2009 Summer Project Week Transrectal Prostate biopsy - Revision history

Lasso: /* Design notes for ProstateNav rework */

2009-07-08T15:32:43Z

Design notes for ProstateNav rework

2009-06-26T16:36:40Z

Future steps

2009-06-26T14:33:30Z

Key Investigators

2009-06-26T14:11:20Z

Key Investigators

2009-06-26T13:56:16Z

Key Investigators

2009-06-26T13:49:07Z

Key Investigators

2009-06-26T13:48:15Z

2009-06-26T13:45:39Z

2009-06-26T13:04:45Z

2009-06-24T18:05:50Z

Design notes for ProstateNav rework

@@ Line 68: / Line 68: @@
 *Classes
 **ProstateBiopsyRobotNode (MRMLNode): holds all robot data (current position, current needle, available needles, status, visualization options?, calibration data), sending command to robot
-**RobotDisplayWidget: observes ProstateBiopsyRobotNode and displays the robot in the viewer
+**RobotDisplayWidget: observes ProstateBiopsyRobotNode and displays the robot in the viewer; specific for each robot, show/hide arm, needle, coverage, calibration object
 **ProstateBiopsyNode (MRMLNode): contain all configuration data, OpenIGTLink, DICOM links, screen config, link to the target list (fiducial list), additional properties for each target (which needle, already completed, etc. – one common superclass to hold data for one target)
 **SetupStep
@@ Line 75: / Line 75: @@
 **VerificationStep
 **ManualStep: robot specific
-**RobotWidget: specific for each robot; show/hide arm, needle, coverage, calibration object
 *User interface

@@ Line 42: / Line 42: @@
 ===Future steps===
 *ProstateSeg module
 **Update the tutorial
-**Determine seed points and background points automatically: image center is in prostate, determine approximate bounding sphere for prostate, use shrinked sphere as seed, expanded sphere for background
+**Determine seed points and background points automatically (e.g., image center is in prostate, determine approximate bounding sphere for prostate, use shrinked sphere as seed, expanded sphere for background)
 **Performance improvement
 ***Reuse current result volume as an initial value for the solution to speed up computations after some changes (adding more seed points or background points)
 ***Use multiresolution technique to get a quick approximate result (then use that result as initial value for the full-resolution computation)
 ***Make use of segmentation on pre-operative images
 *ProstateNav module
 **Merge TRProstateBiopsy features into ProstateNav

@@ Line 30: / Line 30: @@
 <div style="width: 40%; float: left;">
 <h3>Progress</h3>
-*Created ProstateSeg module (in NAMICSandBox\Queens\ProstateSeg; command line module, can be used without ProstateNav).
+*Created ProstateSeg module (available in [http://svn.na-mic.org/NAMICSandBox/trunk/Queens/ProstateSeg/ NAMIC SandBox]; command line module, can be used without ProstateNav).
 *Tested on clinical images. Typical computation time is about 10 seconds (requires manually defined seed and background area).
 *Identified potential solutions for automatic seed and background area definition.

@@ Line 30: / Line 30: @@
 <div style="width: 40%; float: left;">
 <h3>Progress</h3>
-*Created ProstateSeg module (command line module, can be used without ProstateNav).
+*Created ProstateSeg module (in NAMICSandBox\Queens\ProstateSeg; command line module, can be used without ProstateNav).
 *Tested on clinical images. Typical computation time is about 10 seconds (requires manually defined seed and background area).
 *Identified potential solutions for automatic seed and background area definition.

@@ Line 24: / Line 24: @@
 <div style="width: 27%; float: left; padding-right: 3%;">
 <h3>Approach, Plan</h3>
-*Prostate segmentation: There are two algorithms (Algorithm 1: Shape based segmentation. The shape of prostates are learned and then the new image is segmented using the shapes learned. Algorithm 2: It is based on the Random Walks segmentation algorithm. It need more human input but the result could be interactively improved arbitrarily close to user's expectation.), integrate both of them into a standalone module.
+*Prostate segmentation: There are two algorithms (Algorithm 1: Shape based segmentation. The shape of prostates are learned and then the new image is segmented using the shapes learned. Algorithm 2: It is based on the Random Walks segmentation algorithm. It need more human input but the result could be interactively improved arbitrarily close to user's expectation.), integrate them into a standalone module.
 *Prostate robotics: Merge the existing modules (select one prostate robotics module as a base, clean it up, design generic robot and scanner interfaces, and integrate functions and specific robot/scanner support parts from the other module), so that all the functionalities will be available for all robots.
 </div>

@@ Line 5: / Line 5: @@
 Image:ProstateSegSeeds.png|ProstateSeg module: seeds.
 Image:ProstateSegResults.png|ProstateSeg module: segmentation result.
 Image:Capture_20090625_205134.png|Result of a needle insertion experiment on a phantom, using Slicer with a transrectal prostate biopsy robot.
 </gallery>
@@ Line 39: / Line 37: @@
 *Tested on clinical images. Typical computation time is about 10 seconds (requires manually defined seed and background area).
 *Identified potential solutions for automatic seed and background area definition.
 *Agreed in high level design for transrectal and transperineal ProstateNav module merge.
 *Prepared the ProstateNav module for the merge (cleaned up the module to contain only device indpendent parts).

@@ Line 3: / Line 3: @@
 Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
 Image:ProstateNavRework.png|Overview of the ProstateNav / TRProstateBiopsy module rework.
-Image:TRPB_ProstateSegmentation.JPG|Prostate segmentation integrated inside TR Prostate biopsy interactive module
+Image:Capture_20090625_205134.png|Result of a needle insertion experiment on a phantom, using Slicer with a transrectal prostate biopsy robot.
 Image:ShapeBasePstSegSlicer.png|Shape base prostate segmentation in Slicer through command line module.
 </gallery>

@@ Line 60: / Line 60: @@
 *Configuration: configure the module (mostly wizard steps) to use the module for different procedures/devices
 *Wizard steps:
-**Start up: check devices, connections -- Robot/scanner specific
+**Start up: select a configuration XML file and check devices, connections. The XML file contains:
-**Segmentation: just an integrated GUI for ProstateSeg module
+***Robot model
-**Calibration -- Robot/scanner specific
+***OpenIGTLink address, DICOM directory/server
-**Planning: enter targets (could be merged with targeting?)
+***Needles
-**Targeting: driving needle to reach targets -- uses robot/scanner specific functions (display of robot parameters, driving robot, scanner)
+***Screen configuration
-**Manual: manual robot/scanner control -- uses robot/scanner specific functions
+**Calibration
-**Verification:
+**Targeting: driving needle to reach targets
 *User interface
 **Secondary monitor support
 *Communication
 **OpenIGTLink for direct scanner connection
 **OpenIGTLink for DICOM communication with the Scanner
 ==References==