2013 Summer Project Week:Deformable transforms - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T17:12:56Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Pinter: /* Key Investigators */

2013-06-21T02:26:02Z

Key Investigators

Pinter: Moved meeting minutes to a separate wiki page

2013-06-18T13:55:03Z

Moved meeting minutes to a separate wiki page

Pinter: Use cases added

2013-06-17T21:24:04Z

Use cases added

Pinter: /* Key Investigators */

2013-06-17T21:08:14Z

Key Investigators

Pinter at 21:02, 17 June 2013

2013-06-17T21:02:32Z

Pinter: /* Key Investigators */

2013-06-17T20:29:02Z

Key Investigators

Pinter: /* Key Investigators */

2013-06-17T20:14:56Z

Key Investigators

Pinter: /* Key Investigators */

2013-06-17T20:11:09Z

Key Investigators

Pinter at 20:01, 17 June 2013

2013-06-17T20:01:51Z

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 ==References==
 * Relevant tickets in the SlicerRT system: [https://www.assembla.com/spaces/slicerrt/tickets/247#/activity/ticket: #247] and [https://www.assembla.com/spaces/slicerrt/tickets/37#/activity/ticket: #37]
-* [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/Transforms Transforms module documentation]
+* [https://www.slicer.org/wiki/Documentation/4.2/Modules/Transforms Transforms module documentation]

@@ Line 39: / Line 39: @@
 ** RT fractions: Contours are made on the planning CT, which we want to warp to fit the day 2 CT (and be able to warp day 2 dose to match the day 1 dose in terms of geometry so that we can accumulate them)
 ** PET-CT: Follow the progress of a tumor by registering the CT images together and applying this transform to the PET images so that the tumors have the same coordinate frame
 </div>

@@ Line 35: / Line 35: @@
 <h3>Progress</h3>
-* Should it be handled on what level?
+* Meeting minutes of the discussions: [[Handling deformable transforms in Slicer meeting minutes|Handling deformable transforms]]
-** MRML level (Transformable, VolumesLogic?)
+* Use cases:
-** '''Using modules (BRAINSResample, Resample Scalar/Vector/DWI Volume)''' - Subject Hierarchy would know what module can transform what objects using what transforms and use them
+** RT fractions: Contours are made on the planning CT, which we want to warp to fit the day 2 CT (and be able to warp day 2 dose to match the day 1 dose in terms of geometry so that we can accumulate them)
-* Invertability / reversibility
+** PET-CT: Follow the progress of a tumor by registering the CT images together and applying this transform to the PET images so that the tumors have the same coordinate frame
 </div>

@@ Line 35: / Line 35: @@
 <h3>Progress</h3>
-* Should it be handled
+* Should it be handled on what level?
-** on the MRML level (Transformable, VolumesLogic?)
+** MRML level (Transformable, VolumesLogic?)
-** '''or in a CLI (BRAINSResample, Resample Scalar/Vector/DWI Volume)''' - Subject Hierarchy would know what module can transform what objects using what transforms and use them
+** '''Using modules (BRAINSResample, Resample Scalar/Vector/DWI Volume)''' - Subject Hierarchy would know what module can transform what objects using what transforms and use them
 * Invertability / reversibility
 ** '''Should it create clones of the 'hardened' objects?''' - in Subject Hierarchy
@@ Line 58: / Line 58: @@
 * Look at the DICOM transform logic
 ** Make frame of reference concept explicit in Slicer?
 </div>

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 <h3>Progress</h3>
-* Questions
+* Should it be handled
-** Should it be handled on the MRML level (Transformable, VolumesLogic?) or in a CLI (BRAINSResample, Resample Scalar/Vector/DWI Volume)
+** on the MRML level (Transformable, VolumesLogic?)
-** Invertability / reversibility
+** '''or in a CLI (BRAINSResample, Resample Scalar/Vector/DWI Volume)''' - Subject Hierarchy would know what module can transform what objects using what transforms and use them
-*** Should it create clones of the 'hardened' objects?
+* Invertability / reversibility
-*** Should we maintain a history in the hardened nodes?
+** '''Should it create clones of the 'hardened' objects?''' - in Subject Hierarchy
-*** Harden option on drop (I can't display but can resample)
+** Should we maintain a history in the hardened nodes?
-** Plugin mechanism for registering non-linear transforms
+** '''Harden option on drop (I can't display but can resample)''' - in Data and Transforms modules
-*** Modules register themselves in the fashion "I can apply X type of transform to Y type objects"
+* Plugin mechanism for registering non-linear transforms
-**** The application could call these algorithms (from the modules) at first (instead of registering from outside)
+** Modules register themselves in the fashion "I can apply X type of transform to Y type objects"
-*** GUI decision if hardened
+*** The application could call these algorithms (instead of registering from outside)
-** Where?
+** GUI decision if hardened
-*** Data module
+* Where?
-*** Transforms module (display tree, and add a 'Harden' button to the panels)
+** Data module
-** Harden all the way up or until all the parents are linear or just one level a time?
+** Transforms module (display tree, and add a 'Harden' button to the panels)
-** Subject Hierarchy right-click -> apply transform to study
+** Subject Hierarchy right-click -> apply transform to branch
 * Harden all the way up or until all the parents are linear or just one level a time?
 * Extend to contain bounding box
 ** In case of non-linear transforms, go down the edges to specify the output bounding box
 ** Options: resample in source lattice (still cloned), the one above, rsample in target volume
 * Look at the DICOM transform logic
 ** Make frame of reference concept explicit in Slicer?
 </div>
 </div>

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 ==Key Investigators==
 * Queen's: Csaba Pinter, Andras Lasso
-* Isomics: Alex Yarmarkovich
+* Isomics: Alex Yarmarkovich, Steve Pieper
-*?
+* GE Research: Jim Miller
 <div style="margin: 20px;">
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 <h3>Objective</h3>
 Enable handling of deformable transforms in the Transforms module, very similarly to the way linear transforms are handled.
-* Drop TransformableNodes under deformable transform
+* Drop TransformableNodes under deformable transform (possible already but ignored and hardening for rendering not enabled)
 * Harden deformable transform on
 ** Models (should be straightforward)
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 <h3>Approach, Plan</h3>
-The approach is to enhance the Transforms module to be able to use deformable transform nodes as parents to transformable objects.
+The approach is to enhance the Transform node (and Transforms module) to be able to use deformable transform nodes as parents to transformable objects and harden them
 The plan for the project week is to discuss the best way to implement it, and start the implementation.
@@ Line 35: / Line 35: @@
 <h3>Progress</h3>
-*Patient Hierarchy module shows the hierarchy, enables reparenting and adding from outside the Patient Hierarchy.
+* Questions
-*Some steps toward utilization of Patient Hierarchy has been implemented (SlicerRT [https://www.assembla.com/spaces/slicerrt/tickets/278#/activity/ticket: #278])
+** Should it be handled on the MRML level (Transformable, VolumesLogic?) or in a CLI (BRAINSResample)
 </div>
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 ==Delivery Mechanism==
-This work will be delivered to the NA-MIC Kit as an enhancement in the Transforms module in Slicer.
+This work will be delivered to the NA-MIC Kit as an enhancement in Slicer core.
 ==References==
 * Relevant tickets in the SlicerRT system: [https://www.assembla.com/spaces/slicerrt/tickets/247#/activity/ticket: #247] and [https://www.assembla.com/spaces/slicerrt/tickets/37#/activity/ticket: #37]
 * [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Modules/Transforms Transforms module documentation]