diff --git a/scripts/compare_jsons.py b/scripts/compare_jsons.py old mode 100644 new mode 100755 diff --git a/scripts/matlab_conversions.m b/scripts/matlab_conversions.m index 03d7ce49..a5cf1b6b 100644 --- a/scripts/matlab_conversions.m +++ b/scripts/matlab_conversions.m @@ -106,7 +106,7 @@ meta.FrameDuration = 300; meta.FrameTimesStart = 0; meta.ReconFilterType = "none"; - meta.ReconFilterSize = 1; + %meta.ReconFilterSize = 1; dcm2niix4pet(fullfile(source,'SiemensBiographPETMR-NRU'),meta,... 'o',fullfile(destination,['sub-SiemensBiographNRU' filesep 'pet'])); % note we only need to use folders here @@ -169,7 +169,7 @@ meta.AttenuationCorrection = 'MR-corrected'; meta.FrameDuration = 600; meta.FrameTimesStart = 0; - meta.ReconFilterType = "none"; + meta.ReconFilterType = "unknown"; meta.ReconFilterSize = 0; meta.ReconMethodParameterLabels = ["none"]; meta.ReconMethodParameterUnits = ["none"]; @@ -207,7 +207,7 @@ meta.ReconstructionMethod = 'LOR-RAMLA'; meta.FrameDuration = 1798; meta.FrameTimesStart = 0; - meta.ReconFilterType = "none"; + meta.ReconFilterType = "n/a"; meta.ReconFilterSize = 1; dcm2niix4pet(fullfile(source,['PhilipsGeminiPETMR-Unimedizin' filesep 'reqCTAC']),meta,... @@ -250,7 +250,7 @@ meta.ScatterCorrectionMethod = 'SS-SIMUL'; % field added in our library meta.ReconstructionMethod = 'BLOB-OS-TF'; %meta.FrameDuration = repmat(122.238007,20,1); - meta.FrameTimesStart = 0; + %meta.FrameTimesStart = 0; meta.ReconFilterType = "unknown"; meta.ReconFilterSize = 1; @@ -285,8 +285,8 @@ meta.ScatterCorrectionMethod = 'SS-SIMUL'; meta.ReconstructionMethod = 'LOR-RAMLA'; %meta.FrameDuration = repmat(122.238007,40,1); - meta.FrameTimesStart = 0; - meta.ReconFilterType = "unknown"; + %meta.FrameTimesStart = 0; + meta.ReconFilterType = "n/a"; meta.ReconFilterSize = 1; dcm2niix4pet(fullfile(source,'PhilipsIngenuityPETMR-AmsterdamUMC'),meta,... @@ -318,7 +318,7 @@ meta.RandomsCorrectionMethod = 'DLYD'; meta.ReconstructionMethod = 'OSEM:i3s15'; %meta.FrameDuration = repmat(1221.780029,40,1); - meta.FrameTimesStart = 0; + %meta.FrameTimesStart = 0; meta.ReconFilterType = "unknown"; meta.ReconFilterSize = 1; @@ -384,7 +384,7 @@ meta.ImageDecayCorrectionTime = 0; meta.FrameDuration = 98000; meta.FrameTimesStart = 0; - meta.ReconFilterType = "none"; + meta.ReconFilterType = "n/a"; meta.ReconFilterSize = 1; dcm2niix4pet(fullfile(source,'GeneralElectricSignaPETMR-NIMH'),meta,... @@ -412,12 +412,12 @@ meta.AcquisitionMode = 'list mode'; meta.ImageDecayCorrected = 'true'; meta.ImageDecayCorrectionTime = 0; - meta.ScatterCorrectionMethod = 'Gaussian Fit'; + meta.ScatterCorrectionMethod = 'Convolution subtraction'; meta.FrameDuration = 98000; meta.FrameTimesStart = 0; meta.ReconMethodParameterLabels = ["none"]; meta.ReconParameterUnits = ["none"]; - meta.ReconMethodParameterValues = [0]; + meta.ReconMethodParameterValues = [0, 0]; meta.ReconFilterType = "none"; meta.ReconFilterSize = 1; diff --git a/scripts/python_conversions.sh b/scripts/python_conversions.sh old mode 100644 new mode 100755 index 34c7ca4e..5d4d56a3 --- a/scripts/python_conversions.sh +++ b/scripts/python_conversions.sh @@ -72,7 +72,7 @@ FrameTimesStart="[0]" \ FrameDuration=[300] \ ImageDecayCorrected="true" \ ImageDecayCorrectionTime=0 \ -DecayCorrectionFactor=[1] \ +#DecayCorrectionFactor=[1] \ AttenuationCorrection="MR-corrected" \ InjectionStart=0 @@ -124,10 +124,10 @@ ImageDecayCorrected="true" \ ImageDecayCorrectionTime=0 \ AttenuationCorrection="MR-corrected" \ ReconFilterType='unknown' \ -ReconFilterSize=1 \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ -ReconMethodParameterValues="[0, 0]" +ReconFilterSize=0 \ +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ +ReconMethodParameterValues="[0]" # Johannes Gutenberg University of Mainz # -------------------------------------- @@ -152,14 +152,14 @@ AcquisitionMode="list mode" \ ImageDecayCorrected=True \ ImageDecayCorrectionTime=0 \ ReconFilterType='n/a' \ -ReconFilterSize=0 \ +ReconFilterSize=1 \ AttenuationCorrection="CTAC-SG" \ ScatterCorrectionMethod="SS-SIMUL" \ ReconstructionMethod="LOR-RAMLA" \ -ReconMethodParameterValues="[1,1]" \ +ReconMethodParameterValues="[0]" \ FrameDuration=[1798] \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ FrameTimesStart=[0] \ echo "${SOURCE_FOLDER}/PhilipsGeminiPETMR-Unimedizin/reqNAC" @@ -179,14 +179,14 @@ AcquisitionMode="list mode" \ ImageDecayCorrected=True \ ImageDecayCorrectionTime=0 \ ReconFilterType=None \ -ReconFilterSize=0 \ +ReconFilterSize=1 \ AttenuationCorrection="None" \ ScatterCorrectionMethod="None" \ ReconstructionMethod="3D-RAMLA" \ FrameDuration=[1798] \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ -ReconMethodParameterValues="[1,1]" \ +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ +ReconMethodParameterValues="[0]" \ FrameTimesStart=[0] \ @@ -212,16 +212,16 @@ AcquisitionMode="list mode" \ ImageDecayCorrected="true" \ ImageDecayCorrectionTime=0 \ DecayCorrectionFactor=[1] \ -ReconFilterSize=0 \ +ReconFilterSize=1 \ ReconMethodParameterValues=[1] \ AttenuationCorrection="CTAC-SG" \ RandomsCorrectionMethod="DLYD" \ ScatterCorrectionMethod="SS-SIMUL" \ ReconstructionMethod="BLOB-OS-TF" \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ -ReconMethodParameterValues="[0, 0]" \ -ReconFilterType="none" \ +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ +ReconMethodParameterValues="[0]" \ +ReconFilterType="unknown" \ #FrameTimesStart=[0] #TimeZero="12:12:12" \ @@ -245,17 +245,17 @@ AcquisitionMode="list mode" \ ImageDecayCorrected="True" \ ImageDecayCorrectionTime=0 \ ReconFilterType="None" \ -ReconFilterSize=0 \ +ReconFilterSize=1 \ AttenuationCorrection="MRAC" \ RandomsCorrectionMethod="DLYD" \ ScatterCorrectionMethod="SS-SIMUL" \ ReconstructionMethod="LOR-RAMLA" \ ReconMethodParameterValues="[1, 1]" \ -ReconFilterType="['n/a', 'n/a']" \ +ReconFilterType="n/a" \ DecayCorrectionFactor=[1] \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ -ReconMethodParameterValues="[0, 0]" +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ +ReconMethodParameterValues="[0]" # philipsVereosPET-CT # ------------------- @@ -275,13 +275,13 @@ ModeOfAdministration="infusion" \ AcquisitionMode="list mode" \ ImageDecayCorrected="True" \ ImageDecayCorrectionTime=0 \ -ReconFilterType="None" \ -ReconFilterSize=0 \ +ReconFilterType="unknown" \ AttenuationCorrection="CTAC-SG" \ ScatterCorrectionMethod="SS-SIMUL" \ RandomsCorrectionMethod="DLYD" \ ReconstructionMethod="OSEMi3s15" \ -TimeZero="11:40:24" +TimeZero="11:40:24" \ +ReconFilterSize=1 \ #FrameDuration=[1221] @@ -337,9 +337,9 @@ FrameTimesStart="[0]" \ ImageDecayCorrectionTime=0 \ ReconFilterType="n/a" \ ReconFilterSize=1 \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ -ReconMethodParameterValues="[0, 0]" +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ +ReconMethodParameterValues="[0]" # General Electric Medical Systems Advance @@ -385,14 +385,14 @@ InjectionStart=0 \ SpecificRadioactivity=418713.8 \ ModeOfAdministration="infusion" \ FrameTimesStart="[0]" \ -ImageDecayCorrected='false' \ +ImageDecayCorrected='True' \ AttenuationCorrection='measured' \ AcquisitionMode='list mode' \ ImageDecayCorrectionTime="0" \ FrameDuration=[98000] \ ScatterCorrectionMethod="Gaussian Fit" \ ScanStart="0" \ -ReconMethodParameterLabels="[none, none]" \ -ReconMethodParameterUnits="[none, none]" \ -ReconMethodParameterValues="[0, 0]" +ReconMethodParameterLabels="[none]" \ +ReconMethodParameterUnits="[none]" \ +ReconMethodParameterValues="[0]"