Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging

Release of SIRF 2.2.0

We are delighted to announce the release of our Synergistic Image Reconstruction Framework (SIRF) Version 2.2.0.

The main changes of the 2.2.0 release are:

  • Renaming of CCP PETMR to SyneRBI
  • We have now corrected the geometrical information of .h5 images (coming from ISMRMRD and Gadgetron). This means we can now convert them to other SIRF image types (e.g., NiftiImageData and STIRImageData). This is necessary for any kind of synergistic reconstruction. Further, to the best of our knowledge, this is the first ISMRMRD to NIfTI converter out there!
  • NiftyPET projector wrapped (if STIR is built with NiftyPET)
  • SPM registration wrapping (only SPM12 tested). If Matlab and SPM are present, the SPM wrapper is available from C++, Matlab and Python
  • Save STIR images using a parameter file (e.g., for saving as .nii)
  • The adjoint transformation has now been implemented for NiftyResample through the wrapping of NiftyMoMo.
  • Inverse deformation images. Inverse displacements are also possible by converting to and from deformations.

A complete list of changes can be found in our CHANGES file.
DOI for the software is 10.5281/zenodo.3897536 where you can also download the software. Instructions on how to cite this will be on our website in the near future.

Please visit our software framework page for further information and links, including a list with our planned timelines.

We remind you that we supply a Virtual Machine (using Oracle VirtualBox 6.0.14) with Python bindings pre-installed, a Docker container, and procedures for those who want to build the software natively, which should work on Linux and Mac (native installation on Windows is possible but still difficult at present unfortunately).

For those of you who have the previous SIRF 1.x VM, please note that it is not straightforward to upgrade it to SIRF 2.x (due to updated requirements of the dependencies). If you really need this, please send email to our mailing list.

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 10.1016/j.cpc.2019.107087

Our Best Regards,

On behalf of the CCPPETMR Developers

We are delighted to announce the release of our Synergistic Image Reconstruction Framework (SIRF) Version 2.2.0.
News Date: 
Tuesday, June 23, 2020