2007 Project Week MIT QDEC Slicer3 Integration - Revision history

Naucoin: /* Discussion */

2007-05-10T18:41:22Z

Discussion

Naucoin: /* Discussion */

2007-05-10T18:40:55Z

Discussion

Naucoin: /* Discussion */

2007-04-23T21:54:57Z

Discussion

Naucoin: /* Discussion */

2007-04-23T21:52:56Z

Discussion

Naucoin: /* Abstract */

2007-04-23T21:50:09Z

Abstract

Naucoin: /* Discussion */

2007-04-18T22:43:07Z

Discussion

Naucoin: /* Discussion */

2007-04-18T19:35:40Z

Discussion

Naucoin: /* Discussion */

2007-04-18T19:25:07Z

Discussion

Naucoin: /* Discussion */

2007-04-18T19:16:47Z

Discussion

Naucoin at 19:08, 18 April 2007

2007-04-18T19:08:59Z

New page

== Abstract ==

Incorporating the functionality of the MGH developed Freesurfer front end query tool (QDEC) into Slicer 3. Explore related issues of how to better integrate Freesurfer and Slicer3.

== Discussion ==

* What defines a successful integration?
** ?
* What's a list of issues that need a good working solution?
** being able to read volume encoced scalar format - done, changes made to vtkMRMLModelStorageNode
** being able to composite scalars in Slicer3 - done, vtkMRMLModelNode::CompositeScalars
* Identify which parts of this project are:
# internal developments, tightly coupled to the MGH environment
# features that Slicer3 might have in order to provide some qdec-type functionality to a potentially wider audience (say, BIRN users on windows)
## code in slicer for reading mgh file formats (mgz, surfaces, annotations, etc) into ITK and VTK which is duplicated with code used in qdec, scuba, etc.
# what common libraries could be shared by both of those efforts.
## MGH host a publicly readable svn repository, perhaps called libMGH, where all this stuff would be captured as the "official" reference implementation. MGH internal projects also rely on the library so that other users could be confident that the library is up to date and fully compatible.

== Slide ==
[[Image:2007_Project_Week_MIT_QDEC_Slicer3_Integration.ppt|4 block slide]]

== Project Page ==



== Participants ==

*Nicole Aucoin BWH
*Kevin Teich MGH
*Nick Schmansky MGH
*Doug Greve MGH
*Gheorghe Postelnicu MGH
*Steve Pieper Isomics

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[[2007_Programming/Project_Week_MIT|Back to Project week]]

@@ Line 14: / Line 14: @@
 ** being able to read volume encoced scalar format - done, changes made to vtkMRMLModelStorageNode
 ** being able to composite scalars in Slicer3 - done, vtkMRMLModelNode::CompositeScalars (need to save the model in vtk to save the composite in mrml) [[Image:Slicer3ReadMGHVolumeEncodedScalars.jpg | FreeSurfer versus Slicer]]
-** picking points on models - use the fiducials interface to get at vertex ids and index into scalar overlays - done, the vtkSlicerViewerWidget class Pick method sets the picked cell ID, vertex ID - check if the Pick succeeded in finding a model node (PickedNodeName != ""), then use it to get the model node, which contains polydata that can be indexed using the vertix ID (PickedPointID)
+** picking points on models - use the fiducials interface to get at vertex ids and index into scalar overlays - done, the vtkSlicerViewerWidget class Pick method sets the picked cell ID, vertex ID - check if the Pick succeeded in finding a model node (PickedNodeName != ""), then use it to get the model node, which contains polydata that can be indexed using the vertex ID (PickedPointID)
 ** FSGDF plotting
 * Identify which parts of this project are:

@@ Line 14: / Line 14: @@
 ** being able to read volume encoced scalar format - done, changes made to vtkMRMLModelStorageNode
 ** being able to composite scalars in Slicer3 - done, vtkMRMLModelNode::CompositeScalars (need to save the model in vtk to save the composite in mrml) [[Image:Slicer3ReadMGHVolumeEncodedScalars.jpg | FreeSurfer versus Slicer]]
-** picking points on models - use the fiducials interface to get at vertex ids and index into scalar overlays
+** picking points on models - use the fiducials interface to get at vertex ids and index into scalar overlays - done, the vtkSlicerViewerWidget class Pick method sets the picked cell ID, vertex ID - check if the Pick succeeded in finding a model node (PickedNodeName != ""), then use it to get the model node, which contains polydata that can be indexed using the vertix ID (PickedPointID)
 ** FSGDF plotting
 * Identify which parts of this project are:

@@ Line 10: / Line 10: @@
 ** being able to read volume encoced scalar format - done, changes made to vtkMRMLModelStorageNode
 ** being able to composite scalars in Slicer3 - done, vtkMRMLModelNode::CompositeScalars (need to save the model in vtk to save the composite in mrml) [[Image:Slicer3ReadMGHVolumeEncodedScalars.jpg | FreeSurfer versus Slicer]]
-** picking points on models
+** picking points on models - use the fiducials interface to get at vertex ids and index into scalar overlays
 ** FSGDF plotting
 * Identify which parts of this project are:

@@ Line 22: / Line 22: @@
 # what common libraries could be shared by both of those efforts.
 ## MGH host a publicly readable svn repository, perhaps called libMGH, where all this stuff would be captured as the "official" reference implementation.  MGH internal projects also rely on the library so that other users could be confident that the library is up to date and fully compatible.
 == Slide ==

@@ Line 5: / Line 5: @@
 == Discussion ==
-* What defines a successful integration?
+* Slicer will incorporate the basic QDEC functionality:
-** ?
+** load a user-supplied table of subject data (the qdec.table.dat file)
 * What's a list of issues that need a good working solution?
 ** being able to read volume encoced scalar format - done, changes made to vtkMRMLModelStorageNode

@@ Line 1: / Line 1: @@
 == Abstract ==
-Incorporating the functionality of the MGH developed Freesurfer front end query tool (QDEC) into Slicer 3.  Explore related issues of how to better integrate Freesurfer and Slicer3.
+Incorporating some of the functionality of the MGH developed Freesurfer front end query tool (QDEC) into Slicer 3.  Explore related issues of how to better integrate Freesurfer and Slicer3.
 == Discussion ==