Difference between revisions of "Documentation/Nightly/Modules/SUVFactorCalculator"

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__NOTOC__
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<noinclude>{{documentation/versioncheck}}
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</noinclude>
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<!-- ---------------------------- -->
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{{documentation/{{documentation/version}}/module-header}}
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<!-- ---------------------------- -->
  
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==SUV Factor Calculator==
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<!-- ---------------------------- -->
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SUV Factor Calculator
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==Introduction and Acknowledgements==
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{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
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{{documentation/{{documentation/version}}/module-introduction-row}}
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Acknowledgments:
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The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin  QIN] PET DICOM Extension was funded in part by [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin/iowa Quantitative Imaging to Assess Response in Cancer Therapy Trials] NIH grant U01-CA140206 and [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918. <br>
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Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)<br>
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Contributors: Reinhard Beichel (University of Iowa), John Buatti (University of Iowa), Hans Johnson (University of Iowa), Wendy Plesniak (SPL, BWH), Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)<br>
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Contact: <email>qin@iibi.uiowa.edu</email><br>
  
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{|
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License: [http://www.slicer.org/pages/LicenseText Slicer License]
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|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
 
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|}
 
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== General Information ==
 
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{{documentation/{{documentation/version}}/extension-developerinfo}}
 
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===Module Type & Category===
 
  
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Type: CLI
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{{documentation/{{documentation/version}}/module-introduction-row}}
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{{documentation/{{documentation/version}}/module-introduction-logo-gallery
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|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
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|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
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|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
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}}
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{{documentation/{{documentation/version}}/module-introduction-end}}
  
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Category: Quantification
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==General Information==
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The '''SUVFactorCalculator''' Command Line Interface (CLI) takes a PET DICOM series and computes Standardized Uptake Value conversion factors (SUVbw, SUBlbm, SUVbs, SUVibw). Those SUV factors can be stored in a DICOM Real World Value Mapping (RWVM) file and SUV normalized image volumes can be generated.
  
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Depending on the information stored in the PET DICOM header, 4 types of SUV factors can be calculated as summarized here, where weight is in kilograms and height is in centimeters.
  
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===Authors, Collaborators & Contact===
 
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Authors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL, BWH),
 
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Contributors: Markus Van Tol (University of Iowa), Hans Johnson (University of Iowa), Wendy Plesniak (SPL, BWH), Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)
 
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Contact: Ethan Ulrich, <email>ethan-ulrich@uiowa.edu</email><br>
 
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===Module Description===
 
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{| style="color:gray" border="1"
 
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|Program title || SUV Factor Calculator
 
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|-
 
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|Program description || This command line interface module takes a PET DICOM series and creates a Real World Value Mapping (RWVM) file including 4 types of Standardized Uptake Value conversion factors (SUVbw, SUVlbm, SUVbsa, SUVibw).
 
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|-
 
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|Program documentation-url || [http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/SUVFactorCalculator Source code] on GitHub
 
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|-
 
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|}
 
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== Usage ==
 
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{{documentation/{{documentation/version}}/extension-developerinfo}}
 
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===Use Cases, Examples===
 
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The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
 
 
*SUVbw:
 
*SUVbw:
 
**males & females: weight
 
**males & females: weight
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**males: 48.0 + 1.06 * (height - 152)
 
**males: 48.0 + 1.06 * (height - 152)
 
**females: 45.5 + 0.91 * (height - 152)
 
**females: 45.5 + 0.91 * (height - 152)
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===Tutorials===
 
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*
 
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===Quick Tour of Features and Use===
 
  
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A list panels in the interface, their features, what they mean, and how to use them.
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==Use cases==
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{|
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The CLI can be used directly as shown below, but its functionality also integrates into Slicer's DICOM browser GUI via the Sicer [[Documentation/Nightly/Extensions/PETDICOM|PET DICOM Extension]]'s [[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]] and [[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]].
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|
 
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* <span style="color:blue">'''''Input Image'''''</span>:
 
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** <span style="color:green">'''PET DICOM volume path'''</span> [<span style="color:orange">----petDICOMPath</span>] [<span style="color:pink">--p</span>]:
 
  
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* <span style="color:blue">'''''Output'''''</span>:
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Example command line usage:<syntaxhighlight lang="bash">
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** <span style="color:green">'''RWV mapping object DICOM volume path'''</span> [<span style="color:orange">----rwvmDICOMPath</span>] [<span style="color:pink">--r</span>]:
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# list program options
 +
> SUVFactorCalculator --help
  
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** <span style="color:green">'''Radioactivity Units'''</span>  :
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# read PET DICOM image series from folder and calculate SUV normalization factors
 +
> SUVFactorCalculator -p pet_dicom_folder
  
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** <span style="color:green">'''Weight Units'''</span>  :
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# create RWVM DICOM file with calculated SUV normalization factors
 +
> SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm
  
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** <span style="color:green">'''Height Units'''</span> :
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# create SUVbw normalized volume
 +
> SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd
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</syntaxhighlight>A complete list of all parameters is provided in the Module Panel description below.
  
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** <span style="color:green">'''Volume Units'''</span> :  
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==Module Panel==
 +
Parameters:
 +
{|
 +
|
 +
*<span style="color:blue">'''''Input Image'''''</span>:
 +
**<span style="color:green">'''PET DICOM volume path'''</span> [<span style="color:orange">--petDICOMPath</span>] [<span style="color:pink">-p</span>]: Input path to a directory containing a PET DICOM series with header information for SUV computation
 +
**<span style="color:green">'''Instance UID of PET series'''</span> [<span style="color:orange">--petSeriesInstanceUID</span>]: Instance UID of PET series (if multiple series in PET dicom path)
  
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** <span style="color:green">'''Injected Dose'''</span> :  
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*<span style="color:blue">'''''SUV Factor Information'''''</span>:
 +
**<span style="color:green">'''Radioactivity Units'''</span>: DICOM Tag (0054,1001) - Radioactivity Units
 +
**<span style="color:green">'''Weight Units'''</span>: Patient weight units (always assumed to be kg)
 +
**<span style="color:green">'''Height Units'''</span>: Patient weight units (always assumed to be meters)
 +
**<span style="color:green">'''Volume Units'''</span>: Volume units for concentration (always assumed to be mL)
 +
**<span style="color:green">'''Injected Dose'''</span>: DICOM Tag (0018,1074) - Radionuclide Total Dose
 +
**<span style="color:green">'''Patient Weight'''</span>: DICOM Tag (0010,1030) - Patient Weight
 +
**<span style="color:green">'''Patient Height'''</span>: DICOM Tag (0010,1020) - Patient Size
 +
**<span style="color:green">'''Patient Sex'''</span>: DICOM Tag (0010,0040) - Patient Sex
 +
**<span style="color:green">'''Series Reference Time'''</span>: DICOM Tag (0008,0031) - Series Time
 +
**<span style="color:green">'''Injection Time'''</span>: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time
 +
**<span style="color:green">'''Decay Correction'''</span>: DICOM Tag (0054,1102) - Decay Correction
 +
**<span style="color:green">'''Decay Factor'''</span>: DICOM Tag (0054,1321) - Decay Factor
 +
**<span style="color:green">'''Radionuclide Half-life'''</span>: DICOM Tag (0018,1075) - Radionuclide Half-Life
 +
**<span style="color:green">'''Frame Reference Time'''</span>: DICOM Tag (0054,1300) - Frame Reference Time
 +
**<span style="color:green">'''SUVbw Conversion Factor'''</span>: Standardized Uptake Value (body weight) Conversion Factor
 +
**<span style="color:green">'''SUVlbm Conversion Factor'''</span>: Standardized Uptake Value (lean body mass) Conversion Factor
 +
**<span style="color:green">'''SUVbsa Conversion Factor'''</span>: Standardized Uptake Value (body surface area) Conversion Factor
 +
**<span style="color:green">'''SUVibw Conversion Factor'''</span>: Standardized Uptake Value (ideal body weight) Conversion Factor
  
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** <span style="color:green">'''Patient Weight'''</span> :  
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*<span style="color:blue">'''''Real World Value Mapping'''''</span>:
 +
**<span style="color:green">'''RWV mapping object DICOM volume path'''</span> [<span style="color:orange">--rwvmDICOMPath</span>] [<span style="color:pink">-r</span>]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.
 +
**<span style="color:green">'''RWVM DICOM object file'''</span> [<span style="color:orange">--rwvmDICOMFile</span>] [<span style="color:pink">-f</span>]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.
 +
**<span style="color:green">'''Series description'''</span> [<span style="color:orange">--seriesDescription</span>]: Description for the generated RVW object.
 +
**<span style="color:green">'''Series Number'''</span> [<span style="color:orange">--seriesNumber</span>]: Series number for the generated RVW object.
 +
**<span style="color:green">'''Instance number'''</span> [<span style="color:orange">--instanceNumber</span>]: Instance number for the generated RVW object.
  
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** <span style="color:green">'''Patient Height'''</span> :  
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*<span style="color:blue">'''''SUV Normalized Images'''''</span>:
 +
**<span style="color:green">'''SUVbw Volume<'''</span> [<span style="color:orange">--SUVbw</span>]: Output file path for SUVbw normalized volume.
 +
**<span style="color:green">'''SUVlbm Volume<'''</span> [<span style="color:orange">--SUVlbm</span>]: Output file path for SUVlbm normalized volume.
 +
**<span style="color:green">'''SUVbsa Volume<'''</span> [<span style="color:orange">--SUVbsa</span>]: Output file path for SUVbsa normalized volume.
 +
**<span style="color:green">'''SUVibw Volume<'''</span> [<span style="color:orange">--SUVibw</span>]: Output file path for SUVibw normalized volume.
  
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** <span style="color:green">'''Patient Sex'''</span>  :  
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|[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]
 +
|}
  
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** <span style="color:green">'''Series Reference Time'''</span>  :
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==SUV normalization factor calculation - Required metadata==
  
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** <span style="color:green">'''Injection Time'''</span>  :  
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{|
 +
|[[File:PET_DICOM_metadata.png|thumb|500px|DICOM metadata required for SUV normalization. Green: required for all SUV normalization factors. Orange: only required for SUVlbm, SUVbsa, and SUVibw.]]
  
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** <span style="color:green">'''Decay Correction'''</span>  :
 
  
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** <span style="color:green">'''Decay Factor'''</span>  :  
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SUV normalization factor computation is based on the vendor-neutral "happy path only" calculation described on the Quantitative Imaging Biomarkers Alliance (QIBA) wiki page [https://qhttps://qibawiki.rsna.org/index.php/Standardized_Uptake_Value_(SUV)#SUV_Calculation Standardized Uptake Value (SUV)].
 +
The following set of '''DICOM tags with proper values are required''' in the PET DICOM files to calculate SUV normalization factors:
  
−
** <span style="color:green">'''Radionuclide Half-life'''</span>  :
+
*(0008,0021) SeriesDate​
 +
*(0008,0022) AcquisitionDate​
 +
*(0008,0031) SeriesTime​
 +
*(0008,0032) AcquisitionTime​
 +
*(0008,0060) '''Modality must be PT'''​
 +
*(0010,1030) '''PatientWeight >0'''
 +
*(0028,0051) '''CorrectedImage must contain ATTN and DECAY or DECY​'''
 +
*(0054,0016) '''RadiopharmaceuticalInformationSequence​'''
 +
**(0018,1072) RadiopharmaceuticalStartTime or (0018,1078) RadiopharmaceuticalStartDateTime​
 +
**(0018,1074) RadionuclideTotalDose​
 +
**(0018,1075) RadionuclideHalfLife​
 +
*(0054,1001) '''Units must be BQML, *Bq, or *Ci​'''
 +
*(0054,1002) '''DecayCorrection must be START'''
 +
*(0054,1300) FrameReferenceTime​
 +
*(0054,1321) DecayFactor
  
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** <span style="color:green">'''Frame Reference Time'''</span>  :  
+
For calculation of SUVlbm, SUVbsa, and SUVibw in addition:
  
−
** <span style="color:green">'''SUVbw Conversion Factor'''</span>  :
+
*(0010,0040) PatientSex in (M,F) ​
 +
*(0010,1020) PatientSize >0
  
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** <span style="color:green">'''SUVlbm Conversion Factor'''</span>  :  
+
One can check the existence and values of these DICOM tags, using Slicer's DICOM browser, by selecting "View DICOM metadata" from the PET series' context menu:
  
−
** <span style="color:green">'''SUVbsa Conversion Factor'''</span>  :
+
{|
−
 
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|[[File:DICOM_metadata_contextmenu.png|thumb|400px|To display a PET scans DICOM metadata, select "View DICOM metadata" from the series' context menu in the DICOM browser.]]
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** <span style="color:green">'''SUVibw Conversion Factor'''</span>  :
 
−
 
 
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** <span style="color:green">'''RWVM File'''</span>  :
 
−
 
 
−
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
 
 
|}
 
|}
  
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+
==Information for Developers==
−
== Development ==
 
−
{{documentation/{{documentation/version}}/extension-developerinfo}}
 
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===Notes from the Developer(s)===
 
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*
 
−
 
 
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===Tests===
 
−
*
 
−
===Information for Developers===
 
  
 
*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI
 
*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI
  
−
==Other Information==
+
==References==
−
===Acknowledgment===
 
−
This work is funded in part by [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918. <br>
 
−
 
 
−
 
 
−
===References===
 
  
 
Sugawara et al. "Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction." Radiology. 1999.<br>
 
Sugawara et al. "Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction." Radiology. 1999.<br>
 
http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521
 
http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521
 +
|}

Latest revision as of 21:03, 8 April 2022

Home < Documentation < Nightly < Modules < SUVFactorCalculator


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

Acknowledgments: The UIowa QIN PET DICOM Extension was funded in part by Quantitative Imaging to Assess Response in Cancer Therapy Trials NIH grant U01-CA140206 and Quantitative Image Informatics for Cancer Research (QIICR) NIH grant U24 CA180918.
Authors: Andrey Fedorov (SPL), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)
Contributors: Reinhard Beichel (University of Iowa), John Buatti (University of Iowa), Hans Johnson (University of Iowa), Wendy Plesniak (SPL, BWH), Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)
Contact: <email>qin@iibi.uiowa.edu</email>

License: Slicer License

The University of Iowa (UIowa)  
Quantitative Image Informatics for Cancer Research  
National Alliance for Medical Image Computing (NA-MIC)  

General Information

The SUVFactorCalculator Command Line Interface (CLI) takes a PET DICOM series and computes Standardized Uptake Value conversion factors (SUVbw, SUBlbm, SUVbs, SUVibw). Those SUV factors can be stored in a DICOM Real World Value Mapping (RWVM) file and SUV normalized image volumes can be generated.

Depending on the information stored in the PET DICOM header, 4 types of SUV factors can be calculated as summarized here, where weight is in kilograms and height is in centimeters.

  • SUVbw:
    • males & females: weight
  • SUVlbm:
    • males: 1.10 * weight - 128 * (weight/height)^2
    • females: 1.07 * weight - 148 * (weight/height)^2
  • SUVbsa:
    • males & females: weight^0.425 * height^0.725 * 0.007184
  • SUVibw:
    • males: 48.0 + 1.06 * (height - 152)
    • females: 45.5 + 0.91 * (height - 152)

Use cases

The CLI can be used directly as shown below, but its functionality also integrates into Slicer's DICOM browser GUI via the Sicer PET DICOM Extension's DICOM Real World Value Mapping Plugin and DICOM PET SUV Plugin.

Example command line usage:

# list program options
> SUVFactorCalculator --help

# read PET DICOM image series from folder and calculate SUV normalization factors
> SUVFactorCalculator -p pet_dicom_folder

# create RWVM DICOM file with calculated SUV normalization factors
> SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm

# create SUVbw normalized volume 
> SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd

A complete list of all parameters is provided in the Module Panel description below.

Module Panel

Parameters:

  • Input Image:
    • PET DICOM volume path [--petDICOMPath] [-p]: Input path to a directory containing a PET DICOM series with header information for SUV computation
    • Instance UID of PET series [--petSeriesInstanceUID]: Instance UID of PET series (if multiple series in PET dicom path)
  • SUV Factor Information:
    • Radioactivity Units: DICOM Tag (0054,1001) - Radioactivity Units
    • Weight Units: Patient weight units (always assumed to be kg)
    • Height Units: Patient weight units (always assumed to be meters)
    • Volume Units: Volume units for concentration (always assumed to be mL)
    • Injected Dose: DICOM Tag (0018,1074) - Radionuclide Total Dose
    • Patient Weight: DICOM Tag (0010,1030) - Patient Weight
    • Patient Height: DICOM Tag (0010,1020) - Patient Size
    • Patient Sex: DICOM Tag (0010,0040) - Patient Sex
    • Series Reference Time: DICOM Tag (0008,0031) - Series Time
    • Injection Time: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time
    • Decay Correction: DICOM Tag (0054,1102) - Decay Correction
    • Decay Factor: DICOM Tag (0054,1321) - Decay Factor
    • Radionuclide Half-life: DICOM Tag (0018,1075) - Radionuclide Half-Life
    • Frame Reference Time: DICOM Tag (0054,1300) - Frame Reference Time
    • SUVbw Conversion Factor: Standardized Uptake Value (body weight) Conversion Factor
    • SUVlbm Conversion Factor: Standardized Uptake Value (lean body mass) Conversion Factor
    • SUVbsa Conversion Factor: Standardized Uptake Value (body surface area) Conversion Factor
    • SUVibw Conversion Factor: Standardized Uptake Value (ideal body weight) Conversion Factor
  • Real World Value Mapping:
    • RWV mapping object DICOM volume path [--rwvmDICOMPath] [-r]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.
    • RWVM DICOM object file [--rwvmDICOMFile] [-f]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.
    • Series description [--seriesDescription]: Description for the generated RVW object.
    • Series Number [--seriesNumber]: Series number for the generated RVW object.
    • Instance number [--instanceNumber]: Instance number for the generated RVW object.
  • SUV Normalized Images:
    • SUVbw Volume< [--SUVbw]: Output file path for SUVbw normalized volume.
    • SUVlbm Volume< [--SUVlbm]: Output file path for SUVlbm normalized volume.
    • SUVbsa Volume< [--SUVbsa]: Output file path for SUVbsa normalized volume.
    • SUVibw Volume< [--SUVibw]: Output file path for SUVibw normalized volume.
User Interface

SUV normalization factor calculation - Required metadata

DICOM metadata required for SUV normalization. Green: required for all SUV normalization factors. Orange: only required for SUVlbm, SUVbsa, and SUVibw.


SUV normalization factor computation is based on the vendor-neutral "happy path only" calculation described on the Quantitative Imaging Biomarkers Alliance (QIBA) wiki page Standardized Uptake Value (SUV). The following set of DICOM tags with proper values are required in the PET DICOM files to calculate SUV normalization factors:

  • (0008,0021) SeriesDate​
  • (0008,0022) AcquisitionDate​
  • (0008,0031) SeriesTime​
  • (0008,0032) AcquisitionTime​
  • (0008,0060) Modality must be PT​
  • (0010,1030) PatientWeight >0
  • (0028,0051) CorrectedImage must contain ATTN and DECAY or DECY​
  • (0054,0016) RadiopharmaceuticalInformationSequence​
    • (0018,1072) RadiopharmaceuticalStartTime or (0018,1078) RadiopharmaceuticalStartDateTime​
    • (0018,1074) RadionuclideTotalDose​
    • (0018,1075) RadionuclideHalfLife​
  • (0054,1001) Units must be BQML, *Bq, or *Ci​
  • (0054,1002) DecayCorrection must be START
  • (0054,1300) FrameReferenceTime​
  • (0054,1321) DecayFactor

For calculation of SUVlbm, SUVbsa, and SUVibw in addition:

  • (0010,0040) PatientSex in (M,F) ​
  • (0010,1020) PatientSize >0

One can check the existence and values of these DICOM tags, using Slicer's DICOM browser, by selecting "View DICOM metadata" from the PET series' context menu:

To display a PET scans DICOM metadata, select "View DICOM metadata" from the series' context menu in the DICOM browser.

Information for Developers

References

Sugawara et al. "Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction." Radiology. 1999.
http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521

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