From f6d4993e99fdc91508830030b4336fcd7e9d00e8 Mon Sep 17 00:00:00 2001 From: Murat Bilgel Date: Mon, 4 Mar 2024 10:12:18 -0500 Subject: [PATCH] More phantom conversion fixes --- scripts/matlab_conversions.m | 50 ++++++++++++++++++++++------------- scripts/python_conversions.sh | 10 +++---- 2 files changed, 37 insertions(+), 23 deletions(-) diff --git a/scripts/matlab_conversions.m b/scripts/matlab_conversions.m index b6fcdb78..56bcfb71 100644 --- a/scripts/matlab_conversions.m +++ b/scripts/matlab_conversions.m @@ -471,17 +471,23 @@ meta.Units = 'Bq/mL'; meta.TracerName = 'FDG'; meta.TracerRadionuclide = 'F18'; - meta.InjectedRadioactivity = 81.24; % Mbq - meta.SpecificRadioactivity = 1.3019e+04; % ~ 81240000 Bq/ 6240 g + meta.InjectedRadioactivity = 0.788; + meta.InjectedRadioactivityUnits = 'mCi'; + meta.SpecificRadioactivity = 'n/a'; + meta.SpecificRadioactivityUnits = 'n/a'; meta.ModeOfAdministration = 'infusion'; meta.AcquisitionMode = 'list mode'; meta.ImageDecayCorrected = true; % when passing this as string it fails validation meta.ImageDecayCorrectionTime = 0; - meta.ReconFilterType = 'none'; - meta.ReconFilterSize = 0; + meta.ReconFilterType = 'Gaussian'; + meta.ReconFilterSize = 2; meta.AttenuationCorrection = 'transmission scan with a 137Cs point source'; - % meta.FrameDuration = 1200; % not needed, encoded in ecat even for 4D images - % meta.FrameTimesStart = 0; + meta.ScatterCorrectionMethod = 'Single-scatter simulation'; + meta.ScanStart = 0; + meta.InjectionStart = -2183; + meta.ReconMethodParameterLabels = ["subsets" "iterations"]; + meta.ReconMethodParameterLabels = ["none" "none"]; + meta.ReconMethodParameterValues = [16 2]; out = ecat2nii(fullfile(source,['SiemensHRRT-JHU' filesep 'Hoffman.v']),... meta,'gz',true,'FileListOut',fullfile(destination,['sub-SiemensHRRTJHU' filesep 'pet' filesep 'sub-SiemensHRRTJHU.nii'])); @@ -503,23 +509,25 @@ meta.Units = 'Bq/mL'; meta.TracerName = 'FDG'; meta.TracerRadionuclide = 'F18'; - meta.InjectedRadioactivity = 75.8500; % Mbq - meta.SpecificRadioactivity = 418713.8; % ~ 75850000 Bq/ 6240 g + meta.InjectedRadioactivity = 0.788; + meta.InjectedRadioactivityUnits = 'mCi'; + meta.SpecificRadioactivity = 'n/a'; + meta.SpecificRadioactivityUnits = 'n/a'; meta.ModeOfAdministration = 'infusion'; + meta.ScanStart = 0; + meta.InjectionStart = -5336; meta.FrameTimesStart = 0; meta.AcquisitionMode = 'list mode'; meta.ImageDecayCorrected = 'true'; meta.ImageDecayCorrectionTime = 0; - meta.ScatterCorrectionMethod = 'Gaussian Fit'; - meta.FrameDuration = 98000; - meta.FrameTimesStart = 0; - meta.ReconMethodName = 'filtered backprojection with ramp filter'; + meta.ScatterCorrectionMethod = 'Single-scatter simulation'; + meta.ReconMethodName = '3D Reprojection'; meta.ReconMethodParameterLabels = ["none"]; meta.ReconParameterUnits = ["none"]; meta.ReconMethodParameterValues = [0]; meta.ReconFilterType = "none"; - meta.ReconFilterSize = 1; - meta.AttenuationCorrection = '2D-acquired transmission scan with a 68Ge rod source'; + meta.ReconFilterSize = 0; + meta.AttenuationCorrection = '2D-acquired transmission scan with a 68Ge pin'; dcm2niix4pet(fullfile(source,'GeneralElectricAdvance-JHU'),... meta,'o',fullfile(destination,['sub-GeneralElectricAdvanceJHU' filesep 'pet'])); @@ -544,16 +552,22 @@ meta.Units = 'Bq/mL'; meta.TracerName = 'FDG'; meta.TracerRadionuclide = 'F18'; - meta.InjectedRadioactivity = 32.19; % Mbq - meta.SpecificRadioactivity = 32190000/6240; + meta.InjectedRadioactivity = 0.87; + meta.InjectedRadioactivityUnits = 'mCi'; + meta.SpecificRadioactivity = 'n/a'; + meta.SpecificRadioactivityUnits = 'n/a'; meta.ModeOfAdministration = 'infusion'; - meta.FrameTimesStart = 0; + meta.ScanStart = 0; + meta.InjectionStart = -2312; + meta.FrameTimesStart = [0 300 600 900]; meta.AcquisitionMode = 'list mode'; meta.ImageDecayCorrected = 'true'; meta.ImageDecayCorrectionTime = 0; + meta.ReconMethodParameterLabels = ["subsets" "iterations"]; + meta.ReconMethodParameterLabels = ["none" "none"]; meta.ReconMethodParameterValues = [24 5]; meta.ReconFilterType = "Gaussian"; - meta.ReconFilterSize = 2; + meta.ReconFilterSize = 4; dcm2niix4pet(fullfile(source,'CanonCartesionPrimePETCT-NIA'),... meta,'o',fullfile(destination,['sub-CanonCartesionPrimeNIA' filesep 'pet'])); diff --git a/scripts/python_conversions.sh b/scripts/python_conversions.sh index f29c7e19..2ca17816 100644 --- a/scripts/python_conversions.sh +++ b/scripts/python_conversions.sh @@ -408,8 +408,8 @@ ReconMethodParameterUnits="[none, none]" \ ReconMethodParameterValues="[0, 0]" \ --silent -# John Hopkins University -# ----------------------- +# Johns Hopkins University +# ------------------------ # Siemens HRRT # ------------ @@ -433,8 +433,6 @@ ModeOfAdministration='infusion' \ AcquisitionMode='list mode' \ ImageDecayCorrected=true \ ImageDecayCorrectionTime=0 \ -ReconFilterType='none' \ -ReconFilterSize=0 \ AttenuationCorrection='transmission scan with a 137Cs point source' \ ScatterCorrectionMethod='Single-scatter simulation' \ ScanStart=0 \ @@ -467,7 +465,9 @@ AcquisitionMode='list mode' \ ImageDecayCorrected='true' \ ImageDecayCorrectionTime=0 \ ScatterCorrectionMethod='Single-scatter simulation' \ -FrameTimesStart="[0]" \ +ReconMethodParameterLabels='["none"]' \ +ReconMethodParameterUnits='["none"]' \ +ReconMethodParameterValues='[0]' \ ReconFilterType="none" \ ReconFilterSize=0 \ AttenuationCorrection='2D-acquired transmission scan with a 68Ge pin'