Documentation/4.2/Extensions/Reporting - Revision history

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2019-11-21T17:00:05Z

Text replacement - "slicerWiki/index.php" to "wiki"

Fedorov at 17:03, 3 August 2016

2016-08-03T17:03:28Z

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:38:09Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

Fedorov at 23:26, 6 February 2013

2013-02-06T23:26:27Z

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Fedorov at 04:07, 16 November 2012

2012-11-16T04:07:38Z

Fedorov at 02:35, 4 November 2012

2012-11-04T02:35:37Z

Fedorov at 02:32, 4 November 2012

2012-11-04T02:32:11Z

Fedorov at 02:20, 4 November 2012

2012-11-04T02:20:14Z

UpdateBot: Nightly -> 4.2

2012-10-31T22:00:20Z

Nightly -> 4.2

New page

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

{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = 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
}}

{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]]<br>
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>
Author: Andrey Fedorov ({{collaborator|name|spl}}), Nicole Aucoin ({{collaborator|name|spl}}), Steve Pieper ({{collaborator|name|spl}})<br>
Contact: Andrey Fedorov, fedorov at bwh dot harvard dot edu<br>
License: [http://www.slicer.org/pages/LicenseText Slicer License]
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}

{|
|
[[Image:ReportingLogo.png|thumb|128px|]]
|
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:
* point (fiducial)
* 2-d measurement (ruler)
* 3-d segmentation (label map).
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}}

'''Installation:''' Reporting module is available as an extension that can be installed using [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionsManager|Slicer Extension Manager]]. Make sure Extension Manager is enabled in the Application settings (as shown [[Documentation/{{documentation/version}}/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.

'''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.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
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.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
Not available at this time.


{{documentation/{{documentation/version}}/module-section|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 [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|main application GUI]] and [[Documentation/{{documentation/version}}/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 steps to create a new report are the following:
{|
|
# 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/{{documentation/version}}/Modules/DICOM|documentation of the DICOM module]].
# In the Reporting module, new report should be created (see explanation of the module GUI panels below) (Input panel)
# 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.
# The name of the structure should be selected from the Slicer terminology list by clicking the colored patch in the Annotation panel.
# 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.
# To place a new fiducial/ruler markup elements, corresponding controls in the Slicer toolbar should be used (see on the right).
# 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/{{documentation/version}}/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/{{documentation/version}}/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.]]
|}

GUI of the module contains the following elements:
{|
|
* ''Input'' panel
** '''Report''': active report being edited
** '''Annotated volume''': volume being annotated
* ''Annotation'' panel
** 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
** contains the text listing the slice viewers that should be used for placing fiducial/ruler markups.
** 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/{{documentation/version}}/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]]

[[Image:Slicer4-treeWidgetFeatures.png|thumb|280px|Popup menu in the Tree view widget provides some convenient shortcuts]]

[[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/{{documentation/version}}/Modules/Editor|Editor module]] tools provided in the "Edit selected label map" panel.]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}


{{documentation/{{documentation/version}}/module-section|References}}
* [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
* [http://bmir.stanford.edu/projects/view.php/annotation_and_image_markup_aim_project Annotation Image Markup home page]


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
* Source code of the module: https://github.com/fedorov/Reporting
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}
[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]

@@ Line 121: / Line 121: @@
 {{documentation/{{documentation/version}}/module-section|Mapping from SlicerGenericAnatomyColors LUT and DICOM SEG Segmented Property}}
-Currently, only labels that use GeneralAnatomy LUT are supported and can be converted to and from DICOM SEG format. The original LUT is available here: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors. The table below was compiled by David Clunie, Andrey Fedorov and Neha Agrawal to map most of the colors of the LUT to Segmented Property Category, Type and Modifier (when appropriate), which are required for encoding label segments in DICOM SEG.
+Currently, only labels that use GeneralAnatomy LUT are supported and can be converted to and from DICOM SEG format. The original LUT is available here: http://www.slicer.org/wiki/Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors. The table below was compiled by David Clunie, Andrey Fedorov and Neha Agrawal to map most of the colors of the LUT to Segmented Property Category, Type and Modifier (when appropriate), which are required for encoding label segments in DICOM SEG.
 Licensing and redistribution: per agreement between SNOMED and DICOM, "the agreement with SNOMED is to allow any implementer to use the terms included in DICOM in their implementations and products without fee".

@@ Line 123: / Line 123: @@
 Currently, only labels that use GeneralAnatomy LUT are supported and can be converted to and from DICOM SEG format. The original LUT is available here: http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/SlicerApplication/LookupTables/GenericAnatomyColors. The table below was compiled by David Clunie, Andrey Fedorov and Neha Agrawal to map most of the colors of the LUT to Segmented Property Category, Type and Modifier (when appropriate), which are required for encoding label segments in DICOM SEG.
-Licensing and redistribution: per agreement between SNOMED and DICOM, "the agreement with SNOMED is to allow any implementer to use the terms included in DICOM in their implementations and products without fee". DICOM correction proposal CP-1528 (ftp://medical.nema.org/medical/dicom/cp/cp1258_01.pdf, Refactor segment description, extend segment types and anatomy) contains the items included in this table.
+Licensing and redistribution: per agreement between SNOMED and DICOM, "the agreement with SNOMED is to allow any implementer to use the terms included in DICOM in their implementations and products without fee".
 {| class="wikitable sortable labelpage labelpagetable" border="1"

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

@@ Line 107: / Line 107: @@
 * ''Import/Export'' panel allow to export/import the report into AIM format.
-DICOM Segmentation objects that are imported to the user-defined location on disk are also automatically inserted into the local DICOM database. They can be loaded back into Slicer as segmentation labels independently of the report using [Documentation/{{documentation/version}}/Modules/DICOM|DICOM module]].
+DICOM Segmentation objects that are imported to the user-defined location on disk are also automatically inserted into the local DICOM database. They can be loaded back into Slicer as segmentation labels independently of the report using [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM module]].
+|

@@ Line 43: / Line 43: @@
 * 3-d segmentation (label map).
 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.
 |}

@@ Line 76: / Line 76: @@
 {|
+|
-# 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/{{documentation/version}}/Modules/DICOM|documentation of the DICOM module]].
+# A 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/{{documentation/version}}/Modules/DICOM|documentation of the DICOM module]]. '''NOTE''': only volumes loaded from DICOM module can be used in this module!
 # In the Reporting module, new report should be created (see explanation of the module GUI panels below) (Input panel)
 # 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.
@@ Line 84: / Line 84: @@
 # 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/{{documentation/version}}/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/{{documentation/version}}/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.
+# "Export" functionality can be used to save the report into AIM XML format, and the segmentations (if exist) as DICOM Segmentation objects into the specified location. "Import" functionality 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.]]
@@ Line 96: / Line 96: @@
 ** '''Annotated volume''': volume being annotated
 * ''Annotation'' panel
-** 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.
+** 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 standardized lexicon is under development.
 * ''Markup'' panel
 ** contains the text listing the slice viewers that should be used for placing fiducial/ruler markups.
-** 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.
+** Table view widget shows the markups that are associated with the report. The "eye" button toggles visibility of the markup element. Clicking the row with the markup aligns the slices with the location of the markup.
 * ''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/{{documentation/version}}/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.
+* ''Import/Export'' panel allow to export/import the report into AIM format.
+|
-[[Image:Slicer4-Reporting.png|thumb|480px|Module GUI]]
+[[Image:Slicer4-Reporting-4.2.png|thumb|480px|Module GUI]]
 [[Image:Slicer4-SegmentationSelector.png|thumb|280px|New label volume can be created using the "Segmentation volume" selector]]

@@ Line 47: / Line 47: @@
 {{documentation/{{documentation/version}}/module-section|Release Notes}}
-'''Installation:''' Reporting module is available as an extension that can be installed using [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionsManager|Slicer Extension Manager]]. Make sure Extension Manager is enabled in the Application settings (as shown [[Documentation/{{documentation/version}}/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:''' Reporting module is available as an extension that can be installed using [[Documentation/{{documentation/version}}/SlicerApplication/ExtensionsManager|Slicer Extension Manager]]. Make sure Extension Manager is enabled in the Application settings (as shown [[Documentation/{{documentation/version}}/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.
 '''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:
@@ Line 53: / Line 53: @@
 * '''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.