User talk:Tamekue

Time line table

Time	Monday, January 10	Tuesday, January 11	Wednesday, January 12	Thursday, January 13	Friday, January 14
	Project Activities (Canyons)	Project Activities (Canyons)	Project Activities (Canyons)	AHM, EAB (Canyons, Arches, Deer Valley)	Project Activities (Canyons)
7:30-8:00		Breakfast	Breakfast	Breakfast	Breakfast
8:00-10:00		8:00-9:00 DBP Briefing (Ron Kikinis) (Deer Valley) 9:30-10:00 Training Core Strategy Session (Deer Valley) * Project Work	Project Work 8-9:30am: Breakout: Engineering of Multi-Volume Data in Slicer (Arches)	8:00 Introduction, Ron Kikinis 8:05-10:00 Roadmap Projects 8:05-8:25 Atrial Fibrillation, Rob MacLeod (slides (1up)‎ and slides (2up)‎) 8:25-8:45 Huntington's Diseases, Hans Johnson (slides) 8:45-9:05 Head and Neck Cancer, Greg Sharp (slides) 9:05-9:25 Traumatic Brain Injury, Jack Van Horn (slides) 9:25-9:45 Image Guided Therapy, Nobuhiko Hata (slides)	Project Review
10:00-10:30		Coffee	Coffee	Coffee	Coffee
10:30-12:00	Vision10	Breakout: Slicer 4 - Looking Forward (Steve Pieper, Julien Finet, Jean-Christophe Fillion-Robin) (Arches) * Project Work	Breakout: DTI - Next Generation (Hans Johnson, C-F Westin) (Deer Valley) * Project Work	10:30-12:00: Algorithms 10:30-10:45 Overview, Ross Whitaker (slides) 10:45-11:00 Statistical models of anatomy and pathology, Polina Golland (slides) 11:00-11:15 Geometric correspondence, Guido Gerig (pdf slides) (ppt slides w movies) 11:15-11:30 User interactive tools for segmentation, Allen Tannenbaum (pdf slides) (pdf slides) 11:30-11:45 Longitudinal and time-series analysis, Martin Styner (slides)	Project Review
12:00-1:00	Lunch	Lunch	Lunch	Lunch	Boxed Lunch and Adjourn
1:00-3:00	1:00 Welcome Ron Kikinis Segment a spine challenge 1:10pm Project Introductions All Project Leads	1-2pm: Breakout: Pathology and Longitudinal Followup (Guido Gerig) (Deer Valley) 2-3pm: Breakout: Particle Shape Correspondence (Martin Styner, Tom Fletcher, Ross Whitaker) (Arches)	Project Work	1:00-2:30 Engineering 1:00-1:15 2010 Highlights, Aims, Architecture, Will Schroeder (slides) 1:15-1:30 End User Platform Slicer 4, Steve Pieper (slides) 1:30-1:45 Computational Platform, CLI, Jim Miller (slides) 1:45-2:00 Data Management Platform, Stephen Aylward (slides) 2:00-2:15 Software Process, Stephen Aylward (slides) 2:30-3:00 Outreach and Training (Sonia Pujol) (slides)
05:00-07:00		4:30-6:30 How to write a loadable module(J2, JC)		6:00 Optional: Beer at Murphy's (like last year)

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 03/11/11)

• 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

• 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

• 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. DONE

6. Task (until 03/16/11)

• 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 04/01/11)

• 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:

8. Task (until 03/18/11)

• Write a container class in Python to save two coordinates (x,y,z) and a radius. OPEN

9. Task (until 03/23/11)

• Write code in Python to do the following: Use the container from Task 8 to save the results from Task 6. So, these two tasks have to be completed before starting this one. Then, extend Task 6 to store the user click and the touch of the diameter in the container. Finally, use the values of the container to probe an intensity value exactly at the following location: the point on the line between the two coordinates in the container and the distance 2*radius from the first coordinate. OPEN

10. Task (until 03/25/11)

• Use the intensity values from the user clicked point of Task 6 and the probed position of Task 9 to calculate a contrast measure between these two points. The measure should be low (less than 50) if the intensity values are similar and high (around 100-200) if the contrast is high. OPEN

11. Task (until 04/15/11)

• Use the output of task 10 as parameter gamma for Frangi's VesselEnhancement. Use also proper values as discussed for alpha and beta. Also, Integrate the click-to-diameter functionality. Then, you should have a parameter free vesselness module where the user only clicks once to configure the filter. OPEN