AHM2009:JHU - Revision history

Sidd queens: /* Detailed Information about the Pipeline */

2009-01-08T15:25:13Z

Detailed Information about the Pipeline

Gabor: /* Detailed Information about the Pipeline */

2009-01-08T04:56:20Z

Detailed Information about the Pipeline

Gabor: /* Detailed Information about the Pipeline */

2009-01-08T04:51:54Z

Detailed Information about the Pipeline

Gabor at 04:47, 8 January 2009

2009-01-08T04:47:15Z

Gabor at 04:32, 8 January 2009

2009-01-08T04:32:05Z

Sidd queens at 22:36, 7 January 2009

2009-01-07T22:36:14Z

Sidd queens at 22:35, 7 January 2009

2009-01-07T22:35:36Z

Sidd queens at 19:54, 7 January 2009

2009-01-07T19:54:53Z

Sidd queens at 19:53, 7 January 2009

2009-01-07T19:53:57Z

Sidd queens at 19:53, 7 January 2009

2009-01-07T19:53:37Z

@@ Line 58: / Line 58: @@
 The steps in the workflow are as follows:
 #'''Calibration:'''
-#:This is the first step in workflow. The objective is to register the image to the robot via MR fiducials. For this, first a MR scan (calibration volume) is done to optimally image the fiducials. The volume is loaded up inside SLICER, from the TR Prostate Biopsy module's wizard GUI. The registration method is based on first segmenting the fiducials as seen in image. The segmentation algorithm developed by Csaba/Axel at Johns Hopkins, primarily uses morphological operations to localize the fiducials. The parameters of segmentation are available on wizard GUI; these include: approximate physical dimensions of fiducials, thresholds. The semi-automatic segmentation process is initiated by user providing one click each per fiducial. After the fiducials are segmented, the registration is triggered automatically inside, which uses prior knowledge about mechanical design of the device, and knowledge of placement of fiducials. The registration algorithm finds two axis lines (one per pair of fiducials), and computes the angle and distance between those axes. The segmentation, and registration results are displayed in GUI. The registration results (angle and distance between axes) are bench-marked against the mechanically measured ground truth. If the user/clinician are not happy with the results, he/she can modify the parameters and do re-segmentation and recalculate registration.[[Image:TRProstateBiopsy Calibration.JPG|thumb|320px|center|Calibration step GUI.]]
+#:This is the first step in workflow. The objective is to register the image to the robot via MR fiducials. For this, first a MR scan (calibration volume) is done to optimally image the fiducials. The volume is loaded up inside SLICER, from the TR Prostate Biopsy module's wizard GUI. The registration method is based on first segmenting the fiducials as seen in image. The segmentation algorithm developed by Csaba/Axel at Johns Hopkins, primarily uses morphological operations to localize the fiducials. The parameters of segmentation are available on wizard GUI; these include: approximate physical dimensions of fiducials, thresholds. The semi-automatic segmentation process is initiated by user providing one click each per fiducial. After the fiducials are segmented, the registration is triggered automatically inside, which uses prior knowledge about mechanical design of the device, and knowledge of placement of fiducials. The registration algorithm finds two axis lines (one per pair of fiducials), and computes the angle and distance between those axes. The segmentation, and registration results are displayed in GUI. The registration results (angle and distance between axes) are bench-marked against the mechanically measured ground truth. If the user/clinician is not happy with the results, he/she can modify the parameters and do re-segmentation and recalculate registration.[[Image:TRProstateBiopsy Calibration.JPG|thumb|320px|center|Calibration step GUI.]]
 #'''Segmentation:'''
 #:After the robot is registered, the next step (press next on wizard workflow) is to acquire prostate volume, and segment prostate (Algorithm by Yi Gao/ Allen Tannenbaum GeorgiaTech)[[Image:TRPB_ProstateSegmentation.JPG|thumb|320px|center|Segmentation.]]

@@ Line 61: / Line 61: @@
 #'''Segmentation:'''
 #:After the robot is registered, the next step (press next on wizard workflow) is to acquire prostate volume, and segment prostate (Algorithm by Yi Gao/ Allen Tannenbaum GeorgiaTech)[[Image:TRPB_ProstateSegmentation.JPG|thumb|320px|center|Segmentation.]]
-#'''Registration (MR1, MR2,...MRSI -- forthcoming:'''
+#'''Registration:'''
 #'''Targeting:'''
 #:In this step, clinician marks biopsy targets (by click). The robot rotation angle and needle angle is computed along-with needle trajectory and depth (automatically). The information about the target's RAS location, and the needle targeting parameters is populated in the list in wizard GUI. Selecting a particular target in the list brings the target in view in all three slices. Multiple targets can be marked. The clinician selects the target to perform biopsy on. The clinician then dials in the rotation angle, and needle angle on the device, and performs the biopsy. The sensor data from the optical encoders on the robot is continuously read and updated on the SLICER's slice views, about the current depth/orientation of needle. [[Image:TRProstateTargeting.jpg|thumb|320px|center|Trajectory calculation from target locations]]
 #'''Verification:'''
-#:After, the needle is in, a confirmation scan is taken to verify actual biopsy locations against the planned targets. The verification volume is loaded in SLICER from module GUI. The user picks up the target to validated from the list, and then clicks at two needle ends to mark the needle. The distance and angle errors are calculated and populated in the list. [snapshot]
+#:After, the needle is in, a confirmation scan is taken to verify actual biopsy locations against the planned targets. The verification volume is loaded in SLICER from module GUI. The user picks up the target to validated from the list, and then clicks at two needle ends to mark the needle. The distance and angle errors are calculated and populated in the list. [Work in progress...]
 Currently, we have implemented the GUI of all the steps in workflow. The functionality of calibration step is complete. The functionality of segmentation step is being implemented during the project week, working in coordination with Yi/Allen. We are in the process of implementing functionality for the rest of steps.

@@ Line 61: / Line 61: @@
 #'''Segmentation:'''
 #:After the robot is registered, the next step (press next on wizard workflow) is to acquire prostate volume, and segment prostate (Algorithm by Yi Gao/ Allen Tannenbaum GeorgiaTech)[[Image:TRPB_ProstateSegmentation.JPG|thumb|320px|center|Segmentation.]]
 #'''Targeting:'''
 #:In this step, clinician marks biopsy targets (by click). The robot rotation angle and needle angle is computed along-with needle trajectory and depth (automatically). The information about the target's RAS location, and the needle targeting parameters is populated in the list in wizard GUI. Selecting a particular target in the list brings the target in view in all three slices. Multiple targets can be marked. The clinician selects the target to perform biopsy on. The clinician then dials in the rotation angle, and needle angle on the device, and performs the biopsy. The sensor data from the optical encoders on the robot is continuously read and updated on the SLICER's slice views, about the current depth/orientation of needle. [[Image:TRProstateTargeting.jpg|thumb|320px|center|Trajectory calculation from target locations]]
@@ Line 68: / Line 69: @@
 Currently, we have implemented the GUI of all the steps in workflow. The functionality of calibration step is complete. The functionality of segmentation step is being implemented during the project week, working in coordination with Yi/Allen. We are in the process of implementing functionality for the rest of steps.
 This module provides a demonstration of how Slicer modules can be created for specific interventional devices.
 ==Software & documentation==

@@ Line 24: / Line 24: @@
 <center>
 {|
-|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|350px|MR-compatible Trans-Rectal Prostate Robot.]]
+|valign="top"|[[Image:TRProstateCalibration.jpg|thumb|360px|Fiducial calibration of interventional robot]]
 |[[Image:TRPB_ProstateSegmentation.JPG|semi-automatic prostate segmentation|thumb|400px]]
 |}
@@ Line 31: / Line 31: @@
 <center>
 {|
-|[[Image:TRProstateCalibration.jpg|thumb|360px|Fiducial calibration of interventional robot]]
+|valign="top"|[[Image:TRProstateBiopsyRobot.jpg|thumb|350px|MR-compatible Trans-Rectal Prostate Robot.]]
-|valign="top"|[[Image:TRProstateTargeting.jpg|thumb|360px|Trajectory calculation from target locations]]
+|[[Image:TRProstateTargeting.jpg|thumb|360px|Trajectory calculation from target locations]]
 |}
 </center>

@@ Line 3: / Line 3: @@
 __NOTOC__
 ==JHU Roadmap Project==
 <center>

@@ Line 44: / Line 44: @@
 #:After the robot is registered, the next step (press next on wizard workflow) is to acquire prostate volume, and segment prostate (Algorithm by Yi Gao/ Allen Tannenbaum GeorgiaTech)[[Image:ShapeBasedProstateSegmentationResult.png|thumb|320px|center|Segmentation.]]
 #'''Targeting:'''
-#:In this step, clinician marks biopsy targets (by click). The robot rotation angle and needle angle is computed along-with needle trajectory and depth (automatically). The information about the target's RAS location, and the needle targeting parameters is populated in the list in wizard GUI. Selecting a particular target in the list brings the target in view in all three slices. Multiple targets can be marked. The clinician selects the target to perform biopsy on. The clinician then dials in the rotation angle, and needle angle on the device, and performs the biopsy. The sensor data from the optical encoders on the robot is continuously read and updated on the SLICER's slice views, about the current depth/orientation of needle. [snapshot]
+#:In this step, clinician marks biopsy targets (by click). The robot rotation angle and needle angle is computed along-with needle trajectory and depth (automatically). The information about the target's RAS location, and the needle targeting parameters is populated in the list in wizard GUI. Selecting a particular target in the list brings the target in view in all three slices. Multiple targets can be marked. The clinician selects the target to perform biopsy on. The clinician then dials in the rotation angle, and needle angle on the device, and performs the biopsy. The sensor data from the optical encoders on the robot is continuously read and updated on the SLICER's slice views, about the current depth/orientation of needle. [[Image:TRProstateTargeting.jpg|thumb|320px|Trajectory calculation from target locations]]
 #'''Verification:'''
 #:After, the needle is in, a confirmation scan is taken to verify actual biopsy locations against the planned targets. The verification volume is loaded in SLICER from module GUI. The user picks up the target to validated from the list, and then clicks at two needle ends to mark the needle. The distance and angle errors are calculated and populated in the list. [snapshot]