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@ARTICLE{Peter:169904,
      author       = {J. Peter$^*$},
      title        = {{M}usiré: multimodal simulation and reconstruction
                      framework for the radiological imaging sciences.},
      journal      = {Philosophical transactions of the Royal Society of London /
                      A},
      volume       = {379},
      number       = {2204},
      issn         = {0080-4614},
      address      = {London},
      publisher    = {Royal Society},
      reportid     = {DKFZ-2021-01634},
      pages        = {20200190 -},
      year         = {2021},
      note         = {#LA:E020#},
      abstract     = {A software-based workflow is proposed for managing the
                      execution of simulation and image reconstruction for SPECT,
                      PET, CBCT, MRI, BLI and FMI packages in single and
                      multimodal biomedical imaging applications. The workflow is
                      composed of a Bash script, the purpose of which is to
                      provide an interface to the user, and to organize data flow
                      between dedicated programs for simulation and
                      reconstruction. The currently incorporated simulation
                      programs comprise GATE for Monte Carlo simulation of SPECT,
                      PET and CBCT, SpinScenario for simulating MRI, and Lipros
                      for Monte Carlo simulation of BLI and FMI. Currently
                      incorporated image reconstruction programs include CASToR
                      for SPECT and PET as well as RTK for CBCT. MetaImage (mhd)
                      standard is used for voxelized phantom and image data
                      format. Meshlab project (mlp) containers incorporating
                      polygon meshes and point clouds defined by the Stanford
                      triangle format (ply) are employed to represent anatomical
                      structures for optical simulation, and to represent tumour
                      cell inserts. A number of auxiliary programs have been
                      developed for data transformation and adaptive parameter
                      assignment. The software workflow uses fully automatic
                      distribution to, and consolidation from, any number of Linux
                      workstations and CPU cores. Example data are presented for
                      clinical SPECT, PET and MRI systems using the Mida head
                      phantom and for preclinical X-ray, PET and BLI systems
                      employing the Digimouse phantom. The presented method
                      unifies and simplifies multimodal simulation setup and image
                      reconstruction management and might be of value for
                      synergistic image research. This article is part of the
                      theme issue 'Synergistic tomographic image reconstruction:
                      part 2'.},
      keywords     = {CT (Other) / MRI (Other) / Monte Carlo simulation (Other) /
                      PET (Other) / SPECT (Other) / image reconstruction (Other) /
                      optical imaging (Other) / phantoms (Other)},
      cin          = {E020},
      ddc          = {510},
      cid          = {I:(DE-He78)E020-20160331},
      pnm          = {315 - Bildgebung und Radioonkologie (POF4-315)},
      pid          = {G:(DE-HGF)POF4-315},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:34218676},
      doi          = {10.1098/rsta.2020.0190},
      url          = {https://inrepo02.dkfz.de/record/169904},
}