Difference between revisions of "Documentation/4.1/Extensions/Nigthly/LongitudinalPETCT"

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Extension: [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]<br>
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Extension: [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]]<br />
 
Acknowledgments:
 
Acknowledgments:
−
This work is done as part of the [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)] initiative of the National Cancer Institute, and is funded by the National Institutes of Health, National Cancer Institute through the Grant U01 CA151261 (PI Fiona Fennessy).<br>
+
This work is done as part of a master thesis (for the University of Heidelberg) at the Surgical Planning Lab (Brigham and Women’s Hospital and Harvard Medical School)<br />
−
Author: Andrey Fedorov ({{collaborator|name|spl}}), Nicole Aucoin ({{collaborator|name|spl}}), Steve Pieper ({{collaborator|name|spl}})<br>
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Author: Paul Mercea ({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}})<br />
−
Contact: Andrey Fedorov, fedorov at bwh dot harvard dot edu<br>
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Contact: Paul Mercea, pmercea at bwh dot harvard dot edu<br>
 
License: [http://www.slicer.org/pages/LicenseText Slicer License]
 
License: [http://www.slicer.org/pages/LicenseText Slicer License]
 
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{{documentation/{{documentation/version}}/module-section|Module Description}}
 
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{|
 
{|
 
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[[Image:ReportingLogo.png|thumb|128px|]]
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[[Image:LongitudinalPETCTLogo.png|thumb|128px|]]
 
|
 
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The purpose of the Reporting module is to provide Slicer interface for creating image annotations/markup that are stored in a structured form, and can be exported into Annotation Image Markup (AIM) XML-based format. Currently, Reporting module allows to create three types of markup:
+
The purpose of the Longitudinal PET/CT Analysis module is to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data by computing the standardized uptake value (SUV) based on bodyweight for different regions of interest and for different timepoints.<br /><br /><br />
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* point (fiducial)
 
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* 2-d measurement (ruler)
 
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* 3-d segmentation (label map).
 
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The 3-d segmentations are stored as binary image masks, and are serialized into DICOM Segmentation Storage objects, which in turn can be referenced from the AIM XML document.
 
 
|}
 
|}
  
 
{{documentation/{{documentation/version}}/module-section|Release Notes}}
 
{{documentation/{{documentation/version}}/module-section|Release Notes}}
  
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'''Installation:''' Reporting module is available as an extension that can be installed using [[Documentation/4.1/SlicerApplication/ExtensionsManager|Slicer Extension Manager]]. Make sure Extension Manager is enabled in the Application settings (as shown [[Documentation/4.1/SlicerApplication/ExtensionsManager#Extensions_Manager_Settings|here]]). Follow the Extension Manager usage instructions to find and install Reporting extension. Once installed, you need to restart Slicer before you can use the Reporting module. Note that you need to use the latest Slicer nightly package (starting from Aug 19 nightly) to access the Reporting extension.  
+
'''Installation:''' LongitudinalPETCT module is available as an extension that can be installed using [[Documentation/4.1/SlicerApplication/ExtensionsManager|Slicer Extension Manager]]. Make sure Extension Manager is enabled in the Application settings (as shown [[Documentation/4.1/SlicerApplication/ExtensionsManager#Extensions_Manager_Settings|here]]). Follow the Extension Manager usage instructions to find and install the LongitudinalPETCT extension. Once installed, you need to restart Slicer before you can use the LongitudinalPETCT module. Note that you need to use the latest Slicer nightly package (starting from Aug 19 nightly) to access the LongitudinalPETCT extension.  
  
 
'''Potential issues related to extensions and multiple versions of Slicer:''' Slicer settings are stored in a dedicated system-specific location. These settings are not reset when you install a new Slicer version. If you observe unstable behavior, you could try resetting the settings as follows:
 
'''Potential issues related to extensions and multiple versions of Slicer:''' Slicer settings are stored in a dedicated system-specific location. These settings are not reset when you install a new Slicer version. If you observe unstable behavior, you could try resetting the settings as follows:
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{{documentation/{{documentation/version}}/module-section|Use Cases}}
 
{{documentation/{{documentation/version}}/module-section|Use Cases}}
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This module is designed for the use cases that require creation and/or exchange of self-containing documents describing a certain finding in a DICOM image, such as lesions and anatomical structures.
+
This module is designed for the use cases where valid  PET and CT (DICOM) image data for different timepoints is imported from Slicer’s DICOM database to be inspected for oncological lesions and their development at different timepoints. Quantitative analysis of these lesions is performed by segmentation and SUVbw computation. In the end an overview over the analysis workflow is provided with interactive qualitative comparison views of all segmentations and different charts for the quantitative results.  
  
 
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Before you start using the module, you need to be familiar with 3D Slicer interface and main features. Please see instruction on using the [[Documentation/4.1/SlicerApplication/MainApplicationGUI|main application GUI]] and [[Documentation/4.1/Training|various tutorials]] to learn about 3D Slicer.
 
Before you start using the module, you need to be familiar with 3D Slicer interface and main features. Please see instruction on using the [[Documentation/4.1/SlicerApplication/MainApplicationGUI|main application GUI]] and [[Documentation/4.1/Training|various tutorials]] to learn about 3D Slicer.
  
−
Reporting module uses internal data structure called "report" to organize the markup/annotations and associate them with the image volume being annotated.
+
The Longitudinal PET/CT Analysis module uses different internal data structures. The "PET/CT_Report" represents the complete longitudinal analysis for one patient and image data from different timepoints. PET and related CT image data  is represented by a “PET/CT_Study” for every timepoint. Every lesions gets declared as a “PET/CT_Finding” which is present for all timepoints but does not necessarily need to have a segmentation for every timepoint (e.g. lesion dissapearance due to radiation therapy) but only one segmentation per timepoint is supported by the “PET/CT_Finding”.
  
−
The steps to create a new report are the following:
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 +
The steps to create a new Longitudinal PET/CT Report and perform quantification:
 
{|
 
{|
 
|
 
|
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# An DICOM imaging study that will be annotated should be loaded into Slicer DICOM database using Slicer DICOM module. If you are unsure what this means, see [[Documentation/4.1/Modules/DICOM|documentation of the DICOM module]].  
+
# PET/CT DICOM imaging studies from different timepoints should be loaded into Slicer DICOM database using Slicer DICOM module. If you are unsure what this means, see [[Documentation/4.1/Modules/DICOM|documentation of the DICOM module]]. After succesfully imported these studies can be detected and loaded into the scene by the Longitudinal PET/CT Analysis Reader in the DICOM module.
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# In the Reporting module, new report should be created (see explanation of the module GUI panels below) (Input panel)
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# The Report Selection panel can be used to select an imported or loaded Longitudinal PET/CT Analysis Report.
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# The volume that will be annotated should be selected (Input panel). Following this, the slice viewers will be initialized to show the volume being annotated.
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# Adding PET/CT studies to the workflow can be done with the Study Selection panel by checking the respective checkbox in the Study ID colum in the studies table. Adding a study to the workflow will update the slice views and show a volume rendering of the PET volume. A study can also be removed from the workflow by unchecking. Modifications to the volume rendering can be done with the expandable panel on the right. It is possible to stop the spinning of the volume renderer view or to disable it completely. The slider can be used to modify the opacity function of the volume rendering. While imported from the DICOM database the individual PET and related CT volumes are centered in the view. This can be undone by unchecking "Show studies centered".
−
# The name of the structure should be selected from the Slicer terminology list by clicking the colored patch in the Annotation panel.
+
# The Findings panel is the interface helping the user to create and manage the segmentations of lesions for different timepoints. If a lesion has been detected in one of the studies the use case is to create a new PET/CT Finding (see 5. for the possible settings for a Finding) for that lesion and place a region of interest (ROI) fitting the whole lesion on the image data in the viewers (after checking the ROI placement button a first click should be done on the center of the lesion and a second one on the most remote corner of the lesion). Once the ROI is placed, a built-in version of Slicer’s Editor module can be opened and a segmentation can be created or edited. For more detailed instructions on how to use the Editor please see it’s [[Documentation/4.1/Modules/Editor|documentation page]] documentation page. In the end the segmentation can be applied to the current Finding. Segmentations of a lesion at different timepoints should always be added to the same Finding.
−
# Fiducial and ruler markup elements should be placed only in those slice viewers that correspond to the image acquisition plane. Those slice viewers will be listed in the Markup panel of the module.
+
# The Finding Settings Dialog will pop up every time a new PET/CT Finding is created or "Edit current PET/CT Finding" is selected. The use of this dialog is to specify the Finding’s name, it’s type and the color label for it’s segmentations. Please note that a new Finding can never be of the same Type as a previous created Finding in the workflow but the expandable panel at the bottom gives the user the possibility to create new unique Finding Types.
−
# To place a new fiducial/ruler markup elements, corresponding controls in the Slicer toolbar should be used (see on the right).
+
# Once Findings have been created and segmentations have been added the Analysis Panel gets enabled to give an qualitative and quantitative overview for the current workflow. The Qualitative Analysis offers a compare view for all Studies from the different timepoints and the segmentations that have been performed so far. The Quantitative Analysis offers a SUVbw chart of the computed values for all Findings at the different timepoints. A table similar to the one in the Study Selection panel gives the user the possibility to deactive/activate studies for the comparison.
−
# The tree view in the module Markup panel will be showing all markup elements that have been added to the active report.
 
−
# To attach a 3-d segmentation to the report, the segmentation image should be either loaded from file and added to Slicer scene (see [[Documentation/4.1/Modules/Data|instructions on how to use Data module]]), or a new segmentation should be created using the "Segmentation volume" drop-down. Segmentation can then be edited using the Editor panel that is available in the Reporting GUI (see [[Documentation/4.1/Modules/Editor|Editor module]] documentation for using Editor tools).
 
−
# "Save Report into AIM format" button can be used to save the report into AIM XML format. "Load Report from AIM format" button can be used to load the report back into Slicer.
 
−
|
 
−
|[[Image:Slicer4-Reporting-markupToolbar.png|thumb|280px|Slicer toolbar buttons that should be used for placement of fiducial/ruler markups.]]
 
 
|}
 
|}
  
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GUI of the module contains the following elements:
 
−
{|
 
−
|
 
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* ''Input'' panel
 
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** '''Report''': active report being edited
 
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** '''Annotated volume''': volume being annotated
 
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* ''Annotation'' panel
 
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** contains the name of the structure being annotated and the colored patch showing the label color. Clicking the colored patch will bring up the selection of the supported named structures. Currently supported terminology is based on Slicer [[Slicer3:2010_GenericAnatomyColors|General Anatomy Colors lookup table]]. Integration of this table with Radlex terminology is planned for the future.
 
−
* ''Markup'' panel
 
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** contains the text listing the slice viewers that should be used for placing fiducial/ruler markups.
 
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** Tree view widget shows the markups that are associated with the report. The "eye" button toggles visibility of the markup element. Clicking right mouse button over the name of the markup brings up the menu that allows to rename/delete the markup, or to jump to the slice where the markup is placed.
 
−
* ''Segmentation'' panel
 
−
** ''Segmentation volume'' selector allows to choose the volume containing the segmentation, or to create a new segmentation. For an existing label map (segmentation) to be associated with the active report, the geometry of the image volume containing the segmentation should match the geometry of the annotated volume. New segmentation volume can be created to match the geometry of the active volume using the segmentation selector.
 
−
** Once the label volume is selected/created, it can be edited using the [[Documentation/4.1/Modules/Editor|Editor]] tools: these are available by expanding the "Edit Selected Label Map" panel (see figure on the right).
 
−
* ''Save/Load'' buttons allow to export/import the report into AIM format.
 
−
|
 
−
[[Image:Slicer4-Reporting.png|thumb|480px|Module GUI]]
 
−
 
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[[Image:Slicer4-treeWidgetFeatures.png|thumb|280px|Popup menu in the Tree view widget provides some convenient shortcuts]]
 
  
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[[Image:Slicer4-SegmentationSelector.png|thumb|280px|New label volume can be created using the "Segmentation volume" selector]]
 
−
 
−
[[Image:Slicer4-ReportingEditor.png|thumb|280px|Segmentation can be edited using [[Documentation/4.1/Modules/Editor|Editor module]] tools provided in the "Edit selected label map" panel.]]
 
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|}
 
  
 
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
  
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{{documentation/{{documentation/version}}/module-section|References}}
 
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* [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
 
−
* Main page summarizing the scope and development of this functionality: http://wiki.na-mic.org/Wiki/index.php?title=AIM_Annotations_integration_with_3DSlicer
 
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* [http://bmir.stanford.edu/projects/view.php/annotation_and_image_markup_aim_project Annotation Image Markup home page]
 
  
 
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
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* Source code of the module: https://github.com/fedorov/Reporting
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* Source code of the module: https://github.com/paulcm/LongitudinalPETCT
 
{{documentation/{{documentation/version}}/module-developerinfo}}
 
{{documentation/{{documentation/version}}/module-developerinfo}}
  

Revision as of 21:12, 15 October 2012

Home < Documentation < 4.1 < Extensions < Nigthly < LongitudinalPETCT


Work in progress
 WARNING: This module is Work in Progress, which means:
  • the functionality provided by this module may change drastically in the future releases of 3D Slicer
  • the scenes containing data types specific to this module may not be readable by the future versions of Slicer
  • the functionality and user interface may change at any time
  • some functionality may not work as intended
  • testing and documentation is limited

Introduction and Acknowledgements

Extension: LongitudinalPETCT
Acknowledgments: This work is done as part of a master thesis (for the University of Heidelberg) at the Surgical Planning Lab (Brigham and Women’s Hospital and Harvard Medical School)
Author: Paul Mercea (SPL), Andrey Fedorov (SPL)
Contact: Paul Mercea, pmercea at bwh dot harvard dot edu
License: Slicer License

Surgical Planning Laboratory (SPL)  

Module Description

LongitudinalPETCTLogo.png

The purpose of the Longitudinal PET/CT Analysis module is to provide a user friendly Slicer interface for quantification of DICOM PET/CT image data by computing the standardized uptake value (SUV) based on bodyweight for different regions of interest and for different timepoints.


Release Notes

Installation: LongitudinalPETCT module is available as an extension that can be installed using Slicer Extension Manager. Make sure Extension Manager is enabled in the Application settings (as shown here). Follow the Extension Manager usage instructions to find and install the LongitudinalPETCT extension. Once installed, you need to restart Slicer before you can use the LongitudinalPETCT module. Note that you need to use the latest Slicer nightly package (starting from Aug 19 nightly) to access the LongitudinalPETCT extension.

Potential issues related to extensions and multiple versions of Slicer: Slicer settings are stored in a dedicated system-specific location. These settings are not reset when you install a new Slicer version. If you observe unstable behavior, you could try resetting the settings as follows:

  • Linux and Mac: settings are stored in your home directory in .config folder (remove ~/.config or move it to a different location)
  • Windows: settings are located in C:\Users\<your_user_name>\AppData\Roaming\NA-MIC folder -- remove it or move to a different location.

WARNING: the configuration file contains the path to your DICOM database. Once the configuration file is removed, you will need to re-configure the DICOM module to point it to the location of the database!

Please note that this module is under active development, and is being made available for the purposes of beta testing and feedback evaluation! The functionality, GUI and workflows may change in the subsequent releases of the module.

Use Cases

This module is designed for the use cases where valid PET and CT (DICOM) image data for different timepoints is imported from Slicer’s DICOM database to be inspected for oncological lesions and their development at different timepoints. Quantitative analysis of these lesions is performed by segmentation and SUVbw computation. In the end an overview over the analysis workflow is provided with interactive qualitative comparison views of all segmentations and different charts for the quantitative results.

Tutorials

Not available at this time.

Panels and their use

Before you start using the module, you need to be familiar with 3D Slicer interface and main features. Please see instruction on using the main application GUI and various tutorials to learn about 3D Slicer.

The Longitudinal PET/CT Analysis module uses different internal data structures. The "PET/CT_Report" represents the complete longitudinal analysis for one patient and image data from different timepoints. PET and related CT image data is represented by a “PET/CT_Study” for every timepoint. Every lesions gets declared as a “PET/CT_Finding” which is present for all timepoints but does not necessarily need to have a segmentation for every timepoint (e.g. lesion dissapearance due to radiation therapy) but only one segmentation per timepoint is supported by the “PET/CT_Finding”.


The steps to create a new Longitudinal PET/CT Report and perform quantification:

  1. PET/CT DICOM imaging studies from different timepoints should be loaded into Slicer DICOM database using Slicer DICOM module. If you are unsure what this means, see documentation of the DICOM module. After succesfully imported these studies can be detected and loaded into the scene by the Longitudinal PET/CT Analysis Reader in the DICOM module.
  2. The Report Selection panel can be used to select an imported or loaded Longitudinal PET/CT Analysis Report.
  3. Adding PET/CT studies to the workflow can be done with the Study Selection panel by checking the respective checkbox in the Study ID colum in the studies table. Adding a study to the workflow will update the slice views and show a volume rendering of the PET volume. A study can also be removed from the workflow by unchecking. Modifications to the volume rendering can be done with the expandable panel on the right. It is possible to stop the spinning of the volume renderer view or to disable it completely. The slider can be used to modify the opacity function of the volume rendering. While imported from the DICOM database the individual PET and related CT volumes are centered in the view. This can be undone by unchecking "Show studies centered".
  4. The Findings panel is the interface helping the user to create and manage the segmentations of lesions for different timepoints. If a lesion has been detected in one of the studies the use case is to create a new PET/CT Finding (see 5. for the possible settings for a Finding) for that lesion and place a region of interest (ROI) fitting the whole lesion on the image data in the viewers (after checking the ROI placement button a first click should be done on the center of the lesion and a second one on the most remote corner of the lesion). Once the ROI is placed, a built-in version of Slicer’s Editor module can be opened and a segmentation can be created or edited. For more detailed instructions on how to use the Editor please see it’s documentation page documentation page. In the end the segmentation can be applied to the current Finding. Segmentations of a lesion at different timepoints should always be added to the same Finding.
  5. The Finding Settings Dialog will pop up every time a new PET/CT Finding is created or "Edit current PET/CT Finding" is selected. The use of this dialog is to specify the Finding’s name, it’s type and the color label for it’s segmentations. Please note that a new Finding can never be of the same Type as a previous created Finding in the workflow but the expandable panel at the bottom gives the user the possibility to create new unique Finding Types.
  6. Once Findings have been created and segmentations have been added the Analysis Panel gets enabled to give an qualitative and quantitative overview for the current workflow. The Qualitative Analysis offers a compare view for all Studies from the different timepoints and the segmentations that have been performed so far. The Quantitative Analysis offers a SUVbw chart of the computed values for all Findings at the different timepoints. A table similar to the one in the Study Selection panel gives the user the possibility to deactive/activate studies for the comparison.


Similar Modules

Information for Developers

Work in progress
 Section under construction.
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