image Reconstruction Framework) wraps various open source projects in one consistent C++/Python/MATLAB framework. v2.1 adds integration with the CCPi Core Imaging Library (CIL), an interface to the Hybrid Kernel Method for PET image reconstruction using anatomical information from MR, and capability of reconstruction of 3D MR sequences. This new version makes the software much more useful for researchers. The integration with CIL opens the window towards application of advanced optimisation algorithms in PET/MR. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact This version of the software allowed us to train a substantial of ECRs in PET/MR/CT reconstruction with highlight our training school in Chester, November 2019 with about 50 attendees, see https://www.ccppetmr.ac.uk/node/200 
URL http://www.ccppetmr.ac.uk/
 
Title SIRF v2.2 
Description This is an update of our open source software Synergistic Image Reconstruction Framework (SIRF). This framework amalgamates several other open source packages for medical imaging into one consistent package, providing C++, MATLAB and Python interfaces. This release provides several improvement including GPU compute capabilities for PET reconstruction, registration of MR images, access to the SPM registration toolkit, and the basic building blocks for motion corrected image reconstruction (MCIR). 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact This release enabled us to investigate novel ways for motion corrected image reconstruction, with a publication currently in revision and more to come. It also increates the capabilities of SIRF, attracting more interest therefore. 
URL https://www.ccpsynerbi.ac.uk/
 
Title STIR v4.0 
Description This is a major update to our open source Software for Tomographic Image Reconstruction (STIR). STIR provides researchers with the capability to reconstruct PET and SPECT data, completely independently from the manufacturer software (for supported scanners). This release adds several major features, including scatter estimation for PET, the hybrid kernel image reconstruction method, which allows incorporating of anatomical side information, listmode reconstruction, resolution modelling of the PET reconstruction. In addition, STIR can now read data from many Siemens PET scanners, including the mMR PET/MR scanner, as well as output of one of the best known Monte Carlo simulators GATE. 
Type Of Technology Software 
Year Produced 2020 
Open Source License? Yes  
Impact This release is the first to allow image reconstruction of the Siemens mMR PET/MR scanner. This has enabled several researchers to test new algorithms in real data, leading to Sseveral publications. some of these algorithms were then contributed to the open source project. STIR has attracted around 500 citations since its first release in 2000. 
URL http://stir.sourceforge.net/
 
Title STIR: Software for Tomographic Image Reconstruction 
Description Research Software for image reconstruction for Positron Emission Tomography (PET) and Single Photon Emission Tomography (SPECT). STIR is a long-running project (first release in 2001) with contributions from various universities and companies over the years. A major update has now been made available that uses OpenMP for multi-threading and has an interface to Python and MATLAB. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact STIR is widely used as a research tool with a total of more than 260 citations in journals and conference proceedings. It has been used as the initial reconstruction software for the ClearPET preclinical PET scanner, allowing much faster introduction to the market. The scatter correction component of STIR has been used as tools for evaluation of a 3D method and convinced GE Healthcare to modify their own scatter correction software accordingly. The current update considerably enhances usability for research purposes. Previous versions of STIR was command-line based. Cluster-based parallelisation using MPI was already available in STIR. However, many researchers prefer to use interactive languages such that it is easier to try new ideas and get easier feedback via data examination. The multi-threading enhancement speeds-up computation time for interactive use. 
URL http://stir.sourceforge.net/
 
Description 2nd International Training School on PET/MRI 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact The second international training school on PET-MR software engineering for early stage researchers (ESRs) was organised in Leeds from 27th to 30th April. The school was well attended by 35 ESRs from European and Canadian Institutes. The school was financially supported by the EU COST Action TD1007 and the EPSRC CCP-PET-MRI.

The school provided 1 week intensive training on most aspects of PET/MR engineering and physics, although hardware was only briefly covered.
Year(s) Of Engagement Activity 2015
URL http://petmrieu.teiath.gr/PETMR_School_15.html
 
Description Hackathon 1 - 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A two-day Hackathon, in which developers met to tackle outstanding features. This allowed developers to exchange ideas and competencies, which benefitted new users in particular. Furthermore, the general public benefitted as this concentrated effort of code improvement increased the available features.
Year(s) Of Engagement Activity 2018
URL https://www.ccppetmr.ac.uk/hackathon1
 
Description Hackathon 2 - 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact A three-day Hackathon, in which developers met to tackle outstanding features. This allowed developers to exchange ideas and competencies, which benefitted new users in particular. Furthermore, the general public benefitted as this concentrated effort of code improvement increased the available features.

Particular effort was made in this Hackathon to include researchers that had not previously used the software. These efforts helped increase the user-base of the framework (benefitting the project), and allowed the new users to learn in a hands-on environment.
Year(s) Of Engagement Activity 2018
URL https://www.ccppetmr.ac.uk/node/162
 
Description Hackathon 3 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact A three-day Hackathon, in which developers met to get experience with our software SIRF and various Machine Learning frameworks. This hackathon allowed participants to get hands-on experience with novel methods for using Machine Learning for image reconstruction. In addition, we developed extra functionality within our software SIRF to enable this functionality, including GPU computing capability.
Year(s) Of Engagement Activity 2019
URL http://www.ccppetmr.ac.uk/node/190
 
Description Hackathon 4 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact This three day hackathon was a joint event between our CCP PETMR network and CCPi. Its aim was to prepare for a training school on synergistic image reconstruction. We added functionality to both SIRF and CIL and in particular prepared Jupyter notebooks with demos and exercises, lowering the entry-level for using our software, but also expanding its use for educational purposes.
Year(s) Of Engagement Activity 2019
URL http://www.ccppetmr.ac.uk/node/194
 
Description Hackathon 5 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact This three day hackathon involved researchers from UK and Germany and concentrated on adding motion correction capabilities to our SIRF software.
Year(s) Of Engagement Activity 2020
URL http://www.ccppetmr.ac.uk/node/233
 
Description IEEE MIC 2015 Satellite Workshop on Open Source Software in Medical Imaging, San Diego, USA 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In this workshop, we invited the main developers of 6 different open-source projects of image reconstruction in various imaging modalities (PET, SPECT, CT and MR) to present the capabilities and design of their software. Our intention was to disseminate knowledge about these packages, learn from practices by others and to have a platform for discussion on future collaborations.

A concrete outcome of this process is the collaboration between our CCP and the Gadgetron project (developing MR reconstruction software). Hopefully others will follow in the future.
Year(s) Of Engagement Activity 2015
URL http://www.ccppetmr.ac.uk/MIC2015WS_OSSMedImaging
 
Description PET-MRI Image reconstruction Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact A one day workshop educating researchers and industry about PET-MR and image reconstruction techniques, including demonstration of our software.
Year(s) Of Engagement Activity 2016
URL https://www.ccppetmr.ac.uk/node/37
 
Description Regular meetings for methods and software for synergistic image reconstruction 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact As part of our network, we hold regular meetings covering topical issues for synergistic reconstruction in PET/MR and other modalities. They often have an educational component, some seminars, combined with active discussions. The meetings occurred roughly 6 weekly and have an average attendance of around 20 people, about 30% remotely of which about one third internationally.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019,2020,2021
URL https://www.ccppetmr.ac.uk/node/228
 
Description STIR User's and Developer's Meeting 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact 48 attendants, ranging from academic researchers, students and industry representatives attended a 2 hour workshop on our open source software STIR and SIRF. Our own group and external researchers presented their recent work with the software, with lots of interactions with the audience on capabilties, difficulties encountered, and how to access these contributions in the future.
Year(s) Of Engagement Activity 2018
URL http://stir.sourceforge.net/MIC2018UsersMeeting/
 
Description STIR User's and Developer's Meeting 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact about 55 attendants, ranging from academic researchers, students and industry representatives attended a 2 hour workshop on our open source software STIR and SIRF. Our own group and external researchers presented their recent work with the software, with lots of interactions with the audience on capabilties, difficulties encountered, and how to access these contributions in the future.
Year(s) Of Engagement Activity 2019
URL http://stir.sourceforge.net/MIC2019UsersMeeting/
 
Description STIR User's and Developer's Meeting 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact About 40 attendants, ranging from academic researchers, students and industry representatives attended an online 2 hour workshop on our open source software STIR and SIRF. Our own group and external researchers presented their recent work with the software, with lots of interactions with the audience on capabilties, difficulties encountered, and how to access these contributions in the future. This was the first time the event was online which created some challenges with timezones etc, compared to our usual association to a conference. However, it allowed us to get presenters and attendees from all over the world.
Year(s) Of Engagement Activity 2020
URL http://stir.sourceforge.net/2020UsersMeeting/
 
Description STIR Users and Developers Meeting 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact About 40 people attended the annual STIR User's Meeting, with presentations from our team but also others using the software. We also had a presentation on our SIRF open source software. The event generated questions on how to use this software in their research and how they could extended. There were also several new registrations for our software.
Year(s) Of Engagement Activity 2017
URL http://stir.sourceforge.net/MIC2017UsersMeeting/
 
Description Seminar (Johan Nuyts): Reconstruction with MR-prior for PET brain imaging 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Seminar given by external expert (Johan Nuyts - KUL, Belgium) on the subject of: Reconstruction with MR-prior for PET brain imaging.
Year(s) Of Engagement Activity 2018
 
Description Seminar (Simon Stute): CASToR - Customizable and Advanced Software for Tomographic Reconstruction 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Semiar given by external expert on alternative PET reconstruction toolkit. Converstation followed seminar on possibility of collaboration/incorporation of CASToR into our framework.
Year(s) Of Engagement Activity 2018
URL http://www.ccppetmr.ac.uk/node/153
 
Description Seminar (Simon Stute): PET reconstruction of the posterior image probability, including multimodal images 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Seminar by external expert on the subject: PET reconstruction of the posterior image probability, including multimodal images
Year(s) Of Engagement Activity 2018
URL http://www.ccppetmr.ac.uk/node/152
 
Description Seminar from Prof Michel Defrise on Time of Flight imaging with PET 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Prof Defrise is a world-authority on advanced methods for imaging. He gave a seminar on his recent advances in estimating scanner characteristics, enabling better image quality, but also clarifying instabilities in previous methods. Audience reported that the seminar raised many questions, but also answered most of these in a very didactic manner. Future research opportunities were identified.
Year(s) Of Engagement Activity 2020
URL http://www.ccppetmr.ac.uk/node/254
 
Description Stand (touchtable interactions) at Manchester Day Parade (MRI Imaging to the public) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Manchester Brain Box; data showing on touchcreens presentations - two touchtable systems were on offer with PET/MRI data https://mcrbrainbox.wordpress.com/ 19 June 2016 This showed XCT / MRI and PET images for brains from flies to us; all interactively sliced and segmented. Total through the Town Hall was in excess of 5400: 90 people crawled through the 'pretend' MRI scanner and received a scanned image of 'their' brain.
Year(s) Of Engagement Activity 2016
URL https://mcrbrainbox.wordpress.com/
 
Description Symposium on Synergistic Image Reconstruction 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Traditionally, image reconstruction has focussed on estimating 2D or 3D images from a single modality data-set and acquisition. In recent years however, there have been significant developments in hardware and systems that allow extracting multi-parametric images from multiple data-sets. Examples include multi-spectral CT, multi-sequence MR, multi-modality such as PET-MR, and acquisitions from multiple-time points. While it is possible with such data to reconstruct several images independently, each corresponding to a different parameter or time-point, it is often advantageous, although challenging, to synergistically reconstruct all images.

This event brought a group of researchers together from these different fields and application areas, including medical and industrial imaging, to disseminate ideas to, and learn from, researchers both within and outside their usual research field.

This was a joint activity organised together with CCPi.
Year(s) Of Engagement Activity 2019
URL http://www.ccppetmr.ac.uk/symposium2019
 
Description Symposium on current technical challenges in clinical research using PET/MR 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This symposium provided a platform for discussions on how to overcome the remaining barriers in adopting PET/MR in large clinical trials, while also looking at mechanisms for translation of research methods into practice. There was excellent interaction between speakers and audience (many of whom were international), including a discussion panel. Future collaborations were discussed.
Year(s) Of Engagement Activity 2020
URL http://www.ccppetmr.ac.uk/node/231
 
Description Training School in Synergistic Image Reconstruction 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact In this 2 day School we presented theory and practice of up-to-date synergistic reconstruction algorithms for PET, MR and (multi-spectral) CT. A special feature was the hands-on training using the SIRF and CIL software packages. The half day was dedicated for participants to tackle relevant research questions in groups.

The School was organised together with CCPi
Year(s) Of Engagement Activity 2019
URL https://www.ccppetmr.ac.uk/node/200
 
Description Training school on PET/MR reconstruction at PSMR 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact We organised a one day PET-MRI School for students and early stage researchers at PSMR 2018, the 7th Conference on PET-MRI and SPECT-MRI in May 2018, Isle de Elba, Italy, (24 attendants) with a hands-on PET-MR software training session using SIRF. We funded UK attendants to the school.
Year(s) Of Engagement Activity 2018
URL https://www.ccppetmr.ac.uk/psmr2018
 
Description UCL PET/MRI Methodology Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This 3 day workshop focused on development of analysis methods for PET/MRI with the following objectives:
• To present relevant current research at UCL and other centres
• To provide a forum for networking and future planning
• To encourage national collaboration on PET/MRI methods
We had several international of high standing. The workshop was very well received.
Year(s) Of Engagement Activity 2016
URL https://www.ucl.ac.uk/nuclear-medicine/upcomingevents/uclpetmrimethodologyworkshop
 
Description hands-on PET-MR software training session using SIRF 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact We contributed to the PET-MRI School for students and early stage researchers at PSMR 2017, the 6th Conference on PET-MRI and SPECT-MRI in May 2017, Lisbon, Portugal (25 attendants) with a hands-on PET-MR software training session using SIRF. We funded UK attendants to the school.
Year(s) Of Engagement Activity 2017
URL http://psmr2017.pt/index.php/pet-mri-school
 
Description participation in the Siemens PET/MR User's Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We participated in organising a User's Meeting together with Siemens Healthineers. The aim of the meeting was to give a status report of where PET/MR is in clinical practice, but also determine future directions. We also provided some information on our software or image reconstruction SIRF as an open source alternative for the manufacturer's dedicated platform.
Year(s) Of Engagement Activity 2020
 
Description seminar Dr Christoph Kolbitsch on Motion correction for cardiac PET-MR 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Dr Kolbitsch and his PhD student Johannes Mayer gave a joint seminar on their recent work on enabling cardiac PET/MR imaging with motion correction for both respiration and cardiac contraction. The talk included information on clinical progress, but also a software framework, based on our SIRF software, for simulation of the methods, allowing validation with ground truth data.
Year(s) Of Engagement Activity 2020
URL http://www.ccppetmr.ac.uk/node/237