https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=Chribaue 2026-04-08T10:13:03Z User contributions MediaWiki 1.33.0 https://www.slicer.org/w/index.php?title=Documentation/4.6/Extensions/PETTumorSegmentation&diff=64154 2022-07-22T14:34:27Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool 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. &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool provides an Editor-Effect for semi-automated segmentation of tumors and hot lymph nodes in PET scans. A detailed description and evaluation of the method can be found in Beichel et al. (2016): &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4948679 http://dx.doi.org/10.1118/1.4948679]<br /> <br /> [[File:PETTumorSegmentationExtensionIcon.png|PET Tumor Segmentation Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=5o6TvrzbOqk}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentationEffect|PET Tumor Segmentation Editor Effect]]<br /> *PETTumorSegmentation Plugin: This plugin provides the functionality used by the editor effect for the actual processing. It is hidden from the GUI and not intended to be used directly.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETTumorSegmentation<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.8/Extensions/PETTumorSegmentation&diff=64153 2022-07-22T14:34:10Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool 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, [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640.&lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool provides an Editor-Effect for semi-automated segmentation of tumors and hot lymph nodes in PET scans. A detailed description and evaluation of the method can be found in Beichel et al. (2016): &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4948679 http://dx.doi.org/10.1118/1.4948679]<br /> <br /> [[File:PETTumorSegmentationExtensionIcon.png|PET Tumor Segmentation Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=5o6TvrzbOqk}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentationEffect|PET Tumor Segmentation Editor Effect]] for use with Slicer's Labelmap Editor<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentEditorEffect|PET Tumor Segmentation Segment Editor Effect]] for use with Slicer's Segment Editor<br /> *PETTumorSegmentation Plugin: This plugin provides the functionality used by the editor effects for the actual processing. It is hidden from the GUI and not intended to be used directly.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETTumorSegmentation<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.10/Extensions/PETTumorSegmentation&diff=64152 2022-07-22T14:33:46Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool 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, [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640.&lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool provides an Editor-Effect for semi-automated segmentation of tumors and hot lymph nodes in PET scans. A detailed description and evaluation of the method can be found in Beichel et al. (2016): &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4948679 http://dx.doi.org/10.1118/1.4948679]<br /> <br /> [[File:PETTumorSegmentationExtensionIcon.png|PET Tumor Segmentation Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=5o6TvrzbOqk}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentationEffect|PET Tumor Segmentation Editor Effect]] for use with Slicer's Labelmap Editor<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentEditorEffect|PET Tumor Segmentation Segment Editor Effect]] for use with Slicer's Segment Editor<br /> *PETTumorSegmentation Plugin: This plugin provides the functionality used by the editor effects for the actual processing. It is hidden from the GUI and not intended to be used directly.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETTumorSegmentation<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.6/Extensions/PETLiverUptakeMeasurement&diff=64151 2022-07-22T14:32:59Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Liver Uptake Measurement tool 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. &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool allows automated measurement of liver uptake in SUV normalized FDG-18 whole-body PET scans. A detailed description and evaluation of the method can be found in Bauer et al. (2012): &quot;Automated measurement of uptake in cerebellum, liver, and aortic arch in full-body FDG PET/CT scans.&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4711815 http://dx.doi.org/10.1118/1.4711815]<br /> <br /> [[File:PETLiverUptakeMeasurementIcon.png|PET Liver Uptake Measurement Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=Mn9RMsrI1XU}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurement|PET Liver Uptake Measurement]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETLiverUptakeMeasurement<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.8/Extensions/PETLiverUptakeMeasurement&diff=64150 2022-07-22T14:32:41Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Liver Uptake Measurement tool 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. &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool allows automated measurement of liver uptake in SUV normalized FDG-18 whole-body PET scans. Segmented region and measurement results can be exported as DICOM Segmentation (SEG) and Structured Report (SR), respectively. A detailed description and evaluation of the method can be found in Bauer et al. (2012): &quot;Automated measurement of uptake in cerebellum, liver, and aortic arch in full-body FDG PET/CT scans.&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4711815 http://dx.doi.org/10.1118/1.4711815]<br /> <br /> [[File:PETLiverUptakeMeasurementIcon.png|PET Liver Uptake Measurement Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=Mn9RMsrI1XU}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurement|PET Liver Uptake Measurement]]: Module for liver uptake measurement and export to DICOM database<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurementCLI|PET Liver Uptake Measurement CLI]]: Module for liver uptake measurement only<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETLiverUptakeMeasurement<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.10/Extensions/PETLiverUptakeMeasurement&diff=64149 2022-07-22T14:32:22Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Liver Uptake Measurement tool 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. &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: qin{{@}}iibi.uiowa.edu&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool allows automated measurement of liver uptake in SUV normalized FDG-18 whole-body PET scans. Segmented region and measurement results can be exported as DICOM Segmentation (SEG) and Structured Report (SR), respectively. A detailed description and evaluation of the method can be found in Bauer et al. (2012): &quot;Automated measurement of uptake in cerebellum, liver, and aortic arch in full-body FDG PET/CT scans.&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4711815 http://dx.doi.org/10.1118/1.4711815]<br /> <br /> [[File:PETLiverUptakeMeasurementIcon.png|PET Liver Uptake Measurement Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=Mn9RMsrI1XU}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurement|PET Liver Uptake Measurement]]: Module for liver uptake measurement and export to DICOM database<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurementCLI|PET Liver Uptake Measurement CLI]]: Module for liver uptake measurement only<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETLiverUptakeMeasurement<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.6/Extensions/PET-IndiC&diff=64148 2022-07-22T14:31:40Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices.<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=9CIzot8n3hQ}}<br /> <br /> ==USAGE==<br /> PET-IndiC is an extension of the main Editor module in Slicer<br /> {|<br /> |[[Image:PET-IndiC_Screenshot1.png|thumb|800px|PET-IndiC Interface]]<br /> |}<br /> After selecting an input image, a label image is automatically assigned. Window/Level presets are available for PET SUV images. For import of DICOM PET images as SUV images, see the [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM Extension]].<br /> {|<br /> |[[Image:PET-IndiC_Screenshot2.png|thumb|375px|FDG PET (Inverted Grey)]]<br /> |[[Image:PET-IndiC_Screenshot3.png|thumb|375px|FDG PET (Rainbow)]]<br /> |}<br /> Segment the image using the Editor tools. The PET-IndiC Extension is meant to be coupled with the [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PET-SEG Extension]] editor effect.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot4.png|thumb|600px|Editor Effect options]]<br /> |}<br /> Quantitative indices are calculated automatically whenever a new label is created or the current label is modified. Several indices are available for calculation. The output appears as a table that can be copied and pasted into a spreadsheet.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot5.png|thumb|700px|Quantitative indices options and output.]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.8/Extensions/PET-IndiC&diff=64147 2022-07-22T14:31:19Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices.<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=9CIzot8n3hQ}}<br /> <br /> ==USAGE==<br /> PET-IndiC is an extension of the main Editor module in Slicer<br /> {|<br /> |[[Image:PET-IndiC_Screenshot1.png|thumb|800px|PET-IndiC Interface]]<br /> |}<br /> After selecting an input image, a label image is automatically assigned. Window/Level presets are available for PET SUV images. For import of DICOM PET images as SUV images, see the [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM Extension]].<br /> {|<br /> |[[Image:PET-IndiC_Screenshot2.png|thumb|375px|FDG PET (Inverted Grey)]]<br /> |[[Image:PET-IndiC_Screenshot3.png|thumb|375px|FDG PET (Rainbow)]]<br /> |}<br /> Segment the image using the Editor tools. The PET-IndiC Extension is meant to be coupled with the [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PET-SEG Extension]] editor effect.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot4.png|thumb|600px|Editor Effect options]]<br /> |}<br /> Quantitative indices are calculated automatically whenever a new label is created or the current label is modified. Several indices are available for calculation. The output appears as a table that can be copied and pasted into a spreadsheet.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot5.png|thumb|700px|Quantitative indices options and output.]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.10/Extensions/PET-IndiC&diff=64146 2022-07-22T14:30:58Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: qin{{@}}iibi.uiowa.edu&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices.<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=9CIzot8n3hQ}}<br /> <br /> ==USAGE==<br /> PET-IndiC is an extension of the main Editor module in Slicer<br /> {|<br /> |[[Image:PET-IndiC_Screenshot1.png|thumb|800px|PET-IndiC Interface]]<br /> |}<br /> After selecting an input image, a label image is automatically assigned. Window/Level presets are available for PET SUV images. For import of DICOM PET images as SUV images, see the [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM Extension]].<br /> {|<br /> |[[Image:PET-IndiC_Screenshot2.png|thumb|375px|FDG PET (Inverted Grey)]]<br /> |[[Image:PET-IndiC_Screenshot3.png|thumb|375px|FDG PET (Rainbow)]]<br /> |}<br /> Segment the image using the Editor tools. The PET-IndiC Extension is meant to be coupled with the [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PET-SEG Extension]] editor effect.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot4.png|thumb|600px|Editor Effect options]]<br /> |}<br /> Quantitative indices are calculated automatically whenever a new label is created or the current label is modified. Several indices are available for calculation. The output appears as a table that can be copied and pasted into a spreadsheet.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot5.png|thumb|700px|Quantitative indices options and output.]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]]<br /> *[[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.6/Extensions/PETDICOM&diff=64145 2022-07-22T14:30:04Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PETDICOMExtension.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.<br /> *Calculation of Standardized Uptake Value (SUV) conversion factors<br /> *Creation of Real World Value Mapping files<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=cxOuGdVVg8U}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/Slicer-PETDICOMExtension<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.8/Extensions/PETDICOM&diff=64144 2022-07-22T14:29:44Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PETDICOMExtension.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.<br /> *Calculation of Standardized Uptake Value (SUV) conversion factors<br /> *Creation of Real World Value Mapping files<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=cxOuGdVVg8U}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/Slicer-PETDICOMExtension<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.10/Extensions/PETDICOM&diff=64143 2022-07-22T14:29:16Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PETDICOMExtension.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: qin{{@}}iibi.uiowa.edu&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.<br /> *Calculation of Standardized Uptake Value (SUV) conversion factors<br /> *Creation of Real World Value Mapping files<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=cxOuGdVVg8U}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/Slicer-PETDICOMExtension<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PETPhantomAnalysis&diff=64142 2022-07-21T17:18:37Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Phantom Analysis tool 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. &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa)&lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool allows automated analysis of Uniform Cylinder Phantoms in PET scans utilized for quality control purposes. Quantitative verification of calibration and spatial homogeneity of PET scanners is an essential prerequisite for quantitative analysis of clinical PET scans. For this purpose uniform cylindrical phantoms are commonly utilized. The provided extension enables automated analysis of resulting PET scans.<br /> <br /> [[File:PETCPhantomIcon.png|PET Phantom Analysis Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=jimXgez4-5E}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETCPhantomAnalysis|PET Cylinder Phantom Analysis]]: GUI Module for analysis of cylinder phantom PET scans<br /> *PET Cylinder Phantom Analysis CLI: Command line module for actual processing of cylinder phantom PET scans. It is not intended to be used directly.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/SlicerPETPhantomAnalysis<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PETTumorSegmentation&diff=64141 2022-07-21T17:17:48Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool 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, [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640.&lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool provides an Editor-Effect for semi-automated segmentation of tumors and hot lymph nodes in PET scans. A detailed description and evaluation of the method can be found in Beichel et al. (2016): &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4948679 http://dx.doi.org/10.1118/1.4948679]<br /> <br /> [[File:PETTumorSegmentationExtensionIcon.png|PET Tumor Segmentation Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=oYlFhqxdptE}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> &lt;!--<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentationEffect|PET Tumor Segmentation Editor Effect]] for use with Slicer's Labelmap Editor<br /> --&gt;<br /> *[[Documentation/{{documentation/version}}/Modules/PETTumorSegmentEditorEffect|PET Tumor Segmentation Segment Editor Effect]] for use with Slicer's Segment Editor<br /> *PETTumorSegmentation Plugin: This plugin provides the functionality used by the editor effects for the actual processing. It is hidden from the GUI and not intended to be used directly.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETTumorSegmentation<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PETLiverUptakeMeasurement&diff=64140 2022-07-21T17:17:04Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Liver Uptake Measurement tool 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. &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> This tool allows automated measurement of liver uptake in SUV normalized FDG-18 whole-body PET scans. Segmented region and measurement results can be exported as DICOM Segmentation (SEG) and Structured Report (SR), respectively. A detailed description and evaluation of the method can be found in Bauer et al. (2012): &quot;Automated measurement of uptake in cerebellum, liver, and aortic arch in full-body FDG PET/CT scans.&quot;, in Medical Physics. [http://dx.doi.org/10.1118/1.4711815 http://dx.doi.org/10.1118/1.4711815]<br /> <br /> [[File:PETLiverUptakeMeasurementIcon.png|PET Liver Uptake Measurement Extension]]<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=ZhZDS4Nqjeo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurement|PET Liver Uptake Measurement]]: Module for liver uptake measurement and export to DICOM database<br /> *[[Documentation/{{documentation/version}}/Modules/PETLiverUptakeMeasurementCLI|PET Liver Uptake Measurement CLI]]: Module for liver uptake measurement only<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PETLiverUptakeMeasurement<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PETDICOM&diff=64139 2022-07-21T17:14:55Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PETDICOMExtension.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.<br /> <br /> *Calculation of Standardized Uptake Value (SUV) conversion factors<br /> *Creation of Real World Value Mapping files<br /> *Creation of SUV normalized images<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=GMdgXSI8cr0}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64046 2022-04-08T21:03:03Z

<p>Chribaue: /* SUV normalization factor calculation - Required metadata */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)&lt;br&gt;<br /> 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> ==General Information==<br /> 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.<br /> <br /> 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.<br /> <br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> <br /> ==Use cases==<br /> 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]].<br /> <br /> Example command line usage:&lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> # list program options<br /> &gt; SUVFactorCalculator --help<br /> <br /> # read PET DICOM image series from folder and calculate SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder<br /> <br /> # create RWVM DICOM file with calculated SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm<br /> <br /> # create SUVbw normalized volume <br /> &gt; SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd<br /> &lt;/syntaxhighlight&gt;A complete list of all parameters is provided in the Module Panel description below.<br /> <br /> ==Module Panel==<br /> Parameters:<br /> {|<br /> |<br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]<br /> |}<br /> <br /> ==SUV normalization factor calculation - Required metadata==<br /> <br /> {|<br /> |[[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.]]<br /> <br /> <br /> SUV normalization factor computation is based on the vendor-neutral &quot;happy path only&quot; 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)].<br /> The following set of '''DICOM tags with proper values are required''' in the PET DICOM files to calculate SUV normalization factors:<br /> <br /> *(0008,0021) SeriesDate​<br /> *(0008,0022) AcquisitionDate​<br /> *(0008,0031) SeriesTime​<br /> *(0008,0032) AcquisitionTime​<br /> *(0008,0060) '''Modality must be PT'''​<br /> *(0010,1030) '''PatientWeight &gt;0'''<br /> *(0028,0051) '''CorrectedImage must contain ATTN and DECAY or DECY​'''<br /> *(0054,0016) '''RadiopharmaceuticalInformationSequence​'''<br /> **(0018,1072) RadiopharmaceuticalStartTime or (0018,1078) RadiopharmaceuticalStartDateTime​<br /> **(0018,1074) RadionuclideTotalDose​<br /> **(0018,1075) RadionuclideHalfLife​<br /> *(0054,1001) '''Units must be BQML, *Bq, or *Ci​'''<br /> *(0054,1002) '''DecayCorrection must be START'''<br /> *(0054,1300) FrameReferenceTime​<br /> *(0054,1321) DecayFactor<br /> <br /> For calculation of SUVlbm, SUVbsa, and SUVibw in addition:<br /> <br /> *(0010,0040) PatientSex in (M,F) ​<br /> *(0010,1020) PatientSize &gt;0<br /> <br /> One can check the existence and values of these DICOM tags, using Slicer's DICOM browser, by selecting &quot;View DICOM metadata&quot; from the PET series' context menu:<br /> <br /> {|<br /> |[[File:DICOM_metadata_contextmenu.png|thumb|400px|To display a PET scans DICOM metadata, select &quot;View DICOM metadata&quot; from the series' context menu in the DICOM browser.]]<br /> |}<br /> <br /> ==Information for Developers==<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ==References==<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521<br /> |}</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64045 2022-04-08T20:05:14Z

<p>Chribaue: /* SUV normalization factor calculation */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)&lt;br&gt;<br /> 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> ==General Information==<br /> 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.<br /> <br /> 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.<br /> <br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> <br /> ==Use cases==<br /> 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]].<br /> <br /> Example command line usage:&lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> # list program options<br /> &gt; SUVFactorCalculator --help<br /> <br /> # read PET DICOM image series from folder and calculate SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder<br /> <br /> # create RWVM DICOM file with calculated SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm<br /> <br /> # create SUVbw normalized volume <br /> &gt; SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd<br /> &lt;/syntaxhighlight&gt;A complete list of all parameters is provided in the Module Panel description below.<br /> <br /> ==Module Panel==<br /> Parameters:<br /> {|<br /> |<br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]<br /> |}<br /> <br /> ==SUV normalization factor calculation - Required metadata==<br /> <br /> {|<br /> |[[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.]]<br /> <br /> <br /> SUV normalization factor computation is based on the vendor-neutral &quot;happy path only&quot; 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)].<br /> The following set of '''DICOM tags with proper values are required''' in the PET DICOM files to calculate SUV normalization factors:<br /> <br /> *(0008,0021) SeriesDate​<br /> *(0008,0022) AcquisitionDate​<br /> *(0008,0031) SeriesTime​<br /> *(0008,0032) AcquisitionTime​<br /> *(0008,0060) '''Modality must be PT'''​<br /> *(0010,1030) '''PatientWeight &gt;0'''<br /> *(0028,0051) '''CorrectedImage must contain ATTN and DECAY or DECY​'''<br /> *(0054,0016) '''RadiopharmaceuticalInformationSequence​'''<br /> *(0018,1072) RadiopharmaceuticalStartTime or (0018,1078) RadiopharmaceuticalStartDateTime​<br /> *(0018,1074) RadionuclideTotalDose​<br /> *(0018,1075) RadionuclideHalfLife​<br /> *(0054,1001) '''Units must be BQML, *Bq, or *Ci​'''<br /> *(0054,1002) '''DecayCorrection must be START'''<br /> *(0054,1300) FrameReferenceTime​<br /> *(0054,1321) DecayFactor<br /> <br /> For calculation of SUVlbm, SUVbsa, and SUVibw in addition:<br /> <br /> *(0010,0040) PatientSex in (M,F) ​<br /> *(0010,1020) PatientSize &gt;0<br /> <br /> One can check the existence and values of these DICOM tags, using Slicer's DICOM browser, by selecting &quot;View DICOM metadata&quot; from the PET series' context menu:<br /> <br /> {|<br /> |[[File:DICOM_metadata_contextmenu.png|thumb|400px|To display a PET scans DICOM metadata, select &quot;View DICOM metadata&quot; from the series' context menu in the DICOM browser.]]<br /> |}<br /> <br /> ==Information for Developers==<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ==References==<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521<br /> |}</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64044 2022-04-08T20:04:29Z

<p>Chribaue: /* SUV normalization factor calculation */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)&lt;br&gt;<br /> 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> ==General Information==<br /> 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.<br /> <br /> 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.<br /> <br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> <br /> ==Use cases==<br /> 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]].<br /> <br /> Example command line usage:&lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> # list program options<br /> &gt; SUVFactorCalculator --help<br /> <br /> # read PET DICOM image series from folder and calculate SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder<br /> <br /> # create RWVM DICOM file with calculated SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm<br /> <br /> # create SUVbw normalized volume <br /> &gt; SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd<br /> &lt;/syntaxhighlight&gt;A complete list of all parameters is provided in the Module Panel description below.<br /> <br /> ==Module Panel==<br /> Parameters:<br /> {|<br /> |<br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]<br /> |}<br /> <br /> ==SUV normalization factor calculation==<br /> <br /> {|<br /> |[[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.]]<br /> <br /> <br /> SUV normalization factor computation is based on the vendor-neutral &quot;happy path only&quot; 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)].<br /> The following set of '''DICOM tags with proper values are required''' in the PET DICOM files to calculate SUV normalization factors:<br /> <br /> *(0008,0021) SeriesDate​<br /> *(0008,0022) AcquisitionDate​<br /> *(0008,0031) SeriesTime​<br /> *(0008,0032) AcquisitionTime​<br /> *(0008,0060) '''Modality must be PT'''​<br /> *(0010,1030) '''PatientWeight &gt;0'''<br /> *(0028,0051) '''CorrectedImage must contain ATTN and DECAY or DECY​'''<br /> *(0054,0016) '''RadiopharmaceuticalInformationSequence​'''<br /> *(0018,1072) RadiopharmaceuticalStartTime or (0018,1078) RadiopharmaceuticalStartDateTime​<br /> *(0018,1074) RadionuclideTotalDose​<br /> *(0018,1075) RadionuclideHalfLife​<br /> *(0054,1001) '''Units must be BQML, *Bq, or *Ci​'''<br /> *(0054,1002) '''DecayCorrection must be START'''<br /> *(0054,1300) FrameReferenceTime​<br /> *(0054,1321) DecayFactor<br /> <br /> For calculation of SUVlbm, SUVbsa, and SUVibw in addition:<br /> <br /> *(0010,0040) PatientSex in (M,F) ​<br /> *(0010,1020) PatientSize &gt;0<br /> <br /> One can check the existence and values of these DICOM tags, using Slicer's DICOM browser, by selecting &quot;View DICOM metadata&quot; from the PET series' context menu:<br /> <br /> {|<br /> |[[File:DICOM_metadata_contextmenu.png|thumb|400px|To display a PET scans DICOM metadata, select &quot;View DICOM metadata&quot; from the series' context menu in the DICOM browser.]]<br /> |}<br /> <br /> ==Information for Developers==<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ==References==<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521<br /> |}</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64043 2022-04-08T20:03:15Z

<p>Chribaue: added info about required DICOM metadata for SUV factor calculation</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)&lt;br&gt;<br /> 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> ==General Information==<br /> 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.<br /> <br /> 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.<br /> <br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> <br /> == Use cases ==<br /> 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]].<br /> <br /> Example command line usage:&lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> # list program options<br /> &gt; SUVFactorCalculator --help<br /> <br /> # read PET DICOM image series from folder and calculate SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder<br /> <br /> # create RWVM DICOM file with calculated SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm<br /> <br /> # create SUVbw normalized volume <br /> &gt; SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd<br /> &lt;/syntaxhighlight&gt;A complete list of all parameters is provided in the Module Panel description below.<br /> <br /> == Module Panel ==<br /> Parameters:<br /> {|<br /> |<br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]<br /> |}<br /> <br /> ==SUV normalization factor calculation==<br /> <br /> {|<br /> |[[File:PET_DICOM_metadata.png|thumb|500px|DICOM metadata requires for SUV normalization. green: requires for all SUV normalization factors, orange: only required for SUVlbm, SUVbsa, and SUVibw.]]<br /> }<br /> <br /> SUV normalization factor computation is based on the vendor-neutral &quot;happy path only&quot; 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)].<br /> The following set of '''DICOM tags with proper values are required''' in the PET DICOM files to calculate SUV normalization factors:<br /> *(0008,0021) SeriesDate​<br /> *(0008,0022) AcquisitionDate​<br /> *(0008,0031) SeriesTime​<br /> *(0008,0032) AcquisitionTime​<br /> *(0008,0060) '''Modality must be PT'''​<br /> *(0010,1030) '''PatientWeight &gt;0'''<br /> *(0028,0051) '''CorrectedImage must contain ATTN and DECAY or DECY​'''<br /> *(0054,0016) '''RadiopharmaceuticalInformationSequence​'''<br /> *(0018,1072) RadiopharmaceuticalStartTime or (0018,1078) RadiopharmaceuticalStartDateTime​<br /> *(0018,1074) RadionuclideTotalDose​<br /> *(0018,1075) RadionuclideHalfLife​<br /> *(0054,1001) '''Units must be BQML, *Bq, or *Ci​'''<br /> *(0054,1002) '''DecayCorrection must be START'''<br /> *(0054,1300) FrameReferenceTime​<br /> *(0054,1321) DecayFactor<br /> <br /> For calculation of SUVlbm, SUVbsa, and SUVibw in addition:<br /> * (0010,0040) PatientSex in (M,F) ​<br /> * (0010,1020) PatientSize &gt;0<br /> <br /> One can check the existence and values of these DICOM tags, using Slicer's DICOM browser, by selecting &quot;View DICOM metadata&quot; from the PET series' context menu:<br /> <br /> {|<br /> |[[File:DICOM_metadata_contextmenu.png|thumb|400px|To display a PET scans DICOM metadata, select &quot;View DICOM metadata&quot; from the series' context menu in the DICOM browser.]]<br /> |}<br /> <br /> ==Information for Developers==<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ==References==<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521</div>

Chribaue https://www.slicer.org/w/index.php?title=File:PET_DICOM_metadata.png&diff=64042 2022-04-08T19:50:41Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=File:DICOM_metadata_contextmenu.png&diff=64041 2022-04-08T19:50:13Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/PETTumorSegmentEditorEffect&diff=64040 2022-04-04T17:24:08Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool was is 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, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640 &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> Segment Editor Effect for segmentation of tumors and hot lymph nodes in PET scans. Click on a lesion (tumor or hot lymph node) in a PET scan to segment it with one click. For cases where the initial segmentation does not provide the desired result, the tool provides functionality to refine the segmentation with few clicks. Options may help deal with complicated cases such as segmenting individual lymph nodes in a lymph node chain.<br /> <br /> [[File:PETTumorSegmentation_Editor_Effect_options.png|1200px|Screenshot]]<br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;{{documentation/{{documentation/version}}/module-section|Tutorial - Basic Tumor and Lymph Node Segmentation}}<br /> <br /> [[File:PETTumorSegmentation_SegmentEditor_Effect_options.png|thumb|600px|PET Tumor Segmentation Segment Editor Effect Options]]<br /> <br /> Step 1) Load PET scan.<br /> <br /> Step 2) Go to the “Segment Editor” module, select the volume loaded in Step 1 as the “Master Volume”.<br /> <br /> Step 3) Click &quot;Add segment&quot; to create a lesion segment.<br /> <br /> Step 4) Select the [[File:PETTumorSegmentationEffectIcon.png||PETTumorSegmentationEffectIcon]] &quot;PETTumorSegmentationEffect&quot;.<br /> <br /> Step 4) Click on approximately the center of lesion (tumor or hot lymph node) to segment it. The algorithm automatically produces a segmentation, which can be inspected for quality and modified by the user if necessary (see Sections Segmentation Refinement and Tool Options below).<br /> <br /> Step 5) After segmentation of a lesion, click &quot;Add segment&quot; and segment the next lesion.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Segmentation Refinement}}<br /> <br /> In cases where the algorithm was not able to produce the desired segmentation with one click, the user may interactively refine the the segmentation using these three interaction styles:<br /> <br /> *Interaction style &quot;Create new&quot;: Create a new segmentation with the same label as the previous segmentation. After selection, click approximately at the center of the new region to segment.<br /> *Interaction style &quot;Global refinement&quot;: Choose this option in cases where the whole segmentation appears to be too large or too small. After selection, click on a point the new boundary should go through. This changes the whole boundary of the segmentation.<br /> *Interaction style &quot;Local refinement&quot;: Choose this option in cases where most of the segmentation appears correct, but there are local segmentation errors. After selection, click on a point the new boundary should go through. This changes the boundary of the segmentation in the area of the segmentation error.<br /> <br /> All interaction styles can be applied several times until the desired segmentation result is obtained.<br /> {|<br /> |[[File:PETTumorSegmentation InteractionStyles.png|left|800px|thumb|Effect of the different Interaction Styles. 1 and 2 indicate the order of user clicks.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tool Options}}<br /> <br /> After changing segmentation options, click &quot;Apply&quot; to update the segmentation result.<br /> Options:<br /> <br /> *Splitting: Cut off adjacent objects to the target via watershed or local minimum. Useful for lymph node chains. <br /> *Assist Centering: Move the center to the highest voxel within a 7 mm range, without being on or next to other object labels. Improves consistency.<br /> *Sealing: Close single-voxel gaps in the object or between the object and other objects, if above the threshold. Useful for lymph node chains. <br /> *Allow Overwriting: Ignore other object labels.<br /> <br /> {|<br /> |[[File:PETTumorSegmentation_OptionSplitting.png|380px|thumb|Effect of option &quot;Splitting&quot;]]<br /> |[[File:PETTumorSegmentation_OptionSealing.png|430px|thumb|Effect of option &quot;Sealing&quot;]]<br /> |[[File:PETTumorSegmentation_OptionAllowOverwriting.png|560px|thumb|Effect of option &quot;Allow overwriting&quot;]]<br /> |}<br /> <br /> Advanced Options:<br /> <br /> *Necrotic Region: Prevents cutoff from low uptake. Use if placing a center inside a necrotic region.<br /> *Denoise Threshold: Calculates threshold based on median-filtered image. Use only if scan is very noisy.<br /> *Linear Cost: Cost function below threshold is linear rather than based on region. Use only if little/no transition region in uptake.<br /> {|<br /> |[[File:PETTumorSegmentation_OptionNecroticRegion.png|500px|thumb|Example where option &quot;Necrotic Region&quot; is needed and user clicks 1, 2, and 3 with &quot;Local refinement&quot;.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> <br /> *R. R. Beichel, M. Van Tol, E. J. Ulrich, C. Bauer, T. Chang, K. A. Plichta, B. J. Smith, J. J. Sunderland, M. M. Graham, M. Sonka, J. M. Buatti: &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics, 2016. http://dx.doi.org/10.1118/1.4948679<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=File:PETTumorSegmentation_OptionNecroticRegion.png&diff=64039 2022-04-04T17:21:21Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/PETTumorSegmentEditorEffect&diff=64038 2022-04-04T17:15:26Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool was is 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, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640 &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> Segment Editor Effect for segmentation of tumors and hot lymph nodes in PET scans. Click on a lesion (tumor or hot lymph node) in a PET scan to segment it with one click. For cases where the initial segmentation does not provide the desired result, the tool provides functionality to refine the segmentation with few clicks. Options may help deal with complicated cases such as segmenting individual lymph nodes in a lymph node chain.<br /> <br /> [[File:PETTumorSegmentation_Editor_Effect_options.png|1200px|Screenshot]]<br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;{{documentation/{{documentation/version}}/module-section|Tutorial - Basic Tumor and Lymph Node Segmentation}}<br /> <br /> [[File:PETTumorSegmentation_SegmentEditor_Effect_options.png|thumb|600px|PET Tumor Segmentation Segment Editor Effect Options]]<br /> <br /> Step 1) Load PET scan.<br /> <br /> Step 2) Go to the “Segment Editor” module, select the volume loaded in Step 1 as the “Master Volume”.<br /> <br /> Step 3) Click &quot;Add segment&quot; to create a lesion segment.<br /> <br /> Step 4) Select the [[File:PETTumorSegmentationEffectIcon.png||PETTumorSegmentationEffectIcon]] &quot;PETTumorSegmentationEffect&quot;.<br /> <br /> Step 4) Click on approximately the center of lesion (tumor or hot lymph node) to segment it. The algorithm automatically produces a segmentation, which can be inspected for quality and modified by the user if necessary (see Sections Segmentation Refinement and Tool Options below).<br /> <br /> Step 5) After segmentation of a lesion, click &quot;Add segment&quot; and segment the next lesion.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Segmentation Refinement}}<br /> <br /> In cases where the algorithm was not able to produce the desired segmentation with one click, the user may interactively refine the the segmentation using these three interaction styles:<br /> <br /> *Interaction style &quot;Create new&quot;: Create a new segmentation with the same label as the previous segmentation. After selection, click approximately at the center of the new region to segment.<br /> *Interaction style &quot;Global refinement&quot;: Choose this option in cases where the whole segmentation appears to be too large or too small. After selection, click on a point the new boundary should go through. This changes the whole boundary of the segmentation.<br /> *Interaction style &quot;Local refinement&quot;: Choose this option in cases where most of the segmentation appears correct, but there are local segmentation errors. After selection, click on a point the new boundary should go through. This changes the boundary of the segmentation in the area of the segmentation error.<br /> <br /> All interaction styles can be applied several times until the desired segmentation result is obtained.<br /> {|<br /> |[[File:PETTumorSegmentation InteractionStyles.png|left|800px|thumb|Effect of the different Interaction Styles. 1 and 2 indicate the order of user clicks.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tool Options}}<br /> <br /> After changing segmentation options, click &quot;Apply&quot; to update the segmentation result.<br /> Options:<br /> <br /> *Splitting: Cut off adjacent objects to the target via watershed or local minimum. Useful for lymph node chains. <br /> *Assist Centering: Move the center to the highest voxel within a 7 mm range, without being on or next to other object labels. Improves consistency.<br /> *Sealing: Close single-voxel gaps in the object or between the object and other objects, if above the threshold. Useful for lymph node chains. <br /> *Allow Overwriting: Ignore other object labels.<br /> <br /> {|<br /> |[[File:PETTumorSegmentation_OptionSplitting.png|380px|thumb|Effect of option &quot;Splitting&quot;]]<br /> |[[File:PETTumorSegmentation_OptionSealing.png|430px|thumb|Effect of option &quot;Sealing&quot;]]<br /> |[[File:PETTumorSegmentation_OptionAllowOverwriting.png|560px|thumb|Effect of option &quot;Allow overwriting&quot;]]<br /> |}<br /> <br /> Advanced Options:<br /> <br /> *Necrotic Region: Prevents cutoff from low uptake. Use if placing a center inside a necrotic region.<br /> *Denoise Threshold: Calculates threshold based on median-filtered image. Use only if scan is very noisy.<br /> *Linear Cost: Cost function below threshold is linear rather than based on region. Use only if little/no transition region in uptake.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> <br /> *R. R. Beichel, M. Van Tol, E. J. Ulrich, C. Bauer, T. Chang, K. A. Plichta, B. J. Smith, J. J. Sunderland, M. M. Graham, M. Sonka, J. M. Buatti: &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics, 2016. http://dx.doi.org/10.1118/1.4948679<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=File:PETTumorSegmentation_OptionSealing.png&diff=64037 2022-04-04T17:03:16Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=File:PETTumorSegmentation_OptionSplitting.png&diff=64036 2022-04-04T17:02:39Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=File:PETTumorSegmentation_OptionAllowOverwriting.png&diff=64035 2022-04-04T17:01:33Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/PETTumorSegmentEditorEffect&diff=64034 2022-04-04T17:00:48Z

<p>Chribaue: added illustration for interaction styles</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET Tumor Segmentation tool was is 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, and Graph-based Medical Image Segmentation in 3D and 4D NIH grant R01 EB004640 &lt;br&gt;<br /> Authors: Christian Bauer (University of Iowa), Markus van Tol (University of Iowa) &lt;br&gt;<br /> Contributors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> Segment Editor Effect for segmentation of tumors and hot lymph nodes in PET scans. Click on a lesion (tumor or hot lymph node) in a PET scan to segment it with one click. For cases where the initial segmentation does not provide the desired result, the tool provides functionality to refine the segmentation with few clicks. Options may help deal with complicated cases such as segmenting individual lymph nodes in a lymph node chain.<br /> <br /> [[File:PETTumorSegmentation_Editor_Effect_options.png|1200px|Screenshot]]<br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;{{documentation/{{documentation/version}}/module-section|Tutorial - Basic Tumor and Lymph Node Segmentation}}<br /> <br /> [[File:PETTumorSegmentation_SegmentEditor_Effect_options.png|thumb|600px|PET Tumor Segmentation Segment Editor Effect Options]]<br /> <br /> Step 1) Load PET scan.<br /> <br /> Step 2) Go to the “Segment Editor” module, select the volume loaded in Step 1 as the “Master Volume”.<br /> <br /> Step 3) Click &quot;Add segment&quot; to create a lesion segment.<br /> <br /> Step 4) Select the [[File:PETTumorSegmentationEffectIcon.png||PETTumorSegmentationEffectIcon]] &quot;PETTumorSegmentationEffect&quot;.<br /> <br /> Step 4) Click on approximately the center of lesion (tumor or hot lymph node) to segment it. The algorithm automatically produces a segmentation, which can be inspected for quality and modified by the user if necessary (see Sections Segmentation Refinement and Tool Options below).<br /> <br /> Step 5) After segmentation of a lesion, click &quot;Add segment&quot; and segment the next lesion.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Segmentation Refinement}}<br /> <br /> In cases where the algorithm was not able to produce the desired segmentation with one click, the user may interactively refine the the segmentation using these three interaction styles:<br /> <br /> *Interaction style &quot;Create new&quot;: Create a new segmentation with the same label as the previous segmentation. After selection, click approximately at the center of the new region to segment.<br /> *Interaction style &quot;Global refinement&quot;: Choose this option in cases where the whole segmentation appears to be too large or too small. After selection, click on a point the new boundary should go through. This changes the whole boundary of the segmentation.<br /> *Interaction style &quot;Local refinement&quot;: Choose this option in cases where most of the segmentation appears correct, but there are local segmentation errors. After selection, click on a point the new boundary should go through. This changes the boundary of the segmentation in the area of the segmentation error.<br /> <br /> All interaction styles can be applied several times until the desired segmentation result is obtained.<br /> {|<br /> |[[File:PETTumorSegmentation InteractionStyles.png|left|800px|thumb|Effect of the different Interaction Styles. 1 and 2 indicate the order of user clicks.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tool Options}}<br /> <br /> After changing segmentation options, click &quot;Apply&quot; to update the segmentation result.<br /> <br /> Options:<br /> <br /> *Splitting: Cut off adjacent objects to the target via watershed or local minimum. Useful for lymph node chains.<br /> *Assist Centering: Move the center to the highest voxel within a 7 mm range, without being on or next to other object labels. Improves consistency.<br /> *Sealing: Close single-voxel gaps in the object or between the object and other objects, if above the threshold. Useful for lymph node chains.<br /> *Allow Overwriting: Ignore other object labels.<br /> <br /> Advanced Options:<br /> <br /> *Necrotic Region: Prevents cutoff from low uptake. Use if placing a center inside a necrotic region.<br /> *Denoise Threshold: Calculates threshold based on median-filtered image. Use only if scan is very noisy.<br /> *Linear Cost: Cost function below threshold is linear rather than based on region. Use only if little/no transition region in uptake.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> <br /> *R. R. Beichel, M. Van Tol, E. J. Ulrich, C. Bauer, T. Chang, K. A. Plichta, B. J. Smith, J. J. Sunderland, M. M. Graham, M. Sonka, J. M. Buatti: &quot;Semiautomated Segmentation of Head and Neck Cancers in 18F-FDG PET Scans: A Just-Enough-Interaction Approach&quot;, in Medical Physics, 2016. http://dx.doi.org/10.1118/1.4948679<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=File:PETTumorSegmentation_InteractionStyles.png&diff=64033 2022-04-04T16:45:34Z

<p>Chribaue: </p> <hr /> <div>PETTumorSegmentation InteractionStyles</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PET-IndiC&diff=64020 2022-03-18T19:02:22Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows calculation of quantitative indices related to PET scans such as as Peak, Volume, Total lesion Glycolysis (TLG) and includes:<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] GUI module for use with labelmaps<br /> *[[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]] that integrates with Slicer's [https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentstatistics.html Segment Statistics module] module for use with Slicer's Segments.<br /> <br /> <br /> A detailed description of all supported indices can be found in [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI#Index:_Description_.28units_for_SUVbw_images.29|Quantitative Indices CLI]]. To provide proper units for gray-value dependent indices, the image dataset must be loaded from a DICOM dataset via Slicer's [https://slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html DICOM module].<br /> <br /> {|<br /> |[[File:QuantitativeIndicesTool Screenshot3.png.png|thumb|350px|Quantitative Indices Tool GUI module]]<br /> |[[Image:QuantitativeIndicesTool_Screenshot2.png|thumb|350px|Lesion labelmap]]<br /> |}<br /> <br /> {|<br /> |[[File:PETSegmentStatisticsPluginAnnotated.png|thumb|750px|PET Volume Segment Statistics Plugin]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] for use with labelmaps<br /> *[[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]] for use with Slicer Segments<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] for command line usage outside of the Slicer GUI<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PET-IndiC&diff=64019 2022-03-18T19:00:15Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows calculation of quantitative indices related to PET scans such as as Peak, Volume, Total lesion Glycolysis (TLG) and includes:<br /> <br /> * [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] GUI module for use with labelmaps<br /> * [[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]] that integrates with Slicer's [https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentstatistics.html Segment Statistics module] module for use with Slicer's Segments.<br /> <br /> <br /> A detailed description of all supported indices can be found in [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI#Index:_Description_.28units_for_SUVbw_images.29|Quantitative Indices CLI]]. To provide proper units for gray-value dependent indices, the image dataset must be loaded from a DICOM dataset via Slicer's [https://slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html DICOM module].<br /> <br /> {|<br /> |[[File:QuantitativeIndicesTool Screenshot3.png.png|thumb|350px|Quantitative Indices Tool GUI module]]<br /> |[[Image:QuantitativeIndicesTool_Screenshot2.png|thumb|350px|Lesion labelmap]]<br /> |}<br /> <br /> {|<br /> |[[File:PETSegmentStatisticsPluginAnnotated.png||thumb|750px|PET Volume Segment Statistics Plugin]] <br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] for use with labelmaps<br /> *[[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]] for use with Slicer Segments<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] for command line usage outside of the Slicer GUI<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PET-IndiC&diff=64018 2022-03-18T17:52:30Z

<p>Chribaue: Updated description to reflect removal of IndiC module</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows calculation of quantitative indices related to PET scans such as as Peak, Volume, Total lesion Glycolysis (TLG) and includes:<br /> <br /> * [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] GUI module for use with labelmaps<br /> * [[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]] that integrates with Slicer's [https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentstatistics.html Segment Statistics module] module for use with Slicer's Segments.<br /> <br /> <br /> A detailed description of all supported indices can be found in [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI#Index:_Description_.28units_for_SUVbw_images.29|Quantitative Indices CLI]]. To provide proper units for gray-value dependent indices, the image dataset must be loaded from a DICOM dataset via Slicer's [https://slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html DICOM module].<br /> <br /> {|<br /> |[[File:QuantitativeIndicesTool Screenshot3.png.png|thumb|350px|Quantitative Indices Tool GUI module]]<br /> |[[Image:QuantitativeIndicesTool_Screenshot2.png|thumb|350px|Lesion labelmap]]<br /> |}<br /> <br /> {|<br /> |[[File:PETSegmentStatisticsPluginAnnotated.png||thumb|750px|PET Volume Segment Statistics Plugin]] <br /> }<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]] for use with labelmaps<br /> *[[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]] for use with Slicer Segments<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]] for command line usage outside of the Slicer GUI<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64017 2022-03-16T18:19:14Z

<p>Chribaue: updated general information and added command line usage</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Christian Bauer (University of Iowa)&lt;br&gt;<br /> 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> ==General Information==<br /> 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.<br /> <br /> 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.<br /> <br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> <br /> == Use cases ==<br /> 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]].<br /> <br /> Example command line usage:&lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> # list program options<br /> &gt; SUVFactorCalculator --help<br /> <br /> # read PET DICOM image series from folder and calculate SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder<br /> <br /> # create RWVM DICOM file with calculated SUV normalization factors<br /> &gt; SUVFactorCalculator -p pet_dicom_folder -f rwvm.dcm<br /> <br /> # create SUVbw normalized volume <br /> &gt; SUVFactorCalculator -p pet_dicom_folder --SUVbw SUVbw.nrrd<br /> &lt;/syntaxhighlight&gt;A complete list of all parameters is provided in the Module Panel description below.<br /> <br /> == Module Panel ==<br /> Parameters:<br /> {|<br /> |<br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;-f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> *&lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> **&lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;--SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]<br /> |}<br /> ==Information for Developers==<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ==References==<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PETDICOM&diff=64016 2022-03-16T17:35:18Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PETDICOMExtension.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.<br /> <br /> *Calculation of Standardized Uptake Value (SUV) conversion factors<br /> *Creation of Real World Value Mapping files<br /> *Creation of SUV normalized images<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=5JS-fDdG14k}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DICOMPETSUVPlugin&diff=64015 2022-03-16T17:33:34Z

<p>Chribaue: updated GUI screenshot to newer version</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}})&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The DICOM PET SUV Plugin extends the DICOM module to support parsing and loading of PET DICOM series as Standardized Uptake Value (SUV) images.<br /> *If a PET series has an associated Real World Value Mapping (RWVM) object, then options for loading are generated by the RWVM Plugin.<br /> *If no RWVM object is detected, the plugin calls the SUV Factor Calculator CLI to create one.<br /> {|<br /> |[[Image:DICOM_Browser_PET_SUV_Plugin_2022.png|thumb|800px|DICOM Browser with PET SUV Plugin selected]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Dependencies}}<br /> *[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM Module]]<br /> *[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM RWVM Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> * Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/DICOMPETSUVPlugin<br /> ===Known Issues===<br /> [http://www.na-mic.org/Bug/view.php?id=3806 This bug] currently prevents a newly created RWVM object from being added to the DICOM database at load time.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=File:DICOM_Browser_PET_SUV_Plugin_2022.png&diff=64014 2022-03-16T17:32:53Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DICOMRWVMPlugin&diff=64013 2022-03-16T17:32:31Z

<p>Chribaue: updated GUI screenshot to newer version</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}})&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The DICOM RWVM Plugin extends the DICOM module to support parsing and loading of DICOM series associated with Real World Value Mapping (RWVM) objects.&lt;br&gt;<br /> {|<br /> |[[Image:DICOM_Browser_RWVM_Plugin_2022.png|thumb|800px|DICOM Browser with RWVM Plugin selected]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Dependencies}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM Module]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/DICOMRWVMPlugin<br /> *Instructions on performing SUV conversion in batch mode: https://discourse.slicer.org/t/pet-suv-factor-and-rescale-slope/7355/<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=File:DICOM_Browser_RWVM_Plugin_2022.png&diff=64012 2022-03-16T17:31:07Z

<p>Chribaue: </p> <hr /> <div></div>

Chribaue https://www.slicer.org/w/index.php?title=File:SUV_Factor_Calculator_GUI_2022.png&diff=64011 2022-03-16T17:22:50Z

<p>Chribaue: Chribaue uploaded a new version of File:SUV Factor Calculator GUI 2022.png</p> <hr /> <div>SUV Factor Calculator GUI</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64010 2022-03-16T16:39:58Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa)&lt;br&gt;<br /> Contributors: Christian Bauer (University of Iowa), 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> == General Information ==<br /> <br /> ===Module Type &amp; Category===<br /> <br /> Type: CLI<br /> <br /> Category: Quantification<br /> <br /> ===Module Description===<br /> <br /> {| style=&quot;color:gray&quot; border=&quot;1&quot;<br /> |Program title || SUV Factor Calculator<br /> |-<br /> |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).<br /> |-<br /> |Program documentation-url || [https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI Source code] on GitHub<br /> |-<br /> |}<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.<br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> ===Tutorials===<br /> *<br /> ===Quick Tour of Features and Use===<br /> <br /> A list of panels in the interface, their features, what they mean, and how to use them.<br /> {|<br /> |<br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> ** &lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;--p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> ** &lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;--r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;--f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV_Factor_Calculator_GUI_2022.png|thumb|400px|User Interface]]<br /> |}<br /> <br /> <br /> == Development ==<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> ===Information for Developers===<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ===References===<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521</div>

Chribaue https://www.slicer.org/w/index.php?title=File:SUV_Factor_Calculator_GUI_2022.png&diff=64009 2022-03-16T16:38:41Z

<p>Chribaue: Chribaue uploaded a new version of File:SUV Factor Calculator GUI 2022.png</p> <hr /> <div>SUV Factor Calculator GUI</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/SUVFactorCalculator&diff=64008 2022-03-16T16:33:03Z

<p>Chribaue: updated SUVFactorCLI module description</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> ==Introduction and Acknowledgements==<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> 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. &lt;br&gt;<br /> Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa)&lt;br&gt;<br /> Contributors: Christian Bauer (University of Iowa), 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)&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> == General Information ==<br /> <br /> ===Module Type &amp; Category===<br /> <br /> Type: CLI<br /> <br /> Category: Quantification<br /> <br /> ===Module Description===<br /> <br /> {| style=&quot;color:gray&quot; border=&quot;1&quot;<br /> |Program title || SUV Factor Calculator<br /> |-<br /> |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).<br /> |-<br /> |Program documentation-url || [https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI Source code] on GitHub<br /> |-<br /> |}<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.<br /> *SUVbw:<br /> **males &amp; females: weight<br /> *SUVlbm:<br /> **males: 1.10 * weight - 128 * (weight/height)^2<br /> **females: 1.07 * weight - 148 * (weight/height)^2<br /> *SUVbsa:<br /> **males &amp; females: weight^0.425 * height^0.725 * 0.007184<br /> *SUVibw:<br /> **males: 48.0 + 1.06 * (height - 152)<br /> **females: 45.5 + 0.91 * (height - 152)<br /> ===Tutorials===<br /> *<br /> ===Quick Tour of Features and Use===<br /> <br /> A list of panels in the interface, their features, what they mean, and how to use them.<br /> {|<br /> |<br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''Input Image'''''&lt;/span&gt;: <br /> ** &lt;span style=&quot;color:green&quot;&gt;'''PET DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----petDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;--p&lt;/span&gt;]: Input path to a directory containing a PET DICOM series with header information for SUV computation<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Instance UID of PET series'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----petSeriesInstanceUID&lt;/span&gt;]: Instance UID of PET series (if multiple series in PET dicom path)<br /> <br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''SUV Factor Information'''''&lt;/span&gt;:<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Radioactivity Units'''&lt;/span&gt;: DICOM Tag (0054,1001) - Radioactivity Units<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Weight Units'''&lt;/span&gt;: Patient weight units (always assumed to be kg)<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Height Units'''&lt;/span&gt;: Patient weight units (always assumed to be meters)<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Volume Units'''&lt;/span&gt;: Volume units for concentration (always assumed to be mL)<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Injected Dose'''&lt;/span&gt;: DICOM Tag (0018,1074) - Radionuclide Total Dose<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Patient Weight'''&lt;/span&gt;: DICOM Tag (0010,1030) - Patient Weight<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Patient Height'''&lt;/span&gt;: DICOM Tag (0010,1020) - Patient Size<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Patient Sex'''&lt;/span&gt;: DICOM Tag (0010,0040) - Patient Sex<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Series Reference Time'''&lt;/span&gt;: DICOM Tag (0008,0031) - Series Time<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Injection Time'''&lt;/span&gt;: DICOM Tag (0018,1072) - Radiopharmaceutical Start Time<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Decay Correction'''&lt;/span&gt;: DICOM Tag (0054,1102) - Decay Correction<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Decay Factor'''&lt;/span&gt;: DICOM Tag (0054,1321) - Decay Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Radionuclide Half-life'''&lt;/span&gt;: DICOM Tag (0018,1075) - Radionuclide Half-Life<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Frame Reference Time'''&lt;/span&gt;: DICOM Tag (0054,1300) - Frame Reference Time<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body weight) Conversion Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (lean body mass) Conversion Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (body surface area) Conversion Factor<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVibw Conversion Factor'''&lt;/span&gt;: Standardized Uptake Value (ideal body weight) Conversion Factor<br /> <br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''Real World Value Mapping'''''&lt;/span&gt;: <br /> ** &lt;span style=&quot;color:green&quot;&gt;'''RWV mapping object DICOM volume path'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----rwvmDICOMPath&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;--r&lt;/span&gt;]: Output path to a directory to store the RWV object with the SUV computation result. Only used if no file name is provided.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''RWVM DICOM object file'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----rwvmDICOMFile&lt;/span&gt;] [&lt;span style=&quot;color:pink&quot;&gt;--f&lt;/span&gt;]: File name of the RWV object with the SUV computation result. Not required, default is the the DICOM instance UID.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Series description'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----seriesDescription&lt;/span&gt;]: Description for the generated RVW object.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Series Number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----seriesNumber&lt;/span&gt;]: Series number for the generated RVW object.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''Instance number'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----instanceNumber&lt;/span&gt;]: Instance number for the generated RVW object.<br /> <br /> * &lt;span style=&quot;color:blue&quot;&gt;'''''SUV Normalized Images'''''&lt;/span&gt;: <br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVbw&lt;/span&gt;]: Output file path for SUVbw normalized volume.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVlbm Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVlbm&lt;/span&gt;]: Output file path for SUVlbm normalized volume.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVbsa Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVbsa&lt;/span&gt;]: Output file path for SUVbsa normalized volume.<br /> ** &lt;span style=&quot;color:green&quot;&gt;'''SUVibw Volume&lt;'''&lt;/span&gt; [&lt;span style=&quot;color:orange&quot;&gt;----SUVibw&lt;/span&gt;]: Output file path for SUVibw normalized volume.<br /> <br /> |[[File:SUV Factor Calculator GUI 2022.png|thumb|400px|User Interface]]<br /> |}<br /> <br /> <br /> == Development ==<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> ===Information for Developers===<br /> <br /> *Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI<br /> <br /> ===References===<br /> <br /> Sugawara et al. &quot;Reevaluation of the Standardized Uptake Value for FDG: Variation with Body Weight and Methods for Correction.&quot; Radiology. 1999.&lt;br&gt;<br /> http://pubs.rsna.org/doi/pdf/10.1148/radiology.213.2.r99nv37521</div>

Chribaue https://www.slicer.org/w/index.php?title=File:SUV_Factor_Calculator_GUI_2022.png&diff=64007 2022-03-16T16:17:55Z

<p>Chribaue: </p> <hr /> <div>SUV Factor Calculator GUI</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/QuantitativeIndicesTool&diff=64006 2022-03-16T13:55:43Z

<p>Chribaue: updated QuantitativeIndeces GUI screenshot</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] {{documentation/modulename}} 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. &lt;br&gt;<br /> Authors: Ethan Ulrich ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contributors: Markus van Tol ({{collaborator|name|uiowa}}), Andrey Fedorov ({{collaborator|name|spl}}), Christian Bauer ({{collaborator|name|uiowa}}), Reinhard Beichel ({{collaborator|name|uiowa}}), John Buatti ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The {{documentation/modulename}} calculates simple quantitative features from a grayscale volume and label map. Common indices (mean, min, max, median, etc.) may be calculated. The module also includes experimental indices for PET tumor quantification. For detailed descriptions of the indices calculated, see the [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI documentation]].<br /> <br /> {|<br /> |[[File:QuantitativeIndicesTool Screenshot3.png.png|thumb|350px|GUI]]<br /> |[[Image:QuantitativeIndicesTool_Screenshot2.png|thumb|350px|PET image with tumor mask]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Dependencies}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC/tree/master/QuantitativeIndicesTool<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=File:QuantitativeIndicesTool_Screenshot3.png.png&diff=64005 2022-03-16T13:53:02Z

<p>Chribaue: </p> <hr /> <div>QuantitativeIndicesTool main widget</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.10/Extensions/PET-IndiC&diff=63220 2020-05-21T19:11:31Z

<p>Chribaue: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> [[Image:PET-IndiC.png|128px|center|]]<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] PET-IndiC 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. &lt;br&gt;<br /> Authors: Ethan Ulrich (University of Iowa)&lt;br&gt;<br /> Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa)&lt;br&gt;<br /> Contact: qin{{@}}iibi.uiowa.edu&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> The PET-IndiC Extension allows for fast segmentation of regions of interest and calculation of quantitative indices.<br /> <br /> {{#ev:youtube|https://www.youtube.com/watch?v=_JXxFSa_vzc}}<br /> <br /> ==USAGE==<br /> PET-IndiC is an extension of the main Editor module in Slicer<br /> {|<br /> |[[Image:PET-IndiC_Screenshot1.png|thumb|800px|PET-IndiC Interface]]<br /> |}<br /> After selecting an input image, a label image is automatically assigned. Window/Level presets are available for PET SUV images. For import of DICOM PET images as SUV images, see the [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM Extension]].<br /> {|<br /> |[[Image:PET-IndiC_Screenshot2.png|thumb|375px|FDG PET (Inverted Grey)]]<br /> |[[Image:PET-IndiC_Screenshot3.png|thumb|375px|FDG PET (Rainbow)]]<br /> |}<br /> Segment the image using the Editor tools. The PET-IndiC Extension is meant to be coupled with the [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PET-SEG Extension]] editor effect.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot4.png|thumb|600px|Editor Effect options]]<br /> |}<br /> Quantitative indices are calculated automatically whenever a new label is created or the current label is modified. Several indices are available for calculation. The output appears as a table that can be copied and pasted into a spreadsheet.<br /> {|<br /> |[[Image:PET-IndiC_Screenshot5.png|thumb|700px|Quantitative indices options and output.]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]]<br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]]<br /> *[[Documentation/{{documentation/version}}/Modules/PETVolumeSegmentStatisticsPlugin|PET Volume Segment Statistics Plugin]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> * Source code: https://github.com/QIICR/PET-IndiC<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/4.10/Modules/PETVolumeSegmentStatisticsPlugin&diff=63219 2020-05-21T19:10:31Z

<p>Chribaue: PET Volume Segment Statistics Plugin Documentation</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] {{documentation/modulename}} 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. &lt;br&gt;<br /> Authors: Christian Bauer ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contributors: Markus van Tol ({{collaborator|name|uiowa}}), Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich ({{collaborator|name|uiowa}}), Reinhard Beichel ({{collaborator|name|uiowa}}), John Buatti ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The PETVolumeSegmentStatisticsPlugin is SegmentStatistics plugin for calculation of PET related quantitative indices from a PET volume and a segmentation.<br /> <br /> For detailed descriptions of the indices calculated, see the [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI documentation]].<br /> <br /> &lt;br /&gt;[[File:PETSegmentStatisticsPluginAnnotated.png|frameless|974x974px]]<br /> <br /> <br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC/tree/master/PET-IndiC/PETVolumeSegmentStatisticsPlugin</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/PETVolumeSegmentStatisticsPlugin&diff=63218 2020-05-21T19:05:14Z

<p>Chribaue: updated figure</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] {{documentation/modulename}} 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. &lt;br&gt;<br /> Authors: Christian Bauer ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contributors: Markus van Tol ({{collaborator|name|uiowa}}), Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich ({{collaborator|name|uiowa}}), Reinhard Beichel ({{collaborator|name|uiowa}}), John Buatti ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The PETVolumeSegmentStatisticsPlugin is SegmentStatistics plugin for calculation of PET related quantitative indices from a PET volume and a segmentation.<br /> <br /> For detailed descriptions of the indices calculated, see the [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI documentation]].<br /> <br /> &lt;br /&gt;[[File:PETSegmentStatisticsPluginAnnotated.png|frameless|974x974px]]<br /> <br /> <br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC/tree/master/QuantitativeIndicesTool/PETVolumeSegmentStatisticsPlugin</div>

Chribaue https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/PETVolumeSegmentStatisticsPlugin&diff=63217 2020-05-21T18:59:52Z

<p>Chribaue: PET Volume Segment Statistics Plugin Documentation</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}<br /> &lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> Acknowledgments:<br /> The UIowa [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin QIN] {{documentation/modulename}} 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. &lt;br&gt;<br /> Authors: Christian Bauer ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contributors: Markus van Tol ({{collaborator|name|uiowa}}), Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich ({{collaborator|name|uiowa}}), Reinhard Beichel ({{collaborator|name|uiowa}}), John Buatti ({{collaborator|name|uiowa}})&lt;br&gt;<br /> Contact: &lt;email&gt;qin@iibi.uiowa.edu&lt;/email&gt;&lt;br&gt;<br /> <br /> License: [http://www.slicer.org/pages/LicenseText Slicer License]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}<br /> |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}<br /> |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The PETVolumeSegmentStatisticsPlugin is SegmentStatistics plugin for calculation of PET related quantitative indices from a PET volume and a segmentation.<br /> For detailed descriptions of the indices calculated, see the [[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI documentation]].<br /> <br /> <br /> {|<br /> |[[PETSegmentStatisticsPluginAnnotated.png|thumb|350px|GUI]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Dependencies}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesCLI|Quantitative Indices CLI]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> <br /> *Source code: https://github.com/QIICR/PET-IndiC/tree/master/QuantitativeIndicesTool/PETVolumeSegmentStatisticsPlugin<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

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