NAMIC Wiki - User contributions [en]

User talk:Tamekue

2011-10-18T12:19:17Z

Tamekue:

Events:Slicer4-Review-07-2011

2011-07-18T21:18:02Z

Tamekue: /* Attending */

=What=
Slicer 4 review and programming sprint
=When=
July 19, 10 am -21, 4pm 2011

=Who=
Slicer 4 core programmers
=Where=
Demo room, 2nd floor, 1249 Boylston Street, Boston, MA
=Why=
*Identify roadmap for a Slicer 4 product release for the [http://www.na-mic.org/Wiki/index.php/RSNA2011_Planning Nov 27-Dec.2 RSNA demos at the 3DSlicer Booth]

=Work on=
==Main Topics==
*Critical Features
*Bug fixes
*Download setup and integration with the existing Slicer website

== Priority TBD ==
===UI===
[[image:SlicerColorSelector.PNG|400px|right|thumb|SlicerColorSelector]]
* Reformat capabilities: We need a widget and possibly a slider based interface.
* Main GUI
** face lift for the Slice viewers: reduce permanent non-image components. Reduce the number and depth of submenus.
** 3D viewer should have similar appearance to slice viewers
* Update tutorials
** After main gui
** Using GUI Testing
* Volume rendering transfer function
** Jittery, and banding
** Threshold
** Better appearance of the elements of the transfer function. They look ugly and are not antialiased. Check the graph in [https://www.ohloh.net/p/slicer Ohloh] and mouse over it. Looks much nicer!
** Group selection and shifting
*Color selector
**the default color selector should be the one that is slicer customized, not the Qt default.
**add search function to the labels

===Under the hood===
* GPU Volume Rendering
** Support for ATI and MAC
** How many GPU render engines to support/provide?
***Ron says: I just need a single one that works for flythroughs and can handle the combination of volume rendering, cross-sections, surface models, annotations
*hierarchies
**display: the current display is confusing.
**drag and drop capability
* Annotations
** vtkWidgets
** GUI layout
** compositing with volume rendering does not work properly
** Working group (?)

===Infrastructure===
* Move to git/gerrit (TBD - can it be used with git-svn or is the suggestion to retire svn?)
* GUI Testing
** Instrumenting CTK widgets
** Conversion of tutorials to tests
** What will this provide that [http://sikuli.org/ Sikuli] does not? Sonia is ready to use Sikuli unless there is a good reason not to.
* Tk/Tcl
** Removing the last dependencies in core interaction loops
** Maintain functionality for Editor
* Performance optimization
** Module for profiling events
* Extensions
** Support for superbuild
** Requirements for testing, documentation, tutorials, and continued support from developers
*** How to name different levels of compliance
* Downloads
** Statistics on packages and on individual extensions
** Web pages
** Technologies
* Charts
** Reference Implementation (Marcus)
* MIDAS
** sceneviews support
* Interactive CLI modules

=Agenda=

=Attending=
#Ron Kikinis
#Steve Pieper
#Nicole Aucoin
#Julien Finet
#Daniel Haehn (only 07/19)
#Jean-Christophe Fillion-Robin
#Stephen Aylward
#Will Schroeder
#Jim Miller
#Suares Tamekue Tatuebu

2011 Summer Project Week Stenosis Detector

2011-06-30T19:54:18Z

Tamekue: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:VesselnessFilter.png| Vesselness filter
Image:Level Set Segmentation.png| Level set segmentation
Image:Optimization.png| Optimization of the Level set segmentation
Image:CenterlineComputation.png| Centerline computation
</gallery>

==Key Investigators==
* University of Heidelberg, Germany: Suares Tamekue Tatuebu
* UPenn: Daniel Haehn
* [http://www.orobix.com Orobix], Italy: Luca Antiga
* SPL: Ron Kikinis

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.

The tool will be evaluated on datasets.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We changed the graphical user interface. And with the Kitware guys we clarified an issue related events handle in the wizard.
During the coming weeks we will finish all remaining connections between the logic and the graphical user interface. Then we will start valuating the module on datasets.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable [X]
#Other (Please specify)

==References==
* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
</div>

2011 Summer Project Week Stenosis Detector

2011-06-30T19:52:39Z

Tamekue: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:VesselnessFilter.png| Vesselness filter
Image:Level Set Segmentation.png| Level set segmentation
Image:Optimization.png| Optimization of the Level set segmentation
Image:CenterlineComputation.png| Centerline computation
</gallery>

==Key Investigators==
* University of Heidelberg, Germany: Suares Tamekue Tatuebu
* UPenn: Daniel Haehn
* [http://www.orobix.com Orobix], Italy: Luca Antiga
* SPL: Ron Kikinis

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.

The tool will be evaluated on datasets.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We changed the graphical user interface. And with the Kitware guys we clarified an issue related events handle in the wizard.
During the coming weeks we will finish all remaining connections the logic and the graphical user interface. Then we will start valuating the module on datasets.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable [X]
#Other (Please specify)

==References==
* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
</div>

2011 Summer Project Week Stenosis Detector

2011-06-24T14:20:49Z

Tamekue: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:VesselnessFilter.png| Vesselness filter
Image:Level Set Segmentation.png| Level set segmentation
Image:Optimization.png| Optimization of the Level set segmentation
Image:CenterlineComputation.png| Centerline computation
</gallery>

==Key Investigators==
* University of Heidelberg, Germany: Suares Tamekue
* UPenn: Daniel Haehn
* [http://www.orobix.com Orobix], Italy: Luca Antiga
* SPL: Ron Kikinis

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.

The tool will be evaluated on datasets.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We changed the graphical user interface. And with the Kitware guys we clarified an issue related events handle in the wizard.
During the coming weeks we will finish all remaining connections of the logic with the graphical user interface and then we will start valuating the module on datasets.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable [X]
#Other (Please specify)

==References==
* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
</div>

User talk:Tamekue

2011-06-21T13:47:19Z

Tamekue: /* Time line table */

2011-06-17T16:18:29Z

Tamekue: Created page with '__NOTOC__ <gallery> Image:PW-SLC2011.png|Projects List </gallery> ==Key Investigators== * University of Heidelberg, Germany: Suares Tamekue…'

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* University of Heidelberg, Germany: Suares Tamekue
* UPenn: Daniel Haehn
* [http://www.orobix.com Orobix], Italy: Luca Antiga
* SPL: Ron Kikinis

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
We are developing a stenosis detector based on VMTK in Slicer 4. The goal is to be able to visualize stenosis after a vessel segmentation using a wizard-based interface.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach for developing the stenosis detector is: first vessel enhancement, level-set segmentation, network extraction and then quantification and visualization of stenosis.

The tool will be evaluated on datasets.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
A prototyp of the graphical user interface has been designed and implemented.

'''Project Week Update:'''
The week was very productive. We got a lot of feedback from the Kitware guys. Specially on the wizard interface which is based on the CTK library. We also had to clarify an issue concerning the area of the wizard content and the way the different wizard steps interact with each other and with the logic.

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable [X]
#Other (Please specify)

==References==
* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
</div>

2011 Summer Project Week

2011-06-17T16:10:54Z

2011-02-26T01:47:52Z

Tamekue:

=== Diploma Thesis - Tasks ===

1. Task
* Find out how to use .UI files in Python (Slicer4). DONE
* Result: Shown at http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers:Projects:QtSlicer/Tutorials/PythonAndUIFile
2. Task (until 03/04/11)
* Write expose for diploma thesis, find enough references. OPEN
* Result:
3. Task (until 02/24/11)
* Implement a simple program in Python to run through an array (x,y,z,radius), find the points where the radius is < THRESHOLD and save the detected segments in an array. Select a reasonable threshold. This will help to detect stenosis.
* Result: Loop through array realized. Stenosis are now found when radius is below a hard-coded threshold and put into a container DONE
4. Task (until 02/21/11)
* Look at Slicer4/QTScriptedModules/Scripts/Editor.py and Slicer4/QTScriptedModules/EditorLib to figure out how to split Python module to different files in Slicer4. DONE
* Result: The module itself is a .py file in QTScriptedModules/Scripts. It is possible to include a directory with other Python Scripts in QTScriptedModules/XXX where XXX is a custom name. Then, in the .py File in Scripts, an import XXX has to be placed. This will call the XXX/__init__.py file and can include other files.
5. Task (until 03/04/11)
* Modify VMTKCenterlines in Slicer3 to include a button to perform the code of Task 3 on a vtkPolyData object. The centerlines are polyData. Add the new method to the logic class of VMTKCenterlines. This will be the algorithm to detect stenosis. OPEN
6. Task (until 03/04/11)
* A pixel in 2D has always 8 neighbors. Write code in Python to do the following: Create a 2D array (maybe a 16x16 matrix?). Take a random element in the middle of the array and loop in the directions of all 8 neighbors (top, bottom, left, right, diagonal left to top, diagonal left to bottom, diagonal right to top, diagonal right to bottom) until you reach the end of the matrix. If this is finished we can modify it to detect the maximal diameter of a vessel through one click. We will extend it then to 3D. If you want, skip 2D and start directly with 3D (16x16x16 matrix). OPEN
* Result:
7.Task (until 03/20/11)
* We use the gradient (deltaX) to compute the difference between radii of two points to distinguish if a stenosis is present or not in a relative fashion. Prepare the derivation for the formulas used and proof them for the thesis! OPEN
* Result: