Updating scanner configs.

txusser · Sep 4, 2023 · eba66ac · eba66ac
1 parent 3447b66
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diff --git a/configs/params/scanner/discovery_st.yaml b/configs/params/scanner/discovery_st.yaml
@@ -0,0 +1,76 @@
+scanner_name: "GE Discovery ST"
+validation_status: "None"     # None, Partial, Validated
+
+# Scanner Description
+#------------------------------------
+simset_material: 10           # BGO
+average_doi: 0.84             # ¿0.84? cm
+scanner_radius: 44.31         # Scanner radius
+num_rings:  24                # Number of rings
+axial_fov: 15.7               # Axial FOV max (cm)
+transaxial_fov: 88.62         # Transaxial FOV (If unknown use diameter) 
+crystals_per_ring: 420        # Number of crystals per ring ¿Unused?
+
+# Crystal Description
+#------------------------------------
+transaxial_crystal_size: 0.63   # Transaxial Crystal size (cm).
+z_crystal_size: 0.63            # Axial Crystal size (cm)
+crystal_thickness: 3            # Crystal Thickness (cm)
+
+# Energy characteristics
+#-------------------------------------
+energy_resolution: 17          # Energy resolution (%)
+min_energy_window:  375
+max_energy_window:  675
+
+# Sinogram creation
+#-------------------------------------
+# Binning
+num_aa_bins:  210            # Number of views (usualy crystals_per_ring/2)
+num_td_bins:  249            # Number of bins
+
+# Coincidence window (ns)
+coincidence_window: 11.7        # nanoseconds. Used only for random simulation (SimSET)
+
+# Sinograms pre-processing
+psf_value: 1.125
+add_noise: 0
+
+# Corrections
+#--------------------------------------
+# Attenuation correction
+analytical_att_correction: 0    # Performed by SimSET calcattenuation
+stir_recons_att_corr: 1         # Performed in STIR by entering the att image as a normalization map
+
+# Scatter Correction
+analytic_scatt_corr_factor:  0.15    # 0.15 WILL REMOVE 85% of scatter.0 will remove scatter
+stir_scatt_corr_smoothing:   0       # Will use smoothed SimSET scatter as additive_sinogram.
+
+# Randoms Correction
+analytic_randoms_corr_factor: 0.2    # 0.15 WILL REMOVE 85% of scatter.0 will remove randoms
+stir_randoms_corr_smoothing: 0       # Will include smoothed SimSET randoms in the additive_sinogram.
+
+# Reconstruction
+#--------------------------
+recons_type: "OSEM3D"
+max_segment: 23             # Maximum Ring difference on the reconstruction
+
+#Configure Reconstruction output
+zoomFactor: 1               # Zoom factor in x and y
+xyOutputSize: 256
+zOutputSize: 47
+xyOutputVoxelSize: 2        # mm
+zOutputVoxelSize: 3.27      # mm
+numberOfSubsets: 7          # Number of subsets
+numberOfIterations: 32      # Number of iterations
+savingInterval: 8           # The interval that we want to save intermediate subiterations images
+
+# Filter
+inter_iteration_filter: 0 #1 for activate, 0 for deactivate
+subiteration_interval: 4
+x_dir_filter_FWHM: 0 # in mm
+y_dir_filter_FWHM: 0 # in mm
+z_dir_filter_FWHM: 0 # in mm
+
+
+
diff --git a/configs/params/scanner/discovery_ste.yaml b/configs/params/scanner/discovery_ste.yaml
@@ -0,0 +1,76 @@
+scanner_name: "GE Discovery STE"
+validation_status: "None"     # None, Partial, Validated
+
+# Scanner Description
+#-------------------------------
+simset_material: 10           # BGO
+average_doi: 0.84             # ¿0.84? cm
+scanner_radius: 44.31         # Scanner radius
+num_rings:  24                # Number of rings
+axial_fov: 15.7               # Axial FOV max (cm)
+transaxial_fov: 88.62         # Transaxial FOV (cm)
+crystals_per_ring: 560        # Number of crystals per ring ¿Unused?
+
+# Crystal Description
+#--------------------------------
+transaxial_crystal_size: 0.47 # Transaxial Crystal size (cm). En el ST es 0.63
+z_crystal_size: 0.63           # Axial Crystal size (cm)
+crystal_thickness: 3          # Crystal Thickness (cm)
+
+# Energy characteristics
+#---------------------------------
+energy_resolution: 16          # Energy resolution (%)
+min_energy_window:  375
+max_energy_window:  675
+
+# Sinogram creation
+#----------------------------------
+# Binning
+num_aa_bins:  280            # Number of views (Numero de detectores por anillo divido por 2)
+num_td_bins:  293            # Number of bins
+
+# Coincidence window (ns)
+coincidence_window: 11.7        # nanoseconds. Used only for random simulation (SimSET)
+
+# Sinogram pre-processing
+psf_value: 1.125
+add_noise: 0
+
+# Corrections
+#-----------------------------------
+# Attenuation correction
+analytical_att_correction: 0    # Performed by SimSET calcattenuation
+stir_recons_att_corr: 1         # Performed in STIR by entering the att image as a normalization map
+
+# Scatter Correction
+analytic_scatt_corr_factor:  0.15      # 0.15 WILL REMOVE 85% of scatter.0 will remove scatter
+stir_scatt_corr_smoothing:   0      # Will use smoothed SimSET scatter as additive_sinogram.
+
+# Randoms Correction
+analytic_randoms_corr_factor: 0.2     # 0.15 WILL REMOVE 85% of scatter.0 will remove randoms
+stir_randoms_corr_smoothing: 0       # Will include smoothed SimSET randoms in the additive_sinogram.
+
+# Reconstruction
+#-------------------------------------
+recons_type: "OSEM3D"
+max_segment: 23             # Maximum Ring difference on the reconstruction
+
+# Configure Reconstruction output
+zoomFactor: 1.55             # Zoom factor in x and y
+xyOutputSize: 128
+zOutputSize: 47
+xyOutputVoxelSize: 2         # mm
+zOutputVoxelSize: 3.27       # mm
+numberOfSubsets: 7           # Number of subsets
+numberOfIterations: 32       # Number of iterations
+savingInterval: 8            # The interval that we want to save intermediate subiterations images
+
+# Filter
+inter_iteration_filter: 0 #1 for activate, 0 for deactivate
+subiteration_interval: 4 
+x_dir_filter_FWHM: 1.5  # in mm
+y_dir_filter_FWHM: 1.5  # in mm
+z_dir_filter_FWHM: 3  # in mm
+
+
+
diff --git a/configs/params/scanner/ge_advance.yaml b/configs/params/scanner/ge_advance.yaml
@@ -0,0 +1,73 @@
+scanner_name: "GE Advance"
+validation_status: "None"     # None, Partial, Validated
+
+# Scanner Description
+# --------------------------------------
+simset_material: 10           # BGO
+average_doi: 0.0              # cm
+scanner_radius: 46.35         # Scanner radius
+num_rings:  18                # Number of rings
+axial_fov: 15.2               # Axial FOV max (cm) 
+transaxial_fov: 84            # Transaxial FOV (If unknown use diameter) 
+crystals_per_ring: 672        # Number of crystals per ring ¿Unused?
+
+# Crystal Description
+#----------------------------------------
+transaxial_crystal_size: 0.4 # Transaxial Crystal size (cm).
+z_crystal_size: 0.81          # Axial Crystal size (cm)
+crystal_thickness: 3          # Crystal Thickness (cm)
+
+# Energy characteristics
+#-----------------------------------------
+energy_resolution: 20          # Energy resolution (%)
+min_energy_window:  375
+max_energy_window:  675
+
+# Sinogram creation
+#-----------------------------------------
+# Binning
+num_aa_bins:  336            # Number of views (Numero de detectores por anillo divido por 2)
+num_td_bins:  281            # Number of bins
+
+# Coincidence window (ns)
+coincidence_window: 12.5     # nanoseconds. Used only for random simulation (SimSET)
+
+# Sinogram pre-processing
+psf_value: 1.125
+add_noise: 0.01
+
+# Corrections
+#-----------------------------------
+# Attenuation correction
+analytical_att_correction: 1    # Performed by SimSET calcattenuation
+stir_recons_att_corr: 0         # Performed in STIR by entering the att image as a normalization map
+
+# Scatter Correction
+analytic_scatt_corr_factor:  0.15   # 0.15 WILL REMOVE 85% of scatter.0 will remove scatter
+stir_scatt_corr_smoothing:   0      # Will use smoothed SimSET scatter as additive_sinogram.
+
+# Randoms Correction
+analytic_randoms_corr_factor: 0.2    # 0.15 WILL REMOVE 85% of scatter.0 will remove randoms
+stir_randoms_corr_smoothing: 0       # Will include smoothed SimSET randoms in the additive_sinogram.
+
+# Reconstruction
+#-----------------------------------
+recons_type: "OSEM3D"
+max_segment: 11              # Maximum Ring difference on the reconstruction
+
+# Configure Reconstruction output
+zoomFactor: 1.69             # Zoom factor in x and y
+xyOutputSize: 128
+zOutputSize: 35
+xyOutputVoxelSize: 2         # mm
+zOutputVoxelSize: 4.25       # mm
+numberOfSubsets: 14          # Number of subsets
+numberOfIterations: 56       # Number of iterations
+savingInterval: 28           # The interval that we want to save intermediate subiterations images
+
+# Filter
+inter_iteration_filter: 0 #1 for activate, 0 for deactivate
+subiteration_interval: 
+x_dir_filter_FWHM:  # in mm
+y_dir_filter_FWHM:  # in mm
+z_dir_filter_FWHM:  # in mm
diff --git a/scanners/preclinical_Albira_SI.yml → ...params/scanner/preclinical_albira_si.yaml b/scanners/preclinical_Albira_SI.yml → ...params/scanner/preclinical_albira_si.yaml
diff --git a/scanners/preclinical_Inveon.yml → ...gs/params/scanner/preclinical_inveon.yaml b/scanners/preclinical_Inveon.yml → ...gs/params/scanner/preclinical_inveon.yaml
diff --git a/configs/params/scanner/siemens_mct.yaml b/configs/params/scanner/siemens_mct.yaml
@@ -0,0 +1,73 @@
+scanner_name: "Siemens Biograph mCT"
+validation_status: "None"       # None, Partial, Validated
+
+# Scanner Description
+#------------------------------------
+simset_material: 18       # LSO
+average_doi: 0.1          # cm
+scanner_radius: 42.1      # Scanner radius
+num_rings:  52            # Number of rings
+axial_fov: 21.8           # Axial FOV max (cm)
+transaxial_fov: 84.2      # Transaxial FOV (If unknown use diameter) 
+crystal_per_ring: 624     # Number of crystals per ring ¿Unused?
+
+# Crystal Description
+#------------------------------------
+transaxial_crystal_size: 0.4 # Transaxial Crystal size (cm)
+z_crystal_size: 0.4
+crystal_thickness: 2         # Crystal Thickness (cm)
+
+# Energy characteristics
+#-------------------------------------
+energy_resolution: 11.5      # Energy resolution (%)
+min_energy_window:  435
+max_energy_window:  650
+
+# Sinogram creation
+#-------------------------------------
+# Binning
+num_aa_bins:  312         # Number of views (Numero de detectores por anillo divido por 2)
+num_td_bins:  312         # Number of bins
+
+# Coincidence window (ns)
+coincidence_window: 4.1  # nanoseconds. Used only for random simulation (SimSET)
+
+#Sinogram pre-processing
+psf_value: 1 #1.125
+add_noise: 0
+
+# Corrections
+#-------------------------------
+# Attenuation correction 
+analytical_att_correction: 0    # Performed by SimSET calcattenuation
+stir_recons_att_corr: 1        # Performed in STIR by entering the att image as a normalization map
+
+# Scatter Correction
+analytic_scatt_corr_factor:  0.15      # 0.15 WILL REMOVE 85% of scatter.0 will remove scatter
+stir_scatt_corr_smoothing:   0      # Will use smoothed SimSET scatter as additive_sinogram.
+
+# Randoms Correction
+analytic_randoms_corr_factor: 0.2     # 0.15 WILL REMOVE 85% of scatter.0 will remove randoms
+stir_randoms_corr_smoothing: 0       # Will include smoothed SimSET randoms in the additive_sinogram.
+
+# Reconstruction
+#---------------------------------
+recons_type: "OSEM3D"
+max_segment:  49         # Maximum Ring difference on the reconstruction
+
+# Configure Reconstruction output
+zoomFactor: 2.65         # Zoom factor in x and y
+xyOutputSize:  400     
+zOutputSize:  148
+xyOutputVoxelSize: 1.50  # mm  
+zOutputVoxelSize: 1.50   # mm  
+numberOfSubsets:  26     # Number of subsets
+numberOfIterations: 130  # Number of iterations
+savingInterval: 26       # The interval that we want to save intermediate subiterations images
+
+# Filter
+inter_iteration_filter: 0 #1 for activate, 0 for deactivate
+subiteration_interval: 4
+x_dir_filter_FWHM: 0  # in mm
+y_dir_filter_FWHM: 0  # in mm
+z_dir_filter_FWHM: 0  # in mm
diff --git a/configs/params/scanner/siemens_mmr.yaml b/configs/params/scanner/siemens_mmr.yaml
@@ -0,0 +1,73 @@
+scanner_name: "Siemens Biograph mMR"
+validation_status: "None"     # None, Partial, Validated
+
+# Scanner Description
+#-------------------------------------
+simset_material: 18        # LSO
+average_doi: 0.7           # cm
+scanner_radius: 32.8       # Scanner radius
+num_rings: 64              # Number of rings
+axial_fov: 25.8            # Axial FOV max (cm)
+transaxial_fov: 64.0       # Transaxial FOV (If unknown use diameter) 
+crystals_per_ring: 448     # Number of crystals per ring ¿Unused?
+
+# Crystal Description
+#--------------------------------------
+transaxial_crystal_size: 0.4 # Transaxial Crystal size (cm)
+z_crystal_size: 0.4
+crystal_thickness: 2         # Crystal Thickness (cm)
+
+# Energy characteristics
+#---------------------------------------
+energy_resolution: 14.5      # Energy resolution (%)
+min_energy_window:  430
+max_energy_window:  610
+
+# Sinogram creation
+#----------------------------------------
+# Binning
+num_aa_bins:  224         # Number of views (Numero de detectores por anillo divido por 2)
+num_td_bins:  292         # Number of bins
+
+# Coincidence window (ns)
+coincidence_window: 5.86  # nanoseconds. Used only for random simulation (SimSET)
+
+# Sinogram pre-processing
+psf_value: 1 #1.125
+add_noise: 0
+
+# Corrections
+#------------------------------------
+# Attenuation correction
+analytical_att_correction: 0    # Performed by SimSET calcattenuation
+stir_recons_att_corr: 1        # Performed in STIR by entering the att image as a normalization map
+
+# Scatter Correction
+analytic_scatt_corr_factor:  0.15      # 0.15 WILL REMOVE 85% of scatter.0 will remove scatter
+stir_scatt_corr_smoothing:   0      # Will use smoothed SimSET scatter as additive_sinogram.
+
+# Randoms Correction
+analytic_randoms_corr_factor: 0.2     # 0.15 WILL REMOVE 85% of scatter.0 will remove randoms
+stir_randoms_corr_smoothing: 0       # Will include smoothed SimSET randoms in the additive_sinogram.
+
+# Reconstruction
+#-------------------------------------
+recons_type: "OSEM3D"
+max_segment:  60         # Maximum Ring difference on the reconstruction
+
+# Configure Reconstruction output
+zoomFactor: 1.07 #0.91   # Zoom factor in x and y
+xyOutputSize:  344     
+zOutputSize:  127
+xyOutputVoxelSize: 2.0   # mm
+zOutputVoxelSize: 2.0    # mm  
+numberOfSubsets:  28     # Number of subsets
+numberOfIterations: 112  # Number of iterations
+savingInterval: 28       # The interval that we want to save intermediate subiterations images
+
+# Filter
+inter_iteration_filter: 0 #1 for activate, 0 for deactivate
+subiteration_interval: 4
+x_dir_filter_FWHM:  # in mm
+y_dir_filter_FWHM:  # in mm
+z_dir_filter_FWHM:  # in mm