Slicer Wiki - User contributions [en]

Documentation/Nightly/ModuleExtensionListing/Extensions by category

2016-11-04T19:33:08Z

Ejulrich: /* Registration */ add new extension Multi-Level Registration

__NOTOC__
* [[#Extensions_by_category|Extensions by category]]
= Extensions by category =
25 categories:
* [[#Extensions_by_category_Astronomy|Astronomy]]
* [[#Extensions_by_category_Cardiac|Cardiac]]
* [[#Extensions_by_category_Cardiac_MRI_toolkit|Cardiac MRI toolkit]]
* [[#Extensions_by_category_Chest_Imaging_Platform|Chest Imaging Platform]]
* [[#Extensions_by_category_Converters|Converters]]
* [[#Extensions_by_category_Developer_Tools|Developer Tools]]
* [[#Extensions_by_category_Diffusion|Diffusion]]
* [[#Extensions_by_category_Editor_Effects|Editor Effects]]
* [[#Extensions_by_category_Examples|Examples]]
* [[#Extensions_by_category_Exporter|Exporter]]
* [[#Extensions_by_category_Filtering|Filtering]]
* [[#Extensions_by_category_IGT|IGT]]
* [[#Extensions_by_category_Informatics|Informatics]]
* [[#Extensions_by_category_Libraries|Libraries]]
* [[#Extensions_by_category_Mesh_Generation|Mesh Generation]]
* [[#Extensions_by_category_Microscopy|Microscopy]]
* [[#Extensions_by_category_Nuclear_Medicine|Nuclear Medicine]]
* [[#Extensions_by_category_Quantification|Quantification]]
* [[#Extensions_by_category_Radiotherapy|Radiotherapy]]
* [[#Extensions_by_category_Registration|Registration]]
* [[#Extensions_by_category_Scoliosis|Scoliosis]]
* [[#Extensions_by_category_Segmentation|Segmentation]]
* [[#Extensions_by_category_Sequences|Sequences]]
* [[#Extensions_by_category_Shape_Analysis|Shape Analysis]]
* [[#Extensions_by_category_Tractography|Tractography]]
* [[#Extensions_by_category_Training|Training]]
* [[#Extensions_by_category_Ultrasound|Ultrasound]]
* [[#Extensions_by_category_Vascular_Modeling_Toolkit|Vascular Modeling Toolkit]]
* [[#Extensions_by_category_Wizards|Wizards]]

== Astronomy ==
* [[Documentation/Nightly/Extensions/SlicerAstro|Slicer Astro]] [https://github.com/Punzo/SlicerAstro/wiki]

== Cardiac ==
* [[Documentation/Nightly/Extensions/SlicerHeart|Slicer Heart]]
* [http://brainsia.github.io/CardiacAgatstonMeasures/ Cardiac Agatston Measures]

== Cardiac MRI toolkit ==
* [http://capulet.med.utah.edu/namic/cmrslicer/ Cardiac MRI Toolkit]

== Chest Imaging Platform ==
* [http://www.chestimagingplatform.org Chest Imaging Platform]

== Converters ==
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETDICOM PETDICOMExtension]

== Developer Tools ==
* [[Documentation/Nightly/Extensions/DeveloperToolsForExtensions|Developer Tools For Extensions]]
* [[Documentation/Nightly/Extensions/DebuggingTools|Debugging Tools]]
* [[Documentation/Nightly/Extensions/MatlabBridge|Matlab Bridge]]
* [[Documentation/Nightly/Extensions/ImageMaker|Image Maker]]

== Diffusion ==
* [[Documentation/Nightly/Extensions/ResampleDTIlogEuclidean|Resample DTIlog Euclidean]]

== Editor Effects ==
* [[Documentation/Nightly/Extensions/WindowLevelEffect|Window Level Effect]]

== Examples ==
* [[Documentation/Nightly/Extensions/OpenCVExample|OpenCV Example]]

== Exporter ==
* [[Documentation/Nightly/Extensions/SlicerToKiwiExporter|Slicer To Kiwi Exporter]]

== Filtering ==
* [[Documentation/Nightly/Extensions/pyLARSlicerExtension|pyLAR Slicer Extension]]

== IGT ==
* [[Documentation/Nightly/Extensions/NeedleFinder|Needle Finder]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TrackerStabilizer Tracker Stabilizer]
* [[Documentation/Nightly/Extensions/GyroGuide|Gyro Guide]]
* [[Documentation/Nightly/Extensions/CornerAnnotation|Corner Annotation]]
* [https://github.com/SlicerIGT/LumpNav Lump Nav]
* [[Documentation/Nightly/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]]
* [[Documentation/Nightly/Extensions/SlicerIGT|Slicer IGT]]
* [[Documentation/Nightly/Extensions/iGyne|i Gyne]]
* [[Documentation/Nightly/Extensions/ResectionPlanner|Resection Planner]]

== Informatics ==
* [[Documentation/Nightly/Extensions/CurveMaker|Curve Maker]]
* [[Documentation/Nightly/Extensions/LongitudinalPETCT|Longitudinal PETCT]]
* [[Documentation/Nightly/Extensions/Reporting|Reporting]]
* [[Documentation/Nightly/Extensions/mpReview|mp Review]]
* [[Documentation/Nightly/Extensions/TCIABrowser|TCIABrowser]]
* [[Documentation/Nightly/Extensions/SlicerProstate|Slicer Prostate]]

== Libraries ==
* [[Documentation/Nightly/Extensions/SlicerOpenCV|SlicerOpenCV]]

== Mesh Generation ==
* [[Documentation/Nightly/Extensions/CBC_3D_I2MConversion|CBC 3D I2MConversion]]
* [[Documentation/Nightly/Extensions/CleaverExtension|Cleaver Extension]]
* [[Documentation/Nightly/Extensions/Add3DTextExtension|Add3DText Extension]]
* [[Documentation/Nightly/Extensions/PorousScaffoldsExtension|Porous Scaffolds Extension]]


== Microscopy ==
* [[Documentation/Nightly/Extensions/IASEM|IASEM]]

== Nuclear Medicine ==
* [http://gti-fing.github.io/SlicerPetSpectAnalysis Pet Spect Analysis]

== Quantification ==
* [http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis DSCMRIAnalysis]
* [[Documentation/Nightly/Extensions/T1Mapping|T1Mapping]]
* [[Documentation/Nightly/Extensions/DiceComputation|Dice Computation]]
* [[Documentation/Nightly/Extensions/PET-IndiC|PET-Indi C]]
* [[Documentation/Nightly/Extensions/PkModeling|Pk Modeling]]

== Radiotherapy ==
* [[Documentation/Nightly/Extensions/MarginCalculator|Margin Calculator]]
* [[Documentation/Nightly/Extensions/SlicerRT|Slicer RT]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/GelDosimetry Gel Dosimetry Analysis]

== Registration ==
* [[Documentation/Nightly/Extensions/CMFreg|CMFreg]]
* [[Documentation/Nightly/Extensions/PBNRR|PBNRR]]
* [[Documentation/Nightly/Extensions/Multi-LevelRegistration|Multi-LevelRegistration]]


== Scoliosis ==
* [[Documentation/Nightly/Extensions/Scoliosis|Scoliosis]]

== Segmentation ==
* [http://publish.uwo.ca/~dchen285/GraphCutSegment/GraphCutSegment.html Graph Cut Segment]
* [http://www.nitrc.org/projects/abc ABC]
* [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter Carrera Slice]
* [[Documentation/Nightly/Extensions/SkullStripper|Skull Stripper]]
* [[Documentation/Nightly/Extensions/PETTumorSegmentation|PETTumor Segmentation]]
* [[Documentation/Nightly/Extensions/SwissSkullStripper|Swiss Skull Stripper]]
* [[Documentation/Nightly/Extensions/LAScarSegmenter|LAScar Segmenter]]
* [[Documentation/Nightly/Extensions/OpenCAD|Open CAD]]
* [[Documentation/Nightly/Extensions/IntensitySegmenter|Intensity Segmenter]]
* [https://github.com/Tomnl/Slicer-Wasp Wasp]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AirwaySegmentation Airway Segmentation]
* [https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/FastGrowCut Fast Grow Cut Effect]
* [[Documentation/Nightly/Extensions/VolumeClip|Volume Clip]]

== Sequences ==
* [[Documentation/Nightly/Extensions/Sequences|Sequences]]

== Shape Analysis ==
* [[Documentation/Nightly/Extensions/MeshToLabelMap|Mesh To Label Map]]
* [[Documentation/Nightly/Extensions/Q3DC|Q3DC]]
* [[Documentation/Nightly/Extensions/ModelToModelDistance|Model To Model Distance]]
* [[Documentation/Nightly/Extensions/EasyClip|Easy Clip]]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PickAndPaint Pick And Paint Extension]
* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/AnglePlanes Angle Planes Extension]

== Tractography ==
* [[Documentation/Nightly/Extensions/FinslerTractography|Finsler Tractography]]
* [[Documentation/Nightly/Extensions/UKFTractography|UKFTractography]]

== Training ==
* [[Documentation/Nightly/Extensions/PerkTutor|Perk Tutor]]

== Ultrasound ==
* [https://github.com/KitwareMedical/SlicerITKUltrasound SlicerITKUltrasound]


== Vascular Modeling Toolkit ==
* [http://slicer.vmtk.org/ VMTK]

== Wizards ==
* [[Documentation/Nightly/Extensions/ChangeTracker|Change Tracker]]
__NOTOC__

Developer Meetings/20160208

2016-02-08T20:29:15Z

Ejulrich: /* To Discuss */ editor widget

= Update =

= To Discuss=

* Crash closing scene after using CLI GUI http://na-mic.org/Mantis/view.php?id=4141
* Inconsistent behavior with Editor Widget between stable and nightly releases

= Conclusion =

Documentation/Nightly/Modules/QuantitativeIndicesCLI

2015-08-18T21:23:03Z

Ejulrich: adde note for peak

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
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. 
Authors: Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}) 
Contributors: Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa) 
Contact: <email>qin@iibi.uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===
The {{documentation/modulename}} is a simple command line interface module for calculation of quantitative indices inside an image mask. Common indices (mean, min, max, median, etc.) may be calculated. The module also includes experimental indices for PET tumor quantification. For a more user-friendly interface and output, a helper module ([[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]]) has also been developed.

{|
|[[Image:QuantitativeIndicesCLI_Screenshot1.png|thumb|400px|center|CLI input]]
|[[Image:QuantitativeIndicesCLI_Screenshot3.png|thumb|350px|center|PET image with tumor mask]]
|}

[[Image:QuantitativeIndicesCLI_Screenshot2.png|thumb|350px|CLI output]]

===Index: Description (units for SUVbw images)===
* Mean: mean value in region of interest (g/ml)
* Variance: variance in region of interest (g/ml)^2
* Min: minimum value in region of interest (g/ml)
* Max: maximum value in region of interest (g/ml)
* RMS: root-mean-square value in region of interest (g/ml)
* Volume: volume of region of interest (cm^3)
* First Quartile: 25th percentile value in region of interest (g/ml)
* Median: 50th percentile value in region of interest (g/ml)
* Third Quartile: 75th percentile value in region of interest (g/ml)
* Upper Adjacent: first value in region of interest not greater than 1.5 times the interquartile range (g/ml)
* TLG: total lesion glycolysis (g)
* Glycolysis Q1: lesion glycolysis calculated from the first quarter of the grayscale range within the region of interest (g)
* Glycolysis Q2: lesion glycolysis calculated from the second quarter of the grayscale range within the region of interest (g)
* Glycolysis Q3: lesion glycolysis calculated from the third quarter of the grayscale range within the region of interest (g)
* Glycolysis Q4: lesion glycolysis calculated from the fourth quarter of the grayscale range within the region of interest (g)
* Q1 Distibution: percent of gray values that fall within the first quarter of the grayscale range within the region of interest (%)
* Q2 Distibution: percent of gray values that fall within the second quarter of the grayscale range within the region of interest (%)
* Q3 Distibution: percent of gray values that fall within the third quarter of the grayscale range within the region of interest (%)
* Q4 Distibution: percent of gray values that fall within the fourth quarter of the grayscale range within the region of interest (%)
* SAM: standardized added metabolic activity (g)
* SAM mean background: intermediate value for calculating SAM, estimates local background near region of interest (g/ml)
* Peak: maximum average gray value that is calculated from a 1 cubic centimeter sphere placed within the region of interest (g/ml)
** Note: Peak returns NaN when measurement sphere does not fit completely within the region of interest.

===Information for Developers===

*Source code: https://github.com/QIICR/PET-IndiC/tree/master/QuantitativeIndicesCLI

===References===
*Orlhac et al. "Tumor Texture Analysis in 18F-FDG PET: Relationships Between Texture Parameters, Histogram Indices, Standardized Uptake Values, Metabolic Volumes, and Total Lesion Glycolysis." JNM. 2014.
*El-Hafez et al. "Total lesion glycolysis: a possible new prognostic parameter in oral cavity squamous cell carcinoma." Oral Oncology. 2013; 49(3):261–8.
*Mertens et al. "Standardized added metabolic activity (SAM): a partial volume independent marker of total lesion glycolysis in liver metastases." EJNMMI. 2012; 39(9):1441–8.

Documentation/4.4/Modules/QuantitativeIndicesCLI

2015-04-03T18:23:47Z

Ejulrich: add redirect

#REDIRECT [[Documentation/Nightly/Modules/QuantitativeIndicesCLI]]

File:QuantitativeIndicesTool Screenshot2.png

2015-04-02T19:16:20Z

Ejulrich:

File:QuantitativeIndicesTool Screenshot1.png

2015-04-02T19:16:02Z

Ejulrich:

Documentation/Nightly/Modules/QuantitativeIndicesTool

2015-04-02T19:15:40Z

Ejulrich: add Quantitative Indices Tool module

Documentation/Nightly/Modules/QuantitativeIndicesCLI

2015-04-01T16:48:18Z

Ejulrich: add Quantitative Indice CLI module

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
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. 
Authors: Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa), Andrey Fedorov ({{collaborator|name|spl}}) 
Contributors: Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa) 
Contact: <email>qin@iibi.uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===
The {{documentation/modulename}} is a simple command line interface module for calculation of quantitative indices inside an image mask. Common indices (mean, min, max, median, etc.) may be calculated. The module also includes experimental indices for PET tumor quantification. For a more user-friendly interface and output, a helper module ([[Documentation/{{documentation/version}}/Modules/QuantitativeIndicesTool|Quantitative Indices Tool]]) has also been developed.

{|
|[[Image:QuantitativeIndicesCLI_Screenshot1.png|thumb|400px|center|CLI input]]
|[[Image:QuantitativeIndicesCLI_Screenshot3.png|thumb|350px|center|PET image with tumor mask]]
|}

[[Image:QuantitativeIndicesCLI_Screenshot2.png|thumb|350px|CLI output]]

===Index: Description (units for SUVbw images)===
* Mean: mean value in region of interest (g/ml)
* Variance: variance in region of interest (g/ml)^2
* Min: minimum value in region of interest (g/ml)
* Max: maximum value in region of interest (g/ml)
* RMS: root-mean-square value in region of interest (g/ml)
* Volume: volume of region of interest (cm^3)
* First Quartile: 25th percentile value in region of interest (g/ml)
* Median: 50th percentile value in region of interest (g/ml)
* Third Quartile: 75th percentile value in region of interest (g/ml)
* Upper Adjacent: first value in region of interest not greater than 1.5 times the interquartile range (g/ml)
* TLG: total lesion glycolysis (g)
* Glycolysis Q1: lesion glycolysis calculated from the first quarter of the grayscale range within the region of interest (g)
* Glycolysis Q2: lesion glycolysis calculated from the second quarter of the grayscale range within the region of interest (g)
* Glycolysis Q3: lesion glycolysis calculated from the third quarter of the grayscale range within the region of interest (g)
* Glycolysis Q4: lesion glycolysis calculated from the fourth quarter of the grayscale range within the region of interest (g)
* Q1 Distibution: percent of gray values that fall within the first quarter of the grayscale range within the region of interest (%)
* Q2 Distibution: percent of gray values that fall within the second quarter of the grayscale range within the region of interest (%)
* Q3 Distibution: percent of gray values that fall within the third quarter of the grayscale range within the region of interest (%)
* Q4 Distibution: percent of gray values that fall within the fourth quarter of the grayscale range within the region of interest (%)
* SAM: standardized added metabolic activity (g)
* SAM mean background: intermediate value for calculating SAM, estimates local background near region of interest (g/ml)
* Peak: maximum average gray value that is calculated from a 1 cubic centimeter sphere placed within the region of interest (g/ml)

===Information for Developers===

*Source code: https://github.com/QIICR/PET-IndiC/tree/master/QuantitativeIndicesCLI

===References===
*Orlhac et al. "Tumor Texture Analysis in 18F-FDG PET: Relationships Between Texture Parameters, Histogram Indices, Standardized Uptake Values, Metabolic Volumes, and Total Lesion Glycolysis." JNM. 2014.
*El-Hafez et al. "Total lesion glycolysis: a possible new prognostic parameter in oral cavity squamous cell carcinoma." Oral Oncology. 2013; 49(3):261–8.
*Mertens et al. "Standardized added metabolic activity (SAM): a partial volume independent marker of total lesion glycolysis in liver metastases." EJNMMI. 2012; 39(9):1441–8.

File:QuantitativeIndicesCLI Screenshot3.png

2015-04-01T16:12:40Z

Ejulrich:

File:QuantitativeIndicesCLI Screenshot2.png

2015-04-01T16:12:28Z

Ejulrich:

File:QuantitativeIndicesCLI Screenshot1.png

2015-04-01T16:12:14Z

Ejulrich:

Documentation/Nightly/Extensions/PET-IndiC

2015-03-31T22:20:22Z

Ejulrich: update source code URL

Documentation/Nightly/Extensions/PET-IndiC

2015-03-27T15:54:38Z

Ejulrich: added screenshots

File:PET-IndiC Screenshot5.png

2015-03-27T15:19:06Z

Ejulrich:

File:PET-IndiC Screenshot4.png

2015-03-27T15:18:45Z

Ejulrich:

File:PET-IndiC Screenshot3.png

2015-03-27T15:18:17Z

Ejulrich:

File:PET-IndiC Screenshot2.png

2015-03-27T15:17:55Z

Ejulrich:

File:PET-IndiC Screenshot1.png

2015-03-27T15:17:21Z

Ejulrich:

Documentation/4.4/Extensions/PET-IndiC

2015-03-27T14:28:17Z

Ejulrich: created redirect

#REDIRECT [[Documentation/Nightly/Extensions/PET-IndiC]]

File:PET-IndiC.png

2015-03-26T20:43:53Z

Ejulrich:

Documentation/Nightly/Extensions/PET-IndiC

2015-03-26T20:41:48Z

Ejulrich: created

Documentation/Nightly/Extensions

2015-03-26T20:22:15Z

Ejulrich: add PET-IndiC extension

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Kevin Wang, Adam Rankin, Greg Sharp, Andras Lasso, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]


** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)
** [[Documentation/{{documentation/version}}/Extensions/PathRecorder|Path Recorder]] (Alireza Mehrtash)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]] (Francois Budin, Pengdong Xiao, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]] (Andras Lasso, Matt Lougheed)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Atsushi Yamada, Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)
** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]
** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]
* [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)
* [[Documentation/{{documentation/version}}/Extensions/ResectionPlanner|ResectionVolume]] (Matt Lougheed)
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM]] (Andrey Fedorov, Ethan Ulrich)
* [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PETTumorSegmentation]] (Christian Bauer)
* [[Documentation/{{documentation/version}}/Extensions/PET-IndiC|PET-IndiC]] (Ethan Ulrich)
* [[Documentation/{{documentation/version}}/Extensions/CornerAnnotation|CornerAnnotation]] (Atsushi Yamada)
* [[Documentation/{{documentation/version}}/Extensions/Wasp|Watershed Annotation and Segmentation Plugin.]] (Thomas Lawson)
* [[Documentation/{{documentation/version}}/Extensions/SlicerPetSpectAnalysis|SlicerPetSpectAnalysis]] (Martín Bertran,Natalia Martínez, Guillermo Carbajal, Álvaro Gómez)
** [[Documentation/{{documentation/version}}/Modules/dPetBrainQuantification|dPetBrainQuantification]]
* [[Documentation/{{documentation/version}}/Extensions/IGTWizard|IGTWizard]] (Junichi Tokuda and Atsushi Yamada)
* [[Documentation/{{documentation/version}}/Extensions/DeveloperToolsForExtensions|DeveloperToolsForExtensions]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Modules/T1_Mapping|T1_Mapping]] (Xiao Da, Artem Mamonov, Jayashree Kalpathy-Cramer and Andriy Fedorov)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>

Documentation/Nightly/Extensions/PETDICOM

2015-03-13T21:10:45Z

Ejulrich: added new logo

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[Image:PETDICOMExtension.png|128px|center|]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work 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. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa) 
Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa) 
Contact: <email>qin@iibi.uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.
*Calculation of Standardized Uptake Value (SUV) conversion factors
*Creation of Real World Value Mapping files


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]
*[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]
*[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* Source code: https://github.com/QIICR/Slicer-PETDICOMExtension


{{documentation/{{documentation/version}}/extension-footer}}

Documentation/4.4/Extensions/PETDICOM

2015-03-13T21:08:46Z

Ejulrich: added new logo

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}

[[Image:PETDICOMExtension.png|128px|center|]]

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work 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. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa) 
Contributors: Markus van Tol (University of Iowa), Christian Bauer (University of Iowa), Reinhard Beichel (University of Iowa), John Buatti (University of Iowa) 
Contact: <email>qin@iibi.uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
The PET DICOM Extension provides tools to import PET Standardized Uptake Value images from DICOM into Slicer.
*Calculation of Standardized Uptake Value (SUV) conversion factors
*Creation of Real World Value Mapping files


{{documentation/{{documentation/version}}/extension-section|Modules}}
*[[Documentation/{{documentation/version}}/Modules/SUVFactorCalculator|SUV Factor Calculator CLI]]
*[[Documentation/{{documentation/version}}/Modules/DICOMRWVMPlugin|DICOM Real World Value Mapping Plugin]]
*[[Documentation/{{documentation/version}}/Modules/DICOMPETSUVPlugin|DICOM PET SUV Plugin]]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* Source code: https://github.com/QIICR/Slicer-PETDICOMExtension


{{documentation/{{documentation/version}}/extension-footer}}

File:PETDICOMExtension.png

2015-03-13T21:04:19Z

Ejulrich: uploaded a new version of "File:PETDICOMExtension.png"

Documentation/4.4/Modules/DICOMPETSUVPlugin

2015-01-20T18:00:08Z

Ejulrich: update contributors, contact email, and images

Documentation/4.4/Modules/DICOMRWVMPlugin

2015-01-20T17:58:32Z

Ejulrich: update contributors, contact email, and images

Documentation/4.4/Modules/SUVFactorCalculator

2015-01-20T17:57:03Z

Ejulrich: update contributors, contact email, and images

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work 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. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa) 
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) 
Contact: <email>qin@iibi.uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI Source code] on GitHub
|-
|}

== Usage ==

===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list of panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]: Input path to a directory containing a PET DICOM series with header information for SUV computation

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]: Output path to a directory to store the RWV object with the SUV computation result

** '''Radioactivity Units''' : DICOM Tag (0054,1001) - Radioactivity Units

** '''Weight Units''' : Patient weight units (always assumed to be kg)

** '''Height Units''' : Patient weight units (always assumed to be meters)

** '''Volume Units''' : Volume units for concentration (always assumed to be mL)

** '''Injected Dose''' : DICOM Tag (0018,1074) - Radionuclide Total Dose

** '''Patient Weight''' : DICOM Tag (0010,1030) - Patient Weight

** '''Patient Height''' : DICOM Tag (0010,1020) - Patient Size

** '''Patient Sex''' : DICOM Tag (0010,0040) - Patient Sex

** '''Series Reference Time''' : DICOM Tag (0008,0031) - Series Time

** '''Injection Time''' : DICOM Tag (0018,1072) - Radiopharmaceutical Start Time

** '''Decay Correction''' : DICOM Tag (0054,1102) - Decay Correction

** '''Decay Factor''' : DICOM Tag (0054,1321) - Decay Factor

** '''Radionuclide Half-life''' : DICOM Tag (0018,1075) - Radionuclide Half-Life

** '''Frame Reference Time''' : DICOM Tag (0054,1300) - Frame Reference Time

** '''SUVbw Conversion Factor''' : Standardized Uptake Value (body weight) Conversion Factor

** '''SUVlbm Conversion Factor''' : Standardized Uptake Value (lean body mass) Conversion Factor

** '''SUVbsa Conversion Factor''' : Standardized Uptake Value (body surface area) Conversion Factor

** '''SUVibw Conversion Factor''' : Standardized Uptake Value (ideal body weight) Conversion Factor

** '''RWVM File''' : Real World Value Mapping object file

|[[Image:SUV_Factor_Calculator_GUI.png|thumb|400px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}

===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

===References===

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

Documentation/4.4/Extensions/PETDICOM

2015-01-20T17:55:43Z

Ejulrich: update contributors, contact email, and images

Documentation/Nightly/Modules/DICOMPETSUVPlugin

2015-01-19T18:54:09Z

Ejulrich: update contact email

Documentation/Nightly/Modules/DICOMRWVMPlugin

2015-01-19T18:48:22Z

Ejulrich: update contact email

Documentation/Nightly/Modules/SUVFactorCalculator

2015-01-19T18:46:47Z

Ejulrich: update contact email

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work 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. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa) 
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) 
Contact: <email>qin@iibi.uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI Source code] on GitHub
|-
|}

== Usage ==

===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list of panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]: Input path to a directory containing a PET DICOM series with header information for SUV computation

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]: Output path to a directory to store the RWV object with the SUV computation result

** '''Radioactivity Units''' : DICOM Tag (0054,1001) - Radioactivity Units

** '''Weight Units''' : Patient weight units (always assumed to be kg)

** '''Height Units''' : Patient weight units (always assumed to be meters)

** '''Volume Units''' : Volume units for concentration (always assumed to be mL)

** '''Injected Dose''' : DICOM Tag (0018,1074) - Radionuclide Total Dose

** '''Patient Weight''' : DICOM Tag (0010,1030) - Patient Weight

** '''Patient Height''' : DICOM Tag (0010,1020) - Patient Size

** '''Patient Sex''' : DICOM Tag (0010,0040) - Patient Sex

** '''Series Reference Time''' : DICOM Tag (0008,0031) - Series Time

** '''Injection Time''' : DICOM Tag (0018,1072) - Radiopharmaceutical Start Time

** '''Decay Correction''' : DICOM Tag (0054,1102) - Decay Correction

** '''Decay Factor''' : DICOM Tag (0054,1321) - Decay Factor

** '''Radionuclide Half-life''' : DICOM Tag (0018,1075) - Radionuclide Half-Life

** '''Frame Reference Time''' : DICOM Tag (0054,1300) - Frame Reference Time

** '''SUVbw Conversion Factor''' : Standardized Uptake Value (body weight) Conversion Factor

** '''SUVlbm Conversion Factor''' : Standardized Uptake Value (lean body mass) Conversion Factor

** '''SUVbsa Conversion Factor''' : Standardized Uptake Value (body surface area) Conversion Factor

** '''SUVibw Conversion Factor''' : Standardized Uptake Value (ideal body weight) Conversion Factor

** '''RWVM File''' : Real World Value Mapping object file

|[[Image:SUV_Factor_Calculator_GUI.png|thumb|400px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}

===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

===References===

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

Documentation/Nightly/Extensions/PETDICOM

2015-01-19T18:44:54Z

Ejulrich: update contact email

Documentation/Nightly/Modules/DICOMPETSUVPlugin

2015-01-16T19:15:58Z

Ejulrich: include QIN grant and Iowa image

Documentation/Nightly/Modules/DICOMRWVMPlugin

2015-01-16T19:10:51Z

Ejulrich: include QIN grant and Iowa image

Documentation/Nightly/Modules/SUVFactorCalculator

2015-01-16T19:05:50Z

Ejulrich: fix source code link

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work 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. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa) 
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) 
Contact: Ethan Ulrich, <email>ethan-ulrich@uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI Source code] on GitHub
|-
|}

== Usage ==

===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list of panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]: Input path to a directory containing a PET DICOM series with header information for SUV computation

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]: Output path to a directory to store the RWV object with the SUV computation result

** '''Radioactivity Units''' : DICOM Tag (0054,1001) - Radioactivity Units

** '''Weight Units''' : Patient weight units (always assumed to be kg)

** '''Height Units''' : Patient weight units (always assumed to be meters)

** '''Volume Units''' : Volume units for concentration (always assumed to be mL)

** '''Injected Dose''' : DICOM Tag (0018,1074) - Radionuclide Total Dose

** '''Patient Weight''' : DICOM Tag (0010,1030) - Patient Weight

** '''Patient Height''' : DICOM Tag (0010,1020) - Patient Size

** '''Patient Sex''' : DICOM Tag (0010,0040) - Patient Sex

** '''Series Reference Time''' : DICOM Tag (0008,0031) - Series Time

** '''Injection Time''' : DICOM Tag (0018,1072) - Radiopharmaceutical Start Time

** '''Decay Correction''' : DICOM Tag (0054,1102) - Decay Correction

** '''Decay Factor''' : DICOM Tag (0054,1321) - Decay Factor

** '''Radionuclide Half-life''' : DICOM Tag (0018,1075) - Radionuclide Half-Life

** '''Frame Reference Time''' : DICOM Tag (0054,1300) - Frame Reference Time

** '''SUVbw Conversion Factor''' : Standardized Uptake Value (body weight) Conversion Factor

** '''SUVlbm Conversion Factor''' : Standardized Uptake Value (lean body mass) Conversion Factor

** '''SUVbsa Conversion Factor''' : Standardized Uptake Value (body surface area) Conversion Factor

** '''SUVibw Conversion Factor''' : Standardized Uptake Value (ideal body weight) Conversion Factor

** '''RWVM File''' : Real World Value Mapping object file

|[[Image:SUV_Factor_Calculator_GUI.png|thumb|400px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}

===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

===References===

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

Documentation/Nightly/Modules/SUVFactorCalculator

2015-01-16T19:02:57Z

Ejulrich: include QIN grant and Iowa image

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work 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. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa), Markus van Tol (University of Iowa) 
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) 
Contact: Ethan Ulrich, <email>ethan-ulrich@uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|uiowa}}|{{collaborator|longname|uiowa}}
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==

===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/SUVFactorCalculator Source code] on GitHub
|-
|}

== Usage ==

===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list of panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]: Input path to a directory containing a PET DICOM series with header information for SUV computation

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]: Output path to a directory to store the RWV object with the SUV computation result

** '''Radioactivity Units''' : DICOM Tag (0054,1001) - Radioactivity Units

** '''Weight Units''' : Patient weight units (always assumed to be kg)

** '''Height Units''' : Patient weight units (always assumed to be meters)

** '''Volume Units''' : Volume units for concentration (always assumed to be mL)

** '''Injected Dose''' : DICOM Tag (0018,1074) - Radionuclide Total Dose

** '''Patient Weight''' : DICOM Tag (0010,1030) - Patient Weight

** '''Patient Height''' : DICOM Tag (0010,1020) - Patient Size

** '''Patient Sex''' : DICOM Tag (0010,0040) - Patient Sex

** '''Series Reference Time''' : DICOM Tag (0008,0031) - Series Time

** '''Injection Time''' : DICOM Tag (0018,1072) - Radiopharmaceutical Start Time

** '''Decay Correction''' : DICOM Tag (0054,1102) - Decay Correction

** '''Decay Factor''' : DICOM Tag (0054,1321) - Decay Factor

** '''Radionuclide Half-life''' : DICOM Tag (0018,1075) - Radionuclide Half-Life

** '''Frame Reference Time''' : DICOM Tag (0054,1300) - Frame Reference Time

** '''SUVbw Conversion Factor''' : Standardized Uptake Value (body weight) Conversion Factor

** '''SUVlbm Conversion Factor''' : Standardized Uptake Value (lean body mass) Conversion Factor

** '''SUVbsa Conversion Factor''' : Standardized Uptake Value (body surface area) Conversion Factor

** '''SUVibw Conversion Factor''' : Standardized Uptake Value (ideal body weight) Conversion Factor

** '''RWVM File''' : Real World Value Mapping object file

|[[Image:SUV_Factor_Calculator_GUI.png|thumb|400px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}

===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

===References===

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

Documentation/Nightly/Extensions/PETDICOM

2015-01-16T18:54:47Z

Ejulrich: include QIN grant and Iowa image

Documentation/Nightly/Modules/DICOMPETSUVPlugin

2014-08-25T19:24:19Z

Ejulrich:

Documentation/Nightly/Modules/DICOMPETSUVPlugin

2014-08-25T19:22:46Z

Ejulrich: created

Documentation/Nightly/Modules/DICOMRWVMPlugin

2014-08-25T19:04:45Z

Ejulrich: created

File:DICOM Browser PET SUV Plugin.png

2014-08-25T19:04:11Z

Ejulrich:

File:DICOM Browser RWVM Plugin.png

2014-08-25T18:56:19Z

Ejulrich:

Documentation/Nightly/Modules/SUVFactorCalculator

2014-08-25T18:22:44Z

Ejulrich: added GUI screenshot

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is funded in part by [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa) 
Contributors: Markus Van Tol (University of Iowa), Hans Johnson (University of Iowa), Wendy Plesniak (SPL, BWH), Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH) 
Contact: Ethan Ulrich, <email>ethan-ulrich@uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/SUVFactorCalculator Source code] on GitHub
|-
|}

== Usage ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list of panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]: Input path to a directory containing a PET DICOM series with header information for SUV computation

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]: Output path to a directory to store the RWV object with the SUV computation result

** '''Radioactivity Units''' : DICOM Tag (0054,1001) - Radioactivity Units

** '''Weight Units''' : Patient weight units (always assumed to be kg)

** '''Height Units''' : Patient weight units (always assumed to be meters)

** '''Volume Units''' : Volume units for concentration (always assumed to be mL)

** '''Injected Dose''' : DICOM Tag (0018,1074) - Radionuclide Total Dose

** '''Patient Weight''' : DICOM Tag (0010,1030) - Patient Weight

** '''Patient Height''' : DICOM Tag (0010,1020) - Patient Size

** '''Patient Sex''' : DICOM Tag (0010,0040) - Patient Sex

** '''Series Reference Time''' : DICOM Tag (0008,0031) - Series Time

** '''Injection Time''' : DICOM Tag (0018,1072) - Radiopharmaceutical Start Time

** '''Decay Correction''' : DICOM Tag (0054,1102) - Decay Correction

** '''Decay Factor''' : DICOM Tag (0054,1321) - Decay Factor

** '''Radionuclide Half-life''' : DICOM Tag (0018,1075) - Radionuclide Half-Life

** '''Frame Reference Time''' : DICOM Tag (0054,1300) - Frame Reference Time

** '''SUVbw Conversion Factor''' : Standardized Uptake Value (body weight) Conversion Factor

** '''SUVlbm Conversion Factor''' : Standardized Uptake Value (lean body mass) Conversion Factor

** '''SUVbsa Conversion Factor''' : Standardized Uptake Value (body surface area) Conversion Factor

** '''SUVibw Conversion Factor''' : Standardized Uptake Value (ideal body weight) Conversion Factor

** '''RWVM File''' : Real World Value Mapping object file

|[[Image:SUV_Factor_Calculator_GUI.png|thumb|400px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Notes from the Developer(s)===
*

===Tests===
*
===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

==Other Information==
===Acknowledgment===
This work is funded in part by [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918.

===References===

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

File:SUV Factor Calculator GUI.png

2014-08-25T18:11:55Z

Ejulrich:

Documentation/Nightly/Modules/SUVFactorCalculator

2014-08-25T17:54:51Z

Ejulrich: improved Intro & Acknowlegments

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



==Introduction and Acknowledgements==
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Acknowledgments:
This work is funded in part by [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918. 
Authors: Andrey Fedorov ({{collaborator|name|spl}}), Ethan Ulrich (University of Iowa) 
Contributors: Markus Van Tol (University of Iowa), Hans Johnson (University of Iowa), Wendy Plesniak (SPL, BWH), Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH) 
Contact: Ethan Ulrich, <email>ethan-ulrich@uiowa.edu</email> 

License: [http://www.slicer.org/pages/LicenseText Slicer License]

{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}

== General Information ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Module Type & Category===

Type: CLI

Category: Quantification

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/SUVFactorCalculator Source code] on GitHub
|-
|}

== Usage ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]:

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]:

** '''Radioactivity Units''' :

** '''Weight Units''' :

** '''Height Units''' :

** '''Volume Units''' :

** '''Injected Dose''' :

** '''Patient Weight''' :

** '''Patient Height''' :

** '''Patient Sex''' :

** '''Series Reference Time''' :

** '''Injection Time''' :

** '''Decay Correction''' :

** '''Decay Factor''' :

** '''Radionuclide Half-life''' :

** '''Frame Reference Time''' :

** '''SUVbw Conversion Factor''' :

** '''SUVlbm Conversion Factor''' :

** '''SUVbsa Conversion Factor''' :

** '''SUVibw Conversion Factor''' :

** '''RWVM File''' :

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Notes from the Developer(s)===
*

===Tests===
*
===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

==Other Information==
===Acknowledgment===
This work is funded in part by [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918.

===References===

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

Documentation/Nightly/Modules/SUVFactorCalculator

2014-08-25T16:40:44Z

Ejulrich: created

__NOTOC__

==SUV Factor Calculator==
SUV Factor Calculator

{|
|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== General Information ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Module Type & Category===

Type: CLI

Category: Quantification

===Authors, Collaborators & Contact===

Authors: Ethan Ulrich (University of Iowa), Andrey Fedorov (SPL, BWH),

Contributors: Markus Van Tol (University of Iowa), Hans Johnson (University of Iowa), Wendy Plesniak (SPL, BWH), Nicole Aucoin (SPL, BWH), Ron Kikinis (SPL, BWH)

Contact: Ethan Ulrich, <email>ethan-ulrich@uiowa.edu</email> 

===Module Description===

{| style="color:gray" border="1"
|Program title || SUV Factor Calculator
|-
|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).
|-
|Program documentation-url || [http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Modules/SUVFactorCalculator Source code] on GitHub
|-
|}

== Usage ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Use Cases, Examples===
The patient size correction factors are summarized here, where weight is in kilograms and height is in centimeters.
*SUVbw:
**males & females: weight
*SUVlbm:
**males: 1.10 * weight - 128 * (weight/height)^2
**females: 1.07 * weight - 148 * (weight/height)^2
*SUVbsa:
**males & females: weight^0.425 * height^0.725 * 0.007184
*SUVibw:
**males: 48.0 + 1.06 * (height - 152)
**females: 45.5 + 0.91 * (height - 152)
===Tutorials===
*
===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them.
{|
|
* '''''Input Image''''':
** '''PET DICOM volume path''' [----petDICOMPath] [--p]:

* '''''Output''''':
** '''RWV mapping object DICOM volume path''' [----rwvmDICOMPath] [--r]:

** '''Radioactivity Units''' :

** '''Weight Units''' :

** '''Height Units''' :

** '''Volume Units''' :

** '''Injected Dose''' :

** '''Patient Weight''' :

** '''Patient Height''' :

** '''Patient Sex''' :

** '''Series Reference Time''' :

** '''Injection Time''' :

** '''Decay Correction''' :

** '''Decay Factor''' :

** '''Radionuclide Half-life''' :

** '''Frame Reference Time''' :

** '''SUVbw Conversion Factor''' :

** '''SUVlbm Conversion Factor''' :

** '''SUVbsa Conversion Factor''' :

** '''SUVibw Conversion Factor''' :

** '''RWVM File''' :

|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
|}

== Development ==
{{documentation/{{documentation/version}}/extension-developerinfo}}
===Notes from the Developer(s)===
*

===Tests===
*
===Information for Developers===

*Source code: https://github.com/QIICR/Slicer-PETDICOMExtension/tree/master/SUVFactorCalculatorCLI

==Other Information==
===Acknowledgment===
This work is funded in part by [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)] NIH grant U24 CA180918. 

===References===

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

Documentation/Nightly/Extensions/PETDICOM

2014-08-22T20:47:09Z

Ejulrich: created

Documentation/Nightly/Extensions

2014-08-22T20:16:47Z

Ejulrich: added PET DICOM extension page

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>
__TOC__
</noinclude>= Extensions by Category =

==Cat 1==

==Cat 2==
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Kevin Wang, Adam Rankin, Greg Sharp, Andras Lasso, Steve Pieper)
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]


** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]] (Francois Budin, Pengdong Xiao, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)
* [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)
* [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)
** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]
** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]
* [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)
* [[Documentation/{{documentation/version}}/Extensions/ResectionPlanner|ResectionVolume]] (Matt Lougheed)
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM]] (Andrey Fedorov, Ethan Ulrich)

==Cat 3==
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)
<noinclude>
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}
</noinclude>