From 21175ea616cfdbc6525eae4dbe669a14fb823d70 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Fri, 7 Jun 2024 16:22:25 -0400 Subject: [PATCH] update phantom conversion scripts --- scripts/matlab_conversions.m | 142 +++++++++++++++++----------------- scripts/python_conversions.sh | 120 ++++++++++++++-------------- 2 files changed, 133 insertions(+), 129 deletions(-) diff --git a/scripts/matlab_conversions.m b/scripts/matlab_conversions.m index 9d790f3..d3a0168 100644 --- a/scripts/matlab_conversions.m +++ b/scripts/matlab_conversions.m @@ -479,7 +479,9 @@ out = ecat2nii(fullfile(source,['SiemensHRRT-JHU' filesep 'Hoffman.v']),... meta,'gz',true,'FileListOut',fullfile(destination,['sub-SiemensHRRTJHU' filesep 'pet' filesep 'sub-SiemensHRRTJHU.nii'])); - +catch + disp(message); +end %% Johns Hopkins University % ---------------------------------------------- @@ -524,42 +526,42 @@ % General Electric Medical Systems Advance % ----------------------------------------- -try - clear meta - meta.TimeZero = 'ScanStart'; - meta.Manufacturer = 'GE MEDICAL SYSTEMS'; - meta.ManufacturersModelName = 'GE Advance'; - meta.InstitutionName = 'Johns Hopkins University, USA'; - meta.BodyPart = 'Phantom'; - meta.Units = 'Bq/mL'; - meta.TracerName = 'FDG'; - meta.TracerRadionuclide = 'F18'; - 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 = 'Single-scatter simulation'; - meta.ReconMethodName = '3D Reprojection'; - meta.ReconMethodParameterLabels = ["none"]; - meta.ReconParameterUnits = ["none"]; - meta.ReconMethodParameterValues = [0]; - meta.ReconFilterType = "none"; - 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'])); - -catch - disp(message); -end +%try +% clear meta +% meta.TimeZero = 'ScanStart'; +% meta.Manufacturer = 'GE MEDICAL SYSTEMS'; +% meta.ManufacturersModelName = 'GE Advance'; +% meta.InstitutionName = 'Johns Hopkins University, USA'; +% meta.BodyPart = 'Phantom'; +% meta.Units = 'Bq/mL'; +% meta.TracerName = 'FDG'; +% meta.TracerRadionuclide = 'F18'; +% 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 = 'Single-scatter simulation'; +% meta.ReconMethodName = '3D Reprojection'; +% meta.ReconMethodParameterLabels = ["none"]; +% meta.ReconParameterUnits = ["none"]; +% meta.ReconMethodParameterValues = [0]; +% meta.ReconFilterType = "none"; +% 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'])); +% +%catch +% disp(message); +%end %% Chesapeake Medical Imaging % ---------------------------------------------- @@ -567,36 +569,36 @@ % Canon Cartesion Prime PET-CT % ---------------------- -try - clear meta - meta.TimeZero = 'ScanStart'; - meta.Manufacturer = 'Canon Medical Systems'; - meta.ManufacturersModelName = 'Cartesion Prime'; - meta.InstitutionName = 'Chesapeake Medical Imaging, USA'; - meta.BodyPart = 'Phantom'; - meta.Units = 'Bq/mL'; - meta.TracerName = 'FDG'; - meta.TracerRadionuclide = 'F18'; - meta.InjectedRadioactivity = 0.87; - meta.InjectedRadioactivityUnits = 'mCi'; - meta.SpecificRadioactivity = 'n/a'; - meta.SpecificRadioactivityUnits = 'n/a'; - meta.ModeOfAdministration = 'infusion'; - 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 = 4; - - dcm2niix4pet(fullfile(source,'CanonCartesionPrimePETCT-NIA'),... - meta,'o',fullfile(destination,['sub-CanonCartesionPrimeNIA' filesep 'pet'])); - -catch - disp(message); -end +%try +% clear meta +% meta.TimeZero = 'ScanStart'; +% meta.Manufacturer = 'Canon Medical Systems'; +% meta.ManufacturersModelName = 'Cartesion Prime'; +% meta.InstitutionName = 'Chesapeake Medical Imaging, USA'; +% meta.BodyPart = 'Phantom'; +% meta.Units = 'Bq/mL'; +% meta.TracerName = 'FDG'; +% meta.TracerRadionuclide = 'F18'; +% meta.InjectedRadioactivity = 0.87; +% meta.InjectedRadioactivityUnits = 'mCi'; +% meta.SpecificRadioactivity = 'n/a'; +% meta.SpecificRadioactivityUnits = 'n/a'; +% meta.ModeOfAdministration = 'infusion'; +% 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 = 4; +% +% dcm2niix4pet(fullfile(source,'CanonCartesionPrimePETCT-NIA'),... +% meta,'o',fullfile(destination,['sub-CanonCartesionPrimeNIA' filesep 'pet'])); +% +%catch +% disp(message); +%end diff --git a/scripts/python_conversions.sh b/scripts/python_conversions.sh index e10e2df..a736203 100644 --- a/scripts/python_conversions.sh +++ b/scripts/python_conversions.sh @@ -426,63 +426,65 @@ ReconFilterSize=2 # General Electric Medical Systems Advance # ----------------------------------------- -dcm2niix4pet $SOURCE_FOLDER/GeneralElectricAdvance-JHU/ --destination-path $DESTINATION/sub-GeneralElectricAdvanceJHU/pet --kwargs \ -Manufacturer='GE MEDICAL SYSTEMS' \ -ManufacturersModelName='GE Advance' \ -InstitutionName='Johns Hopkins University, USA' \ -BodyPart='Phantom' \ -Units='Bq/mL' \ -TracerName='FDG' \ -TracerRadionuclide='F18' \ -InjectedRadioactivity=0.788 \ -InjectedRadioactivityUnits='mCi' \ -SpecificRadioactivity='n/a' \ -SpecificRadioactivityUnits='n/a' \ -ModeOfAdministration='infusion' \ -ScanStart=0 \ -InjectionStart=-5336 \ -FrameTimesStart="[0]" \ -AcquisitionMode='list mode' \ -ImageDecayCorrected='true' \ -ImageDecayCorrectionTime=0 \ -ScatterCorrectionMethod='Single-scatter simulation' \ -ReconMethodParameterLabels='["none"]' \ -ReconMethodParameterUnits='["none"]' \ -ReconMethodParameterValues='[0]' \ -ReconFilterType="none" \ -ReconFilterSize=0 \ -AttenuationCorrection='2D-acquired transmission scan with a 68Ge pin' - - - -# Chesapeake Medical Imaging -# -------------------------- - - -# Canon Cartesion Prime PET-CT -# ---------------------------- -dcm2niix4pet $SOURCE_FOLDER/CanonCartesionPrimePETCT-NIA --destination-path $DESTINATION/sub-CanonCartesionPrimeNIA/pet --kwargs \ -Manufacturer='Canon Medical Systems' \ -ManufacturersModelName='Cartesion Prime' \ -InstitutionName='Chesapeake Medical Imaging, USA' \ -BodyPart='Phantom' \ -Units='Bq/mL' \ -TracerName='FDG' \ -TracerRadionuclide='F18' \ -InjectedRadioactivity=0.87 \ -InjectedRadioactivityUnits='mCi' \ -SpecificRadioactivity='n/a' \ -SpecificRadioactivityUnits='n/a' \ -ModeOfAdministration='infusion' \ -ScanStart=0 \ -InjectionStart=-2312 \ -FrameTimesStart="[0, 300, 600, 900]" \ -AcquisitionMode='list mode' \ -ImageDecayCorrected='true' \ -ImageDecayCorrectionTime=0 \ -ReconMethodParameterValues="[24, 5]" \ -ReconMethodParameterUnits="['none', 'none']" \ -ReconMethodParameterLabels="['subsets', 'iterations']" \ -ReconFilterType="Gaussian" \ -ReconFilterSize=4 +#echo "${SOURCE_FOLDER}/GeneralElectricAdvance-JHU" +#dcm2niix4pet $SOURCE_FOLDER/GeneralElectricAdvance-JHU/ --destination-path $DESTINATION/sub-GeneralElectricAdvanceJHU/pet --kwargs \ +#Manufacturer='GE MEDICAL SYSTEMS' \ +#ManufacturersModelName='GE Advance' \ +#InstitutionName='Johns Hopkins University, USA' \ +#BodyPart='Phantom' \ +#Units='Bq/mL' \ +#TracerName='FDG' \ +#TracerRadionuclide='F18' \ +#InjectedRadioactivity=0.788 \ +#InjectedRadioactivityUnits='mCi' \ +#SpecificRadioactivity='n/a' \ +#SpecificRadioactivityUnits='n/a' \ +#ModeOfAdministration='infusion' \ +#ScanStart=0 \ +#InjectionStart=-5336 \ +#FrameTimesStart="[0]" \ +#AcquisitionMode='list mode' \ +#ImageDecayCorrected='true' \ +#ImageDecayCorrectionTime=0 \ +#ScatterCorrectionMethod='Single-scatter simulation' \ +#ReconMethodParameterLabels='["none"]' \ +#ReconMethodParameterUnits='["none"]' \ +#ReconMethodParameterValues='[0]' \ +#ReconFilterType="none" \ +#ReconFilterSize=0 \ +#AttenuationCorrection='2D-acquired transmission scan with a 68Ge pin' +# +# +# +## Chesapeake Medical Imaging +## -------------------------- +# +# +## Canon Cartesion Prime PET-CT +## ---------------------------- +#echo "${SOURCE_FOLDER}/CanonCartesionPrimePETCT-NIA" +#dcm2niix4pet $SOURCE_FOLDER/CanonCartesionPrimePETCT-NIA --destination-path $DESTINATION/sub-CanonCartesionPrimeNIA/pet --kwargs \ +#Manufacturer='Canon Medical Systems' \ +#ManufacturersModelName='Cartesion Prime' \ +#InstitutionName='Chesapeake Medical Imaging, USA' \ +#BodyPart='Phantom' \ +#Units='Bq/mL' \ +#TracerName='FDG' \ +#TracerRadionuclide='F18' \ +#InjectedRadioactivity=0.87 \ +#InjectedRadioactivityUnits='mCi' \ +#SpecificRadioactivity='n/a' \ +#SpecificRadioactivityUnits='n/a' \ +#ModeOfAdministration='infusion' \ +#ScanStart=0 \ +#InjectionStart=-2312 \ +#FrameTimesStart="[0, 300, 600, 900]" \ +#AcquisitionMode='list mode' \ +#ImageDecayCorrected='true' \ +#ImageDecayCorrectionTime=0 \ +#ReconMethodParameterValues="[24, 5]" \ +#ReconMethodParameterUnits="['none', 'none']" \ +#ReconMethodParameterLabels="['subsets', 'iterations']" \ +#ReconFilterType="Gaussian" \ +#ReconFilterSize=4