Documentation/4.2/Modules/MultiVolumeExplorer - Revision history

Grundlett: Text replacement - "http://wiki.slicer.org/slicerWiki/images/" to "http://www.slicer.org/w/img_auth.php/"

2019-11-27T12:31:12Z

Text replacement - "http://wiki.slicer.org/slicerWiki/images/" to "http://www.slicer.org/w/img_auth.php/"

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

2013-06-14T07:42:32Z

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

Torabi at 15:45, 28 March 2013

2013-03-28T15:45:03Z

Torabi at 14:58, 28 March 2013

2013-03-28T14:58:45Z

Torabi at 14:47, 28 March 2013

2013-03-28T14:47:34Z

Fedorov at 03:03, 4 November 2012

2012-11-04T03:03:08Z

Fedorov at 02:15, 4 November 2012

2012-11-04T02:15:52Z

UpdateBot: Nightly -> 4.2

2012-10-31T22:01:02Z

Nightly -> 4.2

New page

{{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-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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This work is supported by NA-MIC, NAC, NCIGT, and the Slicer Community. This work is partially supported by the following grants: P41EB015898, P41RR019703, R01CA111288 and U01CA151261.<br>
Author: Andrey Fedorov, Jean-Cristophe Fillion Robin, Julien Finet, Steve Pieper, Ron Kikinis<br>
Contact: Andrey Fedorov <email>fedorov@bwh.harvard.edu</email> <br>
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{{documentation/{{documentation/version}}/module-section|Module Description}}

This module provides support for exploring multivolume (multiframe) data.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
Most frequently used for these scenarios:
* visualization of a DICOM dataset that contains multiple frames that can be separated based on some tag (e.g., DCE MRI data, where individual temporally resolved frames are identified by Trigger Time tag (0018,1060)
* visualization of multiple frames defined in the same coordinate frame, saved as individual volumes in NRRD, NIfTI, or any other [[Documentation/4.1/SlicerApplication/SupportedDataFormat|image format supported by 3D Slicer]]
* exploration of the multivolume data (cine mode visualization, plotting, volume rendering)

[[Image:Screen_Shot_2012-02-23_at_7.53.51_AM.png|400px|thumb|Screenshot of charts derived from the sample data set. The curves represent average signal intensity in the ROI's with corresponding colors, which were drawn in the editor. Please note the arterial input function in red.]]


{{documentation/{{documentation/version}}/module-section|Tutorials}}
* [http://www.youtube.com/watch?v=7zFWRzC31o4 Screencast tutorial] (note that the module is located in '''Modules -> Work in progress -> MultiVolume Support''', not in Modules -> MultiVolume Support, as shown in the video)
* Sample datasets are available:
** [http://wiki.slicer.org/slicerWiki/images/5/56/Case1_DCE.tgz anonymized prostate DCE MRI DICOM series]
** [[File:Cardiac_ECGg_CT.tgz]] (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short [[media:BeatingHeart.mov|movie]]


{{documentation/{{documentation/version}}/module-section|Panels and their use}}

MultiVolume data is represented in this module using two components:
* MultiVolume node: this is the node you select when you import the dataset using [[Documentation/4.1/Modules/MultiVolumeImporter|MultiVolumeImporter module]]
* DisplayNode: this is the node responsible for visualization and storage of the actual image data. The name of that latter node is assigned based on the type of data you are importing. For example, if you import "4D DCE" dataset, it will be called "DCEDisplayNode". This is the node you need to choose in slice viewers to see the multivolume dataset.

{|style="width: 100%"
|
* '''Input''': select the MultiVolume node you would like to explore
* '''Frame control'''
** ''Current frame number'': you can use the slider or spin-box to select the currently shown frame. ''Play'' button can be used to activate 'cine' view mode, with the frames being shown in a continuous mode.
** ''Current frame copy'': you can create and select a conventional scalar volume node in this selector. If ''Enable current frame copying'' button is pressed, each time the currently shown frame is updated, it will be copied to the volume selected. This is useful in situations when you want to do processing of an individual frame (e.g., segmentation), or if you want to show volume rendering of the currently active frame.
* '''Plotting''': there are two modes of plotting that are supported by the module:
** ''Interactive plotting'': this mode of plotting is enabled by default and is facilitated by the chart area located in the ''Plotting'' panel. When enabled, the chart will display the intensity values at the spatial location defined by the current position of the mouse pointer. This mode can be disable from the ''Plotting'' GUI panel.
** ''Static plotting'': This mode of plotting is enabled by the [[Documentation/4.1/SlicerApplication/MainApplicationGUI#Chart_Viewers | Charts]] infrastructure of Slicer, which is exposed in any of the ''Quantitive layouts''. To use this mode, follow these steps:
**# Extract a representative frame from your multivolume dataset, as discussed above.
**# Use the [[Documentation/4.1/Modules/Editor|Editor]] module to create labels for the regions of interest.
**# Select the prepared label volume in the ''Probed label volume'' selector in the ''Plotting'' panel. The ''Charts'' viewer in the Slicer Quantitative layout will be updated with the average intensity values for each of the contoured ROIs. The colors of the plots will be the same as the colors of ROI labels.
|
| align="right" |
|
[[Image:Slicer4-MultiVolumeExplorer_panel1.png|thumb|400px|Settings panel and interactive plotting chart]]
|}

{|
|
|align="center"|
[[Image:Slicer4-MultiVolumeExplorer_static_plotting.png|thumb|800px|Illustration of the static plotting from the explorer module. Note the label overlay in slice viewer with the ROIs corresponding to the femoral artery and an area in the prostate peripheral zone (blue arrow). The label corresponds to the segmentation done for the extracted volume of the 17th frame of the multivolume (green arrow). The same label is selected in the ''Plotting'' panel of the module. The corresponding colors are assigned to the plots in the Chart viewer in the layout (yellow arrow).]]
|
|}


{{documentation/{{documentation/version}}/module-section|Related Modules}}
Before multivolume data can be viewed/explored, it has to be loaded using [[Documentation/4.1/Modules/MultiVolumeImporter|MultVolumeImporter]] module.


{{documentation/{{documentation/version}}/module-section|References}}
* Development of this module was initiated at the 2012 NA-MIC Project week at SLC (see http://wiki.na-mic.org/Wiki/index.php/2012_Project_Week:4DImageSlicer4)


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
This module is an external Slicer module. The source code is available on Github here: https://github.com/fedorov/MultiVolumeExplorer

==Known issues that won't be resolved==
* [http://www.na-mic.org/Bug/view.php?id=1841 bug 1841]: multivolumes that contain less than 7 frames will not be saved correctly and the scene containing such objects will not be loaded correctly by Slicer (limitation of the NRRD IO for DWI)

==Unresolved issues==
* assign correctly title and points for the X axis -- FIXED
* review the comments from JC/J2 on github and fix the code
* bug: repeated loading of a scene that contains a MV node causes crash in onInputChanged() -- FIXED
* improve error reporting!
* look into flickering issue of vtkChart
* improve documentation -- DONE

==Features to be implemented==
* integrate MV importer as a DICOM module plugin -- DONE
* allow the user to speed-up or slow-down the playback, and also turn off "loop"
* report to the user the actual, measured, frame rate
* add an option to report curves in relative SI change in addition to absolute -- DONE

==Features under consideration==
* can we use chart viewer for interactive plotting? -- Discussed with Jim, speedup is possible, but not a priority right now
* should use color names for the legend in the chart viewer -- Will be available as general feature of Charts (Jim)
* interactive update of the active frame based on the point selected in the chart viewer
* should DWI node be a child under the MV hierarchy?
* add GUI elements to update the current frame at the exact time intervals specified in multivolume. If the intervals are non-uniform, I am not sure I can use the timer anymore, so this would require some extra thought.
* import multivolumes from ITK 4d images


{{documentation/{{documentation/version}}/module-footer}}

@@ Line 52: / Line 52: @@
 * Sample datasets are available:
 ** Anonymized prostate DCE MRI DICOM series:
-*** [http://wiki.slicer.org/slicerWiki/images/5/56/Case1_DCE.tgz tgz version]
+*** [http://www.slicer.org/w/img_auth.php/5/56/Case1_DCE.tgz tgz version]
-*** [http://wiki.slicer.org/slicerWiki/images/c/c2/DCE_series.zip zip version]
+*** [http://www.slicer.org/w/img_auth.php/c/c2/DCE_series.zip zip version]
 ** [[File:Cardiac_ECGg_CT.tgz]] (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short [[media:BeatingHeart.mov|movie]]

← Older revision		Revision as of 07:42, 14 June 2013
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@@ Line 52: / Line 52: @@
 ** Anonymized prostate DCE MRI DICOM series:
 *** [http://wiki.slicer.org/slicerWiki/images/5/56/Case1_DCE.tgz tgz version]
-*** [http://wiki.slicer.org/slicerWiki/index.php/File:DCE_series.zip zip version]
+*** [http://wiki.slicer.org/slicerWiki/images/c/c2/DCE_series.zip zip version]
 ** [[File:Cardiac_ECGg_CT.tgz]] (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short [[media:BeatingHeart.mov|movie]]

@@ Line 50: / Line 50: @@
 * [http://www.youtube.com/watch?v=7zFWRzC31o4 Screencast tutorial] (note that the module is located in '''Modules -> Work in progress -> MultiVolume Support''', not in Modules -> MultiVolume Support, as shown in the video)
 * Sample datasets are available:
-** Anonymized prostate DCE MRI DICOM series
+** Anonymized prostate DCE MRI DICOM series:
 *** [http://wiki.slicer.org/slicerWiki/images/5/56/Case1_DCE.tgz tgz version]
 *** [http://wiki.slicer.org/slicerWiki/index.php/File:DCE_series.zip zip version]

@@ Line 41: / Line 41: @@
 Most frequently used for these scenarios:
 * visualization of a DICOM dataset that contains multiple frames that can be separated based on some tag (e.g., DCE MRI data, where individual temporally resolved frames are identified by Trigger Time tag (0018,1060)
-* visualization of multiple frames defined in the same coordinate frame, saved as individual volumes in NRRD, NIfTI, or any other [[Documentation/4.1/SlicerApplication/SupportedDataFormat|image format supported by 3D Slicer]]
+* visualization of multiple frames defined in the same coordinate frame, saved as individual volumes in NRRD, NIfTI, or any other [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|image format supported by 3D Slicer]]
 * exploration of the multivolume data (cine mode visualization, plotting, volume rendering)
@@ Line 71: / Line 71: @@
 ** ''Static plotting'': This mode of plotting is enabled by the [[Documentation/4.2/SlicerApplication/MainApplicationGUI#Chart_Viewers | Charts]] infrastructure of Slicer, which is exposed in any of the ''Quantitive layouts''. To use this mode, follow these steps:
 **# Extract a representative frame from your multivolume dataset, as discussed above.
-**# Use the [[Documentation/4.2/Modules/Editor|Editor]] module to create labels for the regions of interest.
+**# Use the [[Documentation/{{documentation/version}}/Modules/Editor|Editor]] module to create labels for the regions of interest.
 **# Select the prepared label volume in the ''Probed label volume'' selector in the ''Plotting'' panel. The ''Charts'' viewer in the Slicer Quantitative layout will be updated with the average intensity values for each of the contoured ROIs. The colors of the plots will be the same as the colors of ROI labels.
+|
@@ Line 88: / Line 88: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Related Modules}}
-Before multivolume data can be viewed/explored, it has to be loaded using either [[Documentation/4.2/Modules/DICOM|DICOM]] (if the dataset is in DICOM format) or [[Documentation/4.2/Modules/MultiVolumeImporter|MultVolumeImporter]] modules.
+Before multivolume data can be viewed/explored, it has to be loaded using either [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (if the dataset is in DICOM format) or [[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultVolumeImporter]] modules.
 <!-- ---------------------------- -->

@@ Line 58: / Line 58: @@
 MultiVolume data is represented in this module using two components:
-* MultiVolume node: this is the node you select when you import the dataset using [[Documentation/4.1/Modules/MultiVolumeImporter|MultiVolumeImporter module]]
+* MultiVolume node: this is the node you select when you import the dataset using [[Documentation/4.2/Modules/MultiVolumeImporter|MultiVolumeImporter module]]
 * DisplayNode: this is the node responsible for visualization and storage of the actual image data. The name of that latter node is assigned based on the type of data you are importing. For example, if you import "4D DCE" dataset, it will be called "DCEDisplayNode". This is the node you need to choose in slice viewers to see the multivolume dataset.
@@ Line 68: / Line 68: @@
 ** ''Current frame copy'': you can create and select a conventional scalar volume node in this selector. If ''Enable current frame copying'' button is pressed, each time the currently shown frame is updated, it will be copied to the volume selected. This is useful in situations when you want to do processing of an individual frame (e.g., segmentation), or if you want to show volume rendering of the currently active frame.
 * '''Plotting''': there are two modes of plotting that are supported by the module:
-** ''Interactive plotting'': this mode of plotting is enabled by default and is facilitated by the chart area located in the ''Plotting'' panel. When enabled, the chart will display the intensity values at the spatial location defined by the current position of the mouse pointer. This mode can be disable from the ''Plotting'' GUI panel.
+** ''Interactive plotting'': this mode of plotting is enabled by default and is facilitated by the chart area located in the ''Plotting'' panel. When enabled, the chart will display the intensity values at the spatial location defined by the current position of the mouse pointer. This mode can be disable from the ''Plotting'' GUI panel. The range of the Y axis can be either fixed to the maximum intensity over all of the voxels/all frames of the dataset (if the fixed axis extent checkbox is selected), or otherwise will be adjusted dynamically to the signal range of the probed voxel curve.
-** ''Static plotting'': This mode of plotting is enabled by the [[Documentation/4.1/SlicerApplication/MainApplicationGUI#Chart_Viewers | Charts]] infrastructure of Slicer, which is exposed in any of the ''Quantitive layouts''. To use this mode, follow these steps:
+** ''Static plotting'': This mode of plotting is enabled by the [[Documentation/4.2/SlicerApplication/MainApplicationGUI#Chart_Viewers | Charts]] infrastructure of Slicer, which is exposed in any of the ''Quantitive layouts''. To use this mode, follow these steps:
 **# Extract a representative frame from your multivolume dataset, as discussed above.
-**# Use the [[Documentation/4.1/Modules/Editor|Editor]] module to create labels for the regions of interest.
+**# Use the [[Documentation/4.2/Modules/Editor|Editor]] module to create labels for the regions of interest.
 **# Select the prepared label volume in the ''Probed label volume'' selector in the ''Plotting'' panel. The ''Charts'' viewer in the Slicer Quantitative layout will be updated with the average intensity values for each of the contoured ROIs. The colors of the plots will be the same as the colors of ROI labels.
+|
 | align="right" |
+|
-[[Image:Slicer4-MultiVolumeExplorer_panel1.png|thumb|400px|Settings panel and interactive plotting chart]]
+[[Image:Slicer4-MultiVolumeExplorer_4.2.png|thumb|400px|Settings panel and interactive plotting chart]]
 |}
@@ Line 88: / Line 88: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Related Modules}}
-Before multivolume data can be viewed/explored, it has to be loaded using [[Documentation/4.1/Modules/MultiVolumeImporter|MultVolumeImporter]] module.
+Before multivolume data can be viewed/explored, it has to be loaded using either [[Documentation/4.2/Modules/DICOM|DICOM]] (if the dataset is in DICOM format) or [[Documentation/4.2/Modules/MultiVolumeImporter|MultVolumeImporter]] modules.
 <!-- ---------------------------- -->
@@ Line 97: / Line 97: @@
 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
 This module is an external Slicer module. The source code is available on Github here: https://github.com/fedorov/MultiVolumeExplorer
 ==Features to be implemented==
 * allow the user to speed-up or slow-down the playback, and also turn off "loop"
 * report to the user the actual, measured, frame rate
 ==Features under consideration==
 * can we use chart viewer for interactive plotting? -- Discussed with Jim, speedup is possible, but not a priority right now
 * interactive update of the active frame based on the point selected in the chart viewer
 * add GUI elements to update the current frame at the exact time intervals specified in multivolume. If the intervals are non-uniform, I am not sure I can use the timer anymore, so this would require some extra thought.
 * import multivolumes from ITK 4d images
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-footer}}
 <!-- ---------------------------- -->