Documentation/4.0/Modules/ChangeTracker
Introduction and Acknowledgements
This work is supported by NA-MIC, NAC, NCIGT, and the Slicer Community. This work is partially supported by Brain Science Foundation and NIH U01 CA151261. | |||||||
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Module Description
ChangeTracker is a software tool for quantification of the subtle changes in pathology. The module provides a workflow pipeline that combines user input with the medical data. As a result we provide quantitative volumetric measurements of growth/shrinkage together with the volume rendering of the tumor and color-coded visualization of the tumor growth/shrinkage. ChangeTracker is not yet a generic tool for detecting small changes. It has been tuned specifically for meningioma growth analysis. Specifically, the assumptions made by ChangeTracker are
If you want to apply ChangeTracker on non-meningioma data, please let us know. The algorithm is likely to require tuning of the parameters for registration and other processing steps. |
Use Cases
Most frequently used for these scenarios:
- Quantification of small changes in meningioma tumor volume from post-contrast MRI
Tutorials
Under development
The test data can be downloaded automatically by pushing the "Load test data" in the panel of the first step (you will need the internet connection).
Panels and their use
ChangeTracker is organized as a workflow that consists of the following steps:
- Step 1: Define input scans
Use drop-down controls to choose the two scans where you would like to measure pathology development. Currently, we support analysis of the images that correspond to two time points. |
- Step 2: Define volume of interest
This step of wizard includes the following user controls to facilitate Volume of Interest (VOI) selection:
"ROI Widget" refers to the three-dimensional selection box that appears in the 3d slice view once you begin to select VOI. You can define VOI by adjusting the colored handles of the ROI widget in the slice viewer or 3d viewer. |
- Step 3: Segment the analyzed structure
Use threshold control slider to find the intensity that most closely approximates tumor volume. Thresholded volume is rendered interactively in the 3D viewer as you are adjusting the threshold value, and is also visualized as semi-transparent label in the image slice viewers.
Note, that currently ChangeTracker expects that the tissue you monitor is hyperintensive on the image. In the cases when threshold is not effective in segmenting the structure of interest, Advanced tab allows to prescribe the segmentation label image directly, instead of using threshold. (this feature is currently disabled, under development) |
- Step 4: ROI Analysis
We provide two metrics to quantify tumor progression: intensity-based and deformation-based (see details in this paper). Choose the metric(s) you would like to use.
In some cases, the automatic registration functionality in ChangeTracker may not be able to accurately register your data. If this happens, you can use the Advanced tab to register your data, and place Scan2 under the transform. ChangeTracker will use the prescribed transform and will skip registration step. |
- Step 5: ROI Analysis Results
Results are reported as the change in tumor volume, separately for growth and shrinkage component. The quantitative results are reported in voxels, mL and percentage relative the the volume of the structure segmented in the baseline scan.
The visualization of the analysis results includes the following components upon the completion of analysis:
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Similar Modules
- Point to other modules that have similar functionality
References
Publications related to this module go here. Links to pdfs would be useful. For extensions: link to the source code repository and additional documentation
Information for Developers
Section under construction. |
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