CCP SyneRBI
Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging
Release of SIRF 3.1.0
We are delighted to announce the release of our Synergistic Image Reconstruction Framework (SIRF) and associated projects Version 3.1. This release adds a few new features and quite a lot of new notebooks in SIRF-Exercises. It is currently in heavy use in our Training School on Synergistic Image Reconstruction, jointly organised with CCPi.
The main changes of the 3.1 release are:
SIRF v3.1.0:
- MR/Gadgetron
- Golden-angle radial phase encoding (RPE) trajectory is supported if `Gadgetron` toolboxes were found during building
- Added constructor for `GadgetronImagesVector` from `MRAcquisitionData`. This allows setting up an MR acquisition model without having to perform a reconstruction first.
-
PET/STIR
- iterative reconstructors `set_current_estimate` and `get_current_estimate` now create a clone to avoid surprising modifications of arguments. The old behaviour of `set_current_estimate` can still be achieved by `set_estimate`.
- `range_geometry` and `domain_geometry` methods of `AcquisitionModel` classes, required by CIL algorithms, now obtain data via respective C++ `AcquisitionModel` classes accessors, in line with our strategy of keeping interface code minimal
- `sirf.Gadgetron.AcquisitionData.get_info` was renamed to `get_ISMRMRD_info` to avoid confusion with the other `get_info()` methods that return a string. (`get_info` still works but issues a deprecation warning).
SIRF-SuperBuild v3.1.1: (including changes for 3.1.0, v3.1.1 includes some bug fixes for Astra build and docker).
- Docker
- changes related to user permissions and start-up times. Docker container start-up is now a few seconds as opposed to minutes. This has also prepared us for a JupyterHub container, but this work has not been merged yet.
- documentation has also been restructured to (hopefully) be clearer.
- the Docker image now contains CIL as well
- Updated default tags to SIRF 3.1.0, CIL, more synergistic notebooks etc.
A complete list of changes can be found at https://github.com/SyneRBI/SIRF/releases/ and also https://github.com/SyneRBI/SIRF-SuperBuild/releases/. DOI for SIRF is 10.5281/zenodo.4776289.
Please visit our software framework page for further information and links, including to the VM and Docker builds, as well as a list with our planned timelines.
Please try it out and let us know, by mailing to CCP-SYNERBI-USERS@JISCMAIL.AC.UK, whether it worked for you and provide feedback.
Finally, the paper describing SIRF is available at https://doi.org/10.1016/j.cpc.2019.107087. Our new paper "Motion estimation and correction for simultaneous PET/MR using SIRF and CIL" is now published https://doi.org/10.1098/rsta.2020.0208 in Part 2 of the Special Theme on Synergistic Image Reconstruction of the Phil. Trans. R. Soc. A.
Excerpt:
We are delighted to announce the release of our Synergistic Image Reconstruction Framework (SIRF) Version 3.1.0.
News Date:
Tuesday, July 6, 2021
