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touching up conversion inputs, added in philips for matlab
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@bendhouseart
bendhouseart committed Nov 29, 2023
1 parent 9ff7332 commit b043bab
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Showing 3 changed files with 43 additions and 43 deletions.
Empty file modified scripts/compare_jsons.py
100644 → 100755
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20 changes: 10 additions & 10 deletions scripts/matlab_conversions.m
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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"];
Expand Down Expand Up @@ -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,...
Expand Down Expand Up @@ -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;

Expand Down Expand Up @@ -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,...
Expand Down Expand Up @@ -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;

Expand Down Expand Up @@ -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,...
Expand Down Expand Up @@ -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;

Expand Down
66 changes: 33 additions & 33 deletions scripts/python_conversions.sh
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ FrameTimesStart="[0]" \
FrameDuration=[300] \
ImageDecayCorrected="true" \
ImageDecayCorrectionTime=0 \
DecayCorrectionFactor=[1] \
#DecayCorrectionFactor=[1] \
AttenuationCorrection="MR-corrected" \
InjectionStart=0

Expand Down Expand Up @@ -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
# --------------------------------------
Expand All @@ -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"
Expand All @@ -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] \


Expand All @@ -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" \

Expand All @@ -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
# -------------------
Expand All @@ -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]


Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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]"

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