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[[File:LogoCco.png|Cancer Care Ontario]]
[[File:Logo-SparKit.png|SparKit]]
[[File:LogoOCAIRO.jpg|SparKit]]


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Authors: Csaba Pinter (PerkLab, Queen's University), Kevin Alexander (KGH, Queen's University), Jennifer Andrea (PerkLab, Queen's University), Mattea Welch (University of Toronto) 
Contributors: John Schreiner (Kingston General Hospital) 
Contacts:
* Csaba Pinter, <email>csaba.pinter@queensu.ca</email>
* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install SlicerRT extension, restart, install the GelDosimetry extension


{{documentation/{{documentation/version}}/extension-section|Extension Description}}

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|[[Image:GelDosimetry_Logo_128x128.png]]

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* Gel dosimetry analysis is a tool used in commissioning new radiation techniques and to validate the accuracy of radiation treatment by enabling visual comparison of the planned dose to the delivered dose, where correspondence between the two dose distributions is achieved using embedded landmarks. Gel dosimetry is based on imaging chemical systems spatially fixed in gelatin, which exhibit a detectable change upon irradiation. This chemical change is related to the amount of radiation received and can be probed by several imaging techniques, allowing 3D dose information to be obtained.
* The slicelet currently supports CT-optCT clinical dosimetry workflows, with MR-MR preclinical and others coming up. Please contact us if you have a similar workflow you'd like to see supported
* The extension depends on the SlicerRT general radiation therapy extension

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{{documentation/{{documentation/version}}/extension-section|Use Cases}}

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== Gel dosimetry analysis workflow: ==
# Loading planning image (PLANCT) and a planned dose distribution (PLANDOSE)
# Load an on-board imager cone beam CT scan (OBI)
# Register OBI to PLANCT
# Transform PLANDOSE using result transform (to OBI coordinate frame)
# Load 3D optical CT scan of the gel, or a 2D scan of the film. (MEASURED)
# Register MEASURED to OBI using fiducial marks, using rigid transform
# Transform MEASURED using result transform (to OBI coordinate frame)
# Load Percent Depth Dose data (two-column spreadsheet)
# Load experimental CALIBRATION 3D optical CT scan from VFF file
# Get mean optical densities from the central cylinder of the CALIBRATION volume
# Align PDD curve with the curve resulting from previous step
# Calibrate PDD data using RDF and electron MU values input by the user
# Fit polynomial on the optical density vs. dose curve (resulting from the aligned calibration curves)
# Perform a gamma, chi, etc. test between MEASURED and PLANDOSE, yielding another 3D volume COMPARISON
# Extract statistics from COMPARISON

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[[File:GelDosimetryAnalysis_DataFlow_v06.png|thumb|720px|Gel dosimetry data flow diagram]]

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{|
|[[File:20150605_Gamma_98percent.png|thumb|920px|Gel dosimetry screenshot]]

|[[File:GelDosimetryAnalysis_0.1.2_PddCurveAlignment_Small.png|thumb|400px|Pdd aligment curve screenshot]]
 
[[File:GelDosimetryAnalysis_0.1.2_OdVsDoseCurve_Small.png|thumb|400px|Calibration curve screenshot]]

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{{documentation/{{documentation/version}}/extension-section|Tutorials}}
* [http://www.slicer.org/slicerWiki/index.php/File:WC2015_Gel_slicelet_tutorial_final.pdf World Congress 2015 Gel Dosimetry Tutorial]
** [http://slicer.kitware.com/midas3/download/item/205391/WC2015_Gel_Slicelet_Dataset.zip Dataset]


{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]: GelDosimetry uses several modules from the SlicerRT extension


{{documentation/{{documentation/version}}/extension-section|References}}
* Alexander, K. M., et al. "Implementation of an efficient workflow process for gel dosimetry using 3D Slicer." Journal of Physics: Conference Series. Vol. 573. No. 1. IOP Publishing, 2015.
** Please cite this when you refer to Gel Dosimetry in your publication
* Pinter, C., et al. "Performing radiation therapy research using the open-source SlicerRT toolkit." World Congress for Medical Physics and Biomedical Engineering, 2015
* C. Pinter, A. Lasso, A. Wang, D. Jaffray and G. Fichtinger, [http://perk.cs.queensu.ca/sites/perk.cs.queensu.ca/files/Pinter2012_0.pdf "SlicerRT – Radiation therapy research toolkit for 3D Slicer"], Med. Phys., 39(10) pp. 6332-6338, 2012
** Please cite the following paper when referring to SlicerRT in your publication


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* N/A


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

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 {{documentation/{{documentation/version}}/extension-section|Tutorials}}
-* [http://www.slicer.org/slicerWiki/index.php/File:WC2015_Gel_slicelet_tutorial_final.pdf World Congress 2015 Gel Dosimetry Tutorial]
+* [http://www.slicer.org/wiki/File:WC2015_Gel_slicelet_tutorial_final.pdf World Congress 2015 Gel Dosimetry Tutorial]
 ** [http://slicer.kitware.com/midas3/download/item/205391/WC2015_Gel_Slicelet_Dataset.zip Dataset]

Documentation/4.5/Modules/GelDosimetry - Revision history

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