AHM2012-3D-US-Slicer-Breakout - Revision history

Tokuda at 19:57, 27 February 2012

2012-02-27T19:57:07Z

Tokuda at 19:55, 27 February 2012

2012-02-27T19:55:56Z

Lasso at 13:51, 19 January 2012

2012-01-19T13:51:38Z

Lasso at 13:46, 19 January 2012

2012-01-19T13:46:45Z

Lasso: /* Meeting minutes */

2012-01-11T18:38:38Z

Meeting minutes

Noby: /* Meeting minutes */

2012-01-11T18:02:38Z

Meeting minutes

Noby: /* Meeting minutes */

2012-01-11T18:00:00Z

Meeting minutes

Ungi: /* Agenda */

2012-01-11T17:55:10Z

Agenda

Noby: /* Agenda */

2012-01-11T17:04:05Z

Agenda

Noby: /* Agenda */

2012-01-11T16:26:02Z

Agenda

@@ Line 1: / Line 1: @@
   [[AHM_2012#Agenda|Back to AHM Schedule]]
 <gallery>
-image:PW-MIT2011.png|Event logo
+Image:AHM2012-3D-US-Slicer-Breakout-Andras.jpg
-image:Panorama-summer-2011.png|[http://360.io/Afjepd Interactive Panorama of Project Week] (Works on chrome, maybe not on other browsers)
+Image:AHM2012-3D-US-Slicer-Breakout-Tamas.jpg
 </gallery>

← Older revision		Revision as of 19:55, 27 February 2012
Line 1:		Line 1:
	[[AHM_2012#Agenda\|Back to AHM Schedule]]		[[AHM_2012#Agenda\|Back to AHM Schedule]]
		+
		+
		+	[[Image:AHM2012-3D-US-Slicer-Breakout-Andras.jpg]]
		+	[[Image:AHM2012-3D-US-Slicer-Breakout-Tamas.jpg]]
		+
		+	<gallery>
		+	image:PW-MIT2011.png\|Event logo
		+	image:Panorama-summer-2011.png\|[http://360.io/Afjepd Interactive Panorama of Project Week] (Works on chrome, maybe not on other browsers)
		+	</gallery>
		+

	=Objective=		=Objective=

@@ Line 83: / Line 83: @@
 #*CUDA-only is a limitation (no MacOS, nVidia-only), OpenCL would be better
 #**could we bypass CPU?
-#**image source is coming from Ethernet, that could be a bottleneck
+#**image source is coming from Ethernet, that could be a bottleneck - image compression could help (images or image differences could be probably efficiently compressed)
 #**if volume has to be imported into Slicer then the data should be in RAM, not enough to directly send to GPU
 #Junchi Tokuda

@@ Line 39: / Line 39: @@
 #Andras presentation
-#PLUS library
+#*PLUS library
-#	Based on Synchrograb
+#**Based on Synchrograb and its extensions developed at Queen's (QueensOpenIGTLibs) and Robarts (4D Ultrasound module in NAMIC sandbox repository)
-#	Acquire, process, transfer synchronized ultrasound images and position data
+#**Acquire, process, transfer synchronized ultrasound images and position data
-#		Specialized Open IGT Link QueensOpenIGTLibs
+#**Streaming to applications through OpenIGTLink
-#			Separate effort from OPEN IGT Link
+#**Features: calibration (*), B-mode (analog framegrabber or Ultrasonix research interface) and RF-mode (Ultrasonix research interface) image capturing, support for multiple hardware devices
-#			[NH question] any effort toward integration
+#*Sample data can be incorporated without hardware
-#		4D Ultrasound module in NAMIC sandbox repository (*)
+#*Supported hardware: basic image and position data acquisition is available for many devices (any US imaging device with analog output, Ascension, NDI, Claron trackers, brachytherapy steppers), sounds very attractive to most of the investigators
-#	Features: calibration (*), B-mode imaging capturing (video?) RF?, support for multiple hardware devices
+#***Elvis Chen developed a DirectShow video source in VTK, it could be integrated as well ([https://www.assembla.com/spaces/plus/tickets/364 see follow-up])
-#Sample data can be incorporated w/o hardware
+#*Standalone solution: can be downloaded and used as is (binary package is available), device SDK and drivers mostly available only for Windows
-#Supported hardware (not defined well, but sounds very attractive to most of the investigators)
+#*3D Slicer can visualize data that is sent through OpenIGTLink
-#Standalone solution: Device SDK, and drivers
+#*Temporal calibration
-#3D Slicer module
+#**Without that the time offset between position andCorrect 150 msec
-#Temporal calibration
+#**Change detection methods (already available, not very robust)
-#	Change detection methods
+#**Correlation-based ([https://www.assembla.com/spaces/plus/tickets/346 WIP])
-#	Correlation-based (**)
+#*File format: sequence metafile (metaimage with custom fields). We need I/O for this in Slicer, we need module in Slice to handle this kind of data ([https://www.assembla.com/spaces/plus/tickets/421-create-a-sequence-metafile-importer-for-3d-slicer see follow-up])
-#	Correct 150 msec
+#*2D+t data can be interpreted as single-slice-3D+t data. Therefore visualization could be the same as for 3D+t (4D) data
-#File format sequence metafile….. **** we need I/O for this in Slicer, we need module in Slice to handle this kind of data
+#*2D+t as primitive would be useful in Slicer
-#Question… effort to visualize 4D data in Slicer, frames grabbed how does this relates to 4D Volume, or shall we handle this as single frame?
+#*Logging: there is already good support for storing of all events and acquired data in the library
-#2D+t as primitive needed in Slicer?
+#Tamas Ungi
-#Logging ---- within library
+#*Plus image acquisition and data transfer to Slicer
+#*OpenIGTLink send cords of needle and image
+#*2D image primitive with vtkImage updated in the 3D viewer
-#Tamash
+#*images are thrown away (a module could be easily created to record them)
+#*What is needed
-#PLUS image acquisition and data transfer to Slicer
+#**Tracker-model registration module, OR IGT transformation module
-#Open IGT Link send cords of needle and image
+#**Time
-#2D image primitive with vtkImage updated
+#**Recording / replay functions
 #Mehdi Moradi
-#	Prostate cancer
+#*Prostate cancer, ultrasound for tissue characterization
-#	Elastography. Not so much in Slicer. Good platform for translational research
+#*2D+t ultrasound (B or RF) for tissue characterization, elastography
-#	Technical issue
+#*Slicer could be a good platform for translational research, but not so much support for these yet
+#*Technical issues
-#Elvin Cheng
+#**No access to Nucletron's brachy stepper
-#VTK Volume Rendering using CUDA
+#**No access to many ultrasound imaging devices
-#CUDA capable video , CUDA capable driver, SDK,
+#Elvis Chen
-#Qt
+#*VTK Volume Rendering using CUDA
-#Implementation to Slicer 4 in plan
+#*CUDA capable video, CUDA capable driver, SDK are needed
-#Widget support for multi-dimensional transfer function = CTK
+#*Qt
-#Transfer-function tuning
+#*Implementation to Slicer 4 in plan => discuss with Julien Finet
+#*Widget support for multi-dimensional transfer function = CTK
-#Junchi Tokuda presented
+#*Transfer-function tuning
-#4D module, which bundles multiple volumetric data (stored in MRML) and create a 4D volume
+#*Streaming data to GPU is challenging
-#DWI users of 4D image dataset per se.
+#*CUDA-only is a limitation (no MacOS, nVidia-only), OpenCL would be better
-#Population study uses 3D + N
+#**could we bypass CPU?
+#**image source is coming from Ethernet, that could be a bottleneck
-#We agreed that the two approaches should be tried
+#**if volume has to be imported into Slicer then the data should be in RAM, not enough to directly send to GPU
-#	DWI based approach where one MRML node contains all images
+#Junchi Tokuda
-#	Junichi’s node where multiple separate volume is bundled
+#*4D module, which bundles multiple volumetric data (stored in MRML) and create a 4D volume
+#*Use cases for multi-dimensional data
+#**TEE-guided surgery
+#**2D+t live ultrasound
-Plus
+#**2D+t ultrasound (B or RF) for tissue characterization, elastography
-*IGSTK similar
+#**4D US/MRI registration
-*windows-only
+#**Population study uses 3D + N
-*DirectShow video source
+#*We agreed that the two approaches should be tried for multi-dimensional data
+#**4D image dataset per se: DWI based approach where one MRML node contains all images
-OpenIGTLink
+#**Bundle of nodes: Junichi’s node where multiple separate volume is bundled (as it is done for DCE-MRI)
-*single-slice display: similar in LiveUltrasound and OpenIGTLinkIF module => in Slicer4 OpenIGTLinkIF should be enough
+#***bundle node with pointers, so there is no need for memory copy
+#***not just 4D images, but it can be used for any other nodes (transforms, models, ...)
-Ultrasound for tissue characterization
+#***bundles of bundles: arbitrary paremeters (not just t), arbitrary number of bundles could be possible (4D, 5D, 6D, ... data sets can be supported)
-*2D+t ultrasound (B or RF) for tissue characterization, elastography
+#***time (parameter) points should be stored (node attributes can be used for this)
-*Problems
+#*Custom data IO would be useful for sequence metafiles, NRRD files or other multidimensional file formats
-**No access to Nucletron's brachy stepper
+#*OpenIGTLink
-**No access to many ultrasound imaging devices
+#**Single-slice display: similar in LiveUltrasound and OpenIGTLinkIF module => in Slicer4 OpenIGTLinkIF should be enough

← Older revision		Revision as of 18:38, 11 January 2012
Line 93:		Line 93:
	# DWI based approach where one MRML node contains all images		# DWI based approach where one MRML node contains all images
	# Junichi’s node where multiple separate volume is bundled		# Junichi’s node where multiple separate volume is bundled
		+
		+
		+
		+	Plus
		+	*IGSTK similar
		+	*windows-only
		+	*DirectShow video source
		+
		+	OpenIGTLink
		+	*single-slice display: similar in LiveUltrasound and OpenIGTLinkIF module => in Slicer4 OpenIGTLinkIF should be enough
		+
		+	Ultrasound for tissue characterization
		+	*2D+t ultrasound (B or RF) for tissue characterization, elastography
		+	*Problems
		+	**No access to Nucletron's brachy stepper
		+	**No access to many ultrasound imaging devices
		+
		+
		+	4D data - overlapping efforts!
		+	*4D node:
		+	**DWI-like
		+	**DCE-MRI
		+	*bundle node with pointers
		+	**4D ultrasound
		+	**4D images
		+	**bundles of bundles, arbitrary paremeters (not just t), arbitrary nodes, arbitrary number of bundles could be possible
		+	*time (parameter) points should be stored: there could be a subclass with additional
		+	*custom data IO would be useful for sequence metafiles, NRRD files or other xD+t file formats
		+
		+	Volume rendering
		+	*Elvis' GPU renderer=> discuss with Julien Finet
		+	*streaming data to GPU is challenging
		+	*CUDA-only is a limitation (no MacOS, NVidia-only), OpenCL would be betterbetter
		+	**could we bypass CPU?
		+	**image source is coming from Ethernet, that could be a bottleneck
		+	**if volume has to be imported into Slicer then the data should be in RAM, not enough to directly send to GPU
		+
		+	Use cases
		+	*TEE-guided surgery
		+	*2D+t live ultrasound
		+	*2D+t ultrasound (B or RF) for tissue characterization, elastography
		+	*4D US/MRI registration

← Older revision		Revision as of 18:00, 11 January 2012
Line 36:		Line 36:
	*11:30-12:00, Group statement, Action Plan, Plan for the next events		*11:30-12:00, Group statement, Action Plan, Plan for the next events

−	~~=Meeting minutes=~~
	=Meeting minutes=		=Meeting minutes=

@@ Line 18: / Line 18: @@
 *8:20-8:35, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso ([[media:PlusIntro2012Jan.pdf |slides]])
 **Keywords: Plus framework, applications, spatial & temporal calibration, volume reconstruction, ECG
-*Project introduction 2, Tamas Ungi, Tracked real-time 2D ultrasound in Slicer (LiveUltrasound).
+*Project introduction 2, Tamas Ungi, Tracked real-time 2D ultrasound in Slicer (LiveUltrasound) ([[media:LiveUltrasound2012Jan.pdf |slides]])
 **Keywords: OpenIGTLink, needle guidance
 *Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging. The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. We want to integrate the BK RF streaming module with the PLUS/Slicer development.

@@ Line 26: / Line 26: @@
 **Keywords: CUDA, volume rendering, transfer function
 *Project introduction 4, Laurent Chauvin, 4D US rendering
-**Keywords:
+**Keywords: 4D volume rendering, recording/replay
 *Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
 **Keywords: OpenIGTLink, 4D Image Module
@@ Line 38: / Line 35: @@
 *11:00-11:30, Summary of current US projects, Breakdown of core technologies, Identifying unmet needs,
 *11:30-12:00, Group statement, Action Plan, Plan for the next events
 =Meeting minutes=

← Older revision		Revision as of 16:26, 11 January 2012
Line 41:		Line 41:

	=Meeting minutes=		=Meeting minutes=
−	~~=Agenda=~~
−
−	*8:10-8:20, Welcome, Goal of the meeting, Meeting logistics, Note taking in wiki
−	*8:20-8:35, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso ([[media:PlusIntro2012Jan.pdf \|slides]])
−	**Keywords: Plus framework, applications, spatial & temporal calibration, volume reconstruction, ECG
−	*Project introduction 2, Tamas Ungi, Tracked real-time 2D ultrasound in Slicer (LiveUltrasound).
−	**Keywords: OpenIGTLink, needle guidance
−	*Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging. The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. We want to integrate the BK RF streaming module with the PLUS/Slicer development.
−	*short break
−
−	*Project introduction 3, Elvis Chen, GPU volume rendering. We have developed (clean room implementation) a stand-along, CUDA-based, VTK class for volume rendering. It is meant to be a drop-in replacement for vtkVolumeMapper. In addition, we implemented multi-dimentional transfer function, allowing much concise pixel-classification and visualization. Video demo will be given, source code will be made available.
−	**Keywords: CUDA, volume rendering, transfer function
−	*Project introduction 4, Laurent Chauvin, 4D US rendering
−	**Keywords:
−
−
−	**Keywords:
−	*Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
−	**Keywords: OpenIGTLink, 4D Image Module
−	*Project introduction 7, Nobuhiko Hata, review of U.S. US efforts
−	**Keyword: JHU efforts, BWH efforts, more...
−
−
−	*11:00-11:30, Summary of current US projects, Breakdown of core technologies, Identifying unmet needs,
−	*11:30-12:00, Group statement, Action Plan, Plan for the next events
−
−
	=Meeting minutes=		=Meeting minutes=