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Fix phantoms ci (#312)
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* update phantom conversion scripts
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@bendhouseart
bendhouseart committed Jun 7, 2024
1 parent e49524e commit c90be5e
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Showing 3 changed files with 137 additions and 129 deletions.
4 changes: 4 additions & 0 deletions .github/workflows/phantoms.yaml
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Expand Up @@ -144,6 +144,10 @@ jobs:
- name: SetupMatlab
if: ${{ matrix.os == 'ubuntu-20.04' }}
uses: matlab-actions/setup-matlab@v1
# note matlab-actions/setup-matlab@v2 breaks this script, don't update unless you're forced to
#with:
#release: 'R2023a'
#cache: true

- name: Run Matlab Conversion Script on Phantoms
if: ${{ matrix.os == 'ubuntu-20.04' }}
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142 changes: 72 additions & 70 deletions scripts/matlab_conversions.m
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Expand Up @@ -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
% ----------------------------------------------
Expand Down Expand Up @@ -524,79 +526,79 @@

% 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
% ----------------------------------------------

% 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
120 changes: 61 additions & 59 deletions scripts/python_conversions.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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