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Configuration Parameters
Jesús Silva-Rodríguez edited this page Apr 23, 2024
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dir_stir: The directory where STIR is installed. This should be configured during the SimPET installation, but it can be modified if you want to use a different STIR version (compatibility is not guaranteed).
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dir_simset: The directory where SimSET is installed. This should be configured during the SimPET installation, but it can be modified if you want to use a different SimSET version (compatibility is not guaranteed).
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matlab_mcr_path: path to MATLAB MCR, needed to run SPM12 standalone (see Next parameter).
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spm_path: path to SPM12 standalone. This is needed for BrainVISET, to segment the MRI and generate iteration 0 maps. If you don't know how to install SPM12 standalone, please check CAT12 Standalone
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dir_data_path: path to directory with patients or subjects.
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dir_results_path: path to store the results of the simulation + reconstruction.
- interactive_mode: if set to "1" you will see some prompts to prevent you to overwrite existing data. If set to 0 existing data will be overwritten.
- stratification: SimSET variance technique reduction. We recommend setting it to "true"
- forced_detection: SimSET variance technique reduction. We recommend setting it to "true".
- forced_non_absortion: We recommend setting it to "true". We recommend setting it to "true".
- acceptance_angle: SimSET acceptance angle. We recommend setting it to 90.0 but it may need fine tunning for your case.
- positron_range: whether to simulate positron range or not with SimSET. We recommend setting it to "true".
- non_colinearity: whether to simulate non-colinearity of photons with SimSET. We recommend setting it to "true".
- minimum_energy: minimum energy threshold. We recommend setting it to 350.0.
- weight_window_ratio: we recommend setting it to 1.0.
- point_source_voxels: we recommend setting it to "false".
- coherent_scatter_object: we recommend setting it to "false".
- coherent_scatter_detector: we recommend setting it to "false".
See SimSET documentation for further information.
- sim_type: one of SimSET, STIR or GATE (only SimSET working).
- do_simulation: 1 or 0, whether to perform simulation (1) or not (0). This is useful for deactivating simulation when only reconstruction is needed.
- do_reconstruction: 1 or 0, whether to perform reconstruction (1) or not (0).
- divisions: number os subprocesses for parallel simulation.
- scanner_name: name of the PET system.
- model_type: we recommend setting it to "cylindrical".ç
- patient_dirname: name of the subdirectory in dir_data_path where phantoms are located.
- output_dir: name of the attenuation map file (with extension).
- act_map: name of the subdirectory in dir_results_path where the results will be stored.
- att_map: name of the activity map file (with extension).
- center_slice: the slice number to be placed on the center of the scanner. If 0, automatically, the half of the slices will be calculated and used.
- z_min: start of the acquisition, slice.
- z_max: end of the acquisition, slice. We calculate the number of beds based on (z_max - z_min) and the scanner FOV.
- mri_image: MRI filename with extension.
- ct_image: CT filename with extension.
- pet_image: PET filename with extension.
- maximumIteration: maximum number of iterations when using BrainVISET.
- total_dose: dose in mCi.
- simulation_time: time to be simulated in s.
- sampling_photons: set to 0 to avoid importance sampling. We recommend the use of importance sampling and setting this parameter to 20000000 as a starting point.
- photons: set to 0 to do a realistic noise simulation.
- add_randoms: 1 activate randoms simulation (will force sampling_photons=0 and photons=0). It can kill the process is there is not enough RAM.
- phglistmode: history Files from the phg module (needed for LM reconstruction, potentially very big).
- detlistmode: history Files from the detector module (you need this for adding randoms, if add_randoms=1 will be forced).
- scanner_name: name of the scanner.
- simset_material: material of the scanner, see SimSET for available materials.
- average_doi: depth of interaction.
- scanner_radius: radius of the scanner in cm.
- num_rings: number of rings of the scanner.
- axial_fov: axial FOV of the scanner in cm.
- z_crystal_size: size of the crystal in the axial direction in cm.
- transaxial_crystal_size: size of the cristal in the transaxial size in cm.
- crystal_thickness: thickness of the crystal in cm.
- energy_resolution: FWHM in keV it will be divided by reference energy (511 keV).
- min_energy_window: min energy threshold in keV.
- max_energy_window: max energy threshold in keV.
- num_aa_bins: number of views (half of the number of detectors per ring).
- num_td_bins: number of radial bins.
- coincidence_window: used only for randoms simulation, in ns.
- psf_value: sinogram preprocessing parameter.
- add_noise: sinogram preprocessing parameter.
- analytical_att_correction: performed by SimSET calcattenuation.
- stir_recons_att_corr: performed in STIR by entering the att image as a normalization map.
- analytic_scatt_corr_factor: 0.15 will remove 85% of scatter, 0 will remove scatter.
- stir_scatt_corr_smoothing: will use smoothed SimSET scatter as additive_sinogram.
- analytic_randoms_corr_factor: 0.15 will remove 85% of scatter, 0 will remove randoms.
- stir_randoms_corr_smoothing: will include smoothed SimSET randoms in the additive_sinogram.
- recons_type: one of OSEM3D, OSEM2D, FBP2D, FBP3D.
- max_segment: maximum Ring difference on the reconstruction.
- zoomFactor: relation between sinogram bin size and X, Y voxel size.
- xyOutputSize: output matrix X,Y size in reconstruction.
- zOutputSize: output marix Z size in reconstruction.
- numberOfSubsets: number of subsets in reconstruction.
- numberOfIterations: number of iterations in iterative reconstruction.
- savingInterval: interval that to save intermediate subiterations images.
- inter_iteration_filter: 1 for activation, 0 for deactivation.
- subiteration_interval:
- x_dir_filter_FWHM: postprocessing filter X size in mm.
- y_dir_filter_FWHM: postprocessing filter Y size in mm.
- z_dir_filter_FWHM: postprocessing filter Z size in mm.
SimSET and SimPET simulation