Documentation/Nightly/Modules/MultiVolumeExplorer

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Introduction and Acknowledgements

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. Author: Andrey Fedorov, Jean-Cristophe Fillion Robin, Julien Finet, Steve Pieper, Ron Kikinis Contact: Andrey Fedorov <email>fedorov@bwh.harvard.edu</email>

National Center for Image Guided Therapy (NCIGT)   National Alliance for Medical Image Computing (NA-MIC)   Surgical Planning Laboratory (SPL)   Kitware, Inc.   Neuroimage Analysis Center (NAC)

Module Description

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

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 image format supported by 3D Slicer
• exploration of the multivolume data (cine mode visualization, plotting, volume rendering)

Tutorials

Screencast tutorial Sample datasets are available: Anonymized prostate DCE MRI DICOM series: tgz version zip version The same series saved in MultiVolume-specific 4d NRRD format using Slicer: File:DCE series.nrrd.zip File:Cardiac ECGg CT.tgz (ECG-gated contrast-enhanced cardiac CT) (use "User-defined non-DICOM" parameter option to load it into MultiVolumeImporter). Short movie Tutorial: Meysam Torabi and Andrey Fedorov, Exploration and Study of MultiVolume Image Data using 3D Slicer

Panels and their use

Input data Before the module can be used, you should import the data into a MultiVolume node that you can choose as input in this module. There are two options to do this:

1. If your data is in DICOM format, you should first import it into Slicer DICOM database using DICOM module. Once imported, you should click on the series containing the multi-frame data in the DICOM browser. If DICOM module detects multi-frame dataset in the series, you should see the MultiVolume option in the list of load options for the series.
2. If your data is stored as a collection of NRRD/NIFTI/etc volumes per time-point, you should use MultiVolume Importer module to first create a MultiVolume node from your file collection, and then use the resulting MultiVolume node as input for the Explorer module.

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. 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 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 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.

Settings panel and interactive plotting chart

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).

Related Modules

Before multivolume data can be viewed/explored, it has to be loaded using either DICOM (if the dataset is in DICOM format) or MultVolumeImporter modules.

Documentation/Nightly/Modules/PkModeling extension can be used for pharmacokinetic analysis of the DCE MRI data.

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)

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