Difference between revisions of "ChangeTracker"
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= What's New = | = What's New = | ||
| − | * | + | *Jan 25, 2009, use of 3d box widget with tumor volume rendering for ROI selection |
| + | *Jan 12, 2009, New visualization features integrated | ||
| + | *Jan 4-9, 2009, ChangeTracker project on NA-MIC AHM/Programming Week at Salt Lake City. See summary and results [http://wiki.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_ChangeTracker here] | ||
| + | *Dec 27, 2008, DiameterEstimator tool is available for automatic estimation of tumor diameter from the binary image | ||
=Background= | =Background= | ||
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=User information / Tutorials= | =User information / Tutorials= | ||
| − | * Detecting subtle change in pathology: [ | + | * Detecting subtle change in pathology: [https://na-mic.org/w/images/8/8b/Slicer3Training_ChangeTracker.ppt slides], [https://na-mic.org/w/images/1/19/ChangeTracker-Tutorial-Data.zip data] |
| + | * ChangeTracker module documentation page on Slicer Wiki [http://wiki.slicer.org/slicerWiki/index.php?title=Modules:ChangeTracker-Documentation here] | ||
=Technical details= | =Technical details= | ||
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* during "Analysis type step", Slicer crashes if "Analyze" button is hit more than once | * during "Analysis type step", Slicer crashes if "Analyze" button is hit more than once | ||
| − | * registration of a new volume node with the scene results in update of the slice views | + | * registration of a new volume node with the scene results in update of the slice views: ''Resolved: this appeared to be due to a lacking functionality in SliceCompositeNode, which invoked PropagateVolumeUpdate() on image load. This functionality can now be controlled via the DoPropagatVolumeUpdate in SliceComposite MRML node'' |
| − | * incorrect setting of the registration parameters results in registration producing empty volume, no error messages from the module: '' | + | * incorrect setting of the registration parameters results in registration producing empty volume, no error messages from the module: ''Resolved: committed a fix to CommandLineModuleLogic to update the module node status correctly to indicate the error, if module entry point returns non-zero. TODO: update ChangeTracker logic to account for this change'' |
* need to investigate reproducibility of registration and impact of the random seed initialization: ''Linear registration updated with metric seed reinitialization'' | * need to investigate reproducibility of registration and impact of the random seed initialization: ''Linear registration updated with metric seed reinitialization'' | ||
| − | * investigate reasons for segfault with the weird dataset from Yanling | + | * investigate reasons for segfault with the weird dataset from Yanling: ''Resolved (?): data is intrinsically very difficult to align. Registration must be solved prior to using ChangeTrcker'' |
* check and clean up file output procedures (..-TG directories) | * check and clean up file output procedures (..-TG directories) | ||
=Feature requests/Features under development= | =Feature requests/Features under development= | ||
| − | * multi-color volume rendering for tumor growth results | + | * multi-color volume rendering for tumor growth results: DONE |
| − | * use ''Compare view'' | + | * use ''Compare view'': DONE |
| − | * 3d box widget for ROI selection | + | * 3d box widget for ROI selection DONE |
* analysis of multiple time points | * analysis of multiple time points | ||
| − | * testing | + | * testing IN PROGRESS |
| − | * Jean-Jacques: would be nice to combine growth results with the 3D rendering of the estimated tumor volume | + | * improved tumor segmentation to exclude prominent non-tumor regions (vessels, scull, falx) |
| + | * Jean-Jacques Lemaire: would be nice to combine growth results with the 3D rendering of the estimated tumor volume | ||
| + | * Jean-Jacques Lemaire: improve user interface for tumor boundary identification -- something missing in the existing tools; would like to see better robustness of segmentation | ||
| + | * Ron wish list: get user input for inside/outside locations of points for tracked structure, use this for threshold selection and initial segmentation; ROI centering; sync ROI scales colors with the 3d box colors; review naming conventions for intermediate volumes; allow for separate show/hide functionality for 3d box and volume rendering; link compare views; support scene snapshots; fix bottom layout panel random popup issue | ||
| + | * graceful error handling | ||
| + | |||
| + | =Use cases= | ||
| + | |||
| + | * Meningioma growth analysis | ||
| + | * [http://wiki.na-mic.org/Wiki/index.php/ChangeTracker:Lupus_DBP Longitudinal lesion analysis for Lupus DBP] | ||
=People= | =People= | ||
Latest revision as of 18:27, 10 July 2017
Home < ChangeTrackerOverview
THIS PAGE IS UNDER CONSTRUCTION -- CHECK BACK OFTEN!
ChangeTracker is a 3D Slicer GUI module for monitoring slowly evolving tumors. This page will host the relevant information about ChangeTracker.
What's New
- Jan 25, 2009, use of 3d box widget with tumor volume rendering for ROI selection
- Jan 12, 2009, New visualization features integrated
- Jan 4-9, 2009, ChangeTracker project on NA-MIC AHM/Programming Week at Salt Lake City. See summary and results here
- Dec 27, 2008, DiameterEstimator tool is available for automatic estimation of tumor diameter from the binary image
Background
User information / Tutorials
- Detecting subtle change in pathology: slides, data
- ChangeTracker module documentation page on Slicer Wiki here
Technical details
Bugs / Known issues
- during "Analysis type step", Slicer crashes if "Analyze" button is hit more than once
- registration of a new volume node with the scene results in update of the slice views: Resolved: this appeared to be due to a lacking functionality in SliceCompositeNode, which invoked PropagateVolumeUpdate() on image load. This functionality can now be controlled via the DoPropagatVolumeUpdate in SliceComposite MRML node
- incorrect setting of the registration parameters results in registration producing empty volume, no error messages from the module: Resolved: committed a fix to CommandLineModuleLogic to update the module node status correctly to indicate the error, if module entry point returns non-zero. TODO: update ChangeTracker logic to account for this change
- need to investigate reproducibility of registration and impact of the random seed initialization: Linear registration updated with metric seed reinitialization
- investigate reasons for segfault with the weird dataset from Yanling: Resolved (?): data is intrinsically very difficult to align. Registration must be solved prior to using ChangeTrcker
- check and clean up file output procedures (..-TG directories)
Feature requests/Features under development
- multi-color volume rendering for tumor growth results: DONE
- use Compare view: DONE
- 3d box widget for ROI selection DONE
- analysis of multiple time points
- testing IN PROGRESS
- improved tumor segmentation to exclude prominent non-tumor regions (vessels, scull, falx)
- Jean-Jacques Lemaire: would be nice to combine growth results with the 3D rendering of the estimated tumor volume
- Jean-Jacques Lemaire: improve user interface for tumor boundary identification -- something missing in the existing tools; would like to see better robustness of segmentation
- Ron wish list: get user input for inside/outside locations of points for tracked structure, use this for threshold selection and initial segmentation; ROI centering; sync ROI scales colors with the 3d box colors; review naming conventions for intermediate volumes; allow for separate show/hide functionality for 3d box and volume rendering; link compare views; support scene snapshots; fix bottom layout panel random popup issue
- graceful error handling
Use cases
- Meningioma growth analysis
- Longitudinal lesion analysis for Lupus DBP
People
- Ron Kikinis
- Kilian Pohl
- Andriy Fedorov
Funding
Publications
- E.Konukoglu, W.M.Wells, S.Novellas, N.Ayache, R.Kikinis, P.M.Black, K.M.Pohl. Monitoring Slowly Evolving Tumors. Proc. of 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2008, pp.812-815 link
Contact
Please contact Andriy Fedorov for further information.
