SyneRBI SIRF v2.2.0 Release Candidate 1

• A passthrough for both the maximum and minimum relative change during OSMAPOSL reconstruction has been added.
• 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!
• The adjoint transformation has now been implemented for NiftyResample through the wrapping of NiftyMoMo.
• Resample::process() has been marked as deprecated. Instead, the following methods have been added to C++, python and matlab NiftyResample:
  • out = forward(in)
  • forward(out, in)
  • out = adjoint(in)
  • adjoint(out, in)
  • out = backward(in) <- alias for adjoint
  • backward(out, in) <- alias for adjoint
• Inverse deformation images. Inverse displacements are also possible by converting to and from deformations.
• NiftyPET projector wrapped (if STIR is built with NiftyPET)
• Added set_image_data_processor to PETAcquisitionModel. This allows for instance image-based PSF modelling.
• Resampling of complex images.
• SPM registration wrapping (only SPM12 tested). If Matlab and SPM are present, the SPM wrapper is available from C++, Matlab and Python.
• Support for registering multiple floating images has been added. This is only available for certain algorithms (currently only SPM). There are therefore new methods add_floating_image and clear_floating_images on top of the original set_floating_image. Methods extracting the results of registrations can now be called with an index (get_output(idx = 0), get_transformation_matrix_forward(idx = 0), etc.). This index defaults to the first to maintain backwards compatibility.
• Ability to pad NiftiImageData, e.g., a.pad([10,10,0],[10,10,0]) to add 10 voxels to the minimum and maximum of the x- and y-directions.
• Ability to set and get STIR verbosity from python.
• Save STIR images using a parameter file (e.g., for saving as .nii)
• Default F3d to using non-symmetric version (previously, symmetric was used). Option to use the symmetric in C++, but currently exposed to python and matlab as we suspect there is an upstream bug there.