NAMIC Wiki - User contributions [en]

Slicer3:Volume Rendering With Cuda

2008-05-12T12:37:18Z

Bensch: /* Feature Wishlist */

= Overview =
On this page a description of the ''Volume Rendering algorithm with CUDA For Slicer3'' is presented.
A link to the IGT project page can be found on [[Slicer-IGT/GPU-IGT]].

Involved in this projects are Benjamin Grauer (integration into vtk/Slicer3), Nicholas Harlambang (cuda algorithms) and Nobuhiko Hata (project supervisor).

== Objective ==
The goal of this project is to implement a CUDA based Volume Rendering Technique inside of [http://www.vtk.org VTK] and Slicer3.

== Project Outline ==
Several steps have to be made to integrating a CUDA based volume rendering technique into vtk.
#Implement and Integrate a '''CUDA Volume Rendering algorithm'''.
#Integrate '''CUDA runtime API''' support into VTK using a class based approach.
#Integrate the algorithm into a '''VTK pipeline''' (described below)
#Create a '''user interface''' to control the flow of the Volume Rendering within Slicer3.

= Cuda Volume Rendering Algorithm =
The Code that we use so far has been implemented by Nicholas Harlambang and can be viewed at [http://svn.orxonox.net/subprojects/volrenSample].

== Feature Wishlist ==
{| border=1 cellspacing
|- bgcolor="#9badcf"
! Relevance || Feature || Status || Dependency || Description
|-
| +++ || Z-Buffer || 80% || Current Z-buffer to CUDA || Render and stop at the Z-buffer information
|-
| ++ || Different Data Types || 100% || || uchar, char, float, double, short, ushort, int
|-
| +++ || Sample Distance || 80% || || The sampling step distance along the ray.
|-
| ++ || Transfer Function || 100% || ||
|-
| + || Lighting Model || 30% || ||
|-
| = || Multiple Lights || 0% || ||
|-
| - || Shading Model || 0% || Lighting Model || Use Shaders to render
|-
| +++ || Perspective and Planar Projection || 100% || || Perspective Projection using vtkCamera Projection Matrix
|-
| = || Memory To Texture || 100% || || Render CUDA directly onto Texture (for GeForce Cards only)
|-
| - || Partial Memory Update || 50% || || Partial Updates of the Input data for animation
|-
| -- || vtkCudaVolumeProperty || 100% || Transfer Function, || Implement all the features of [http://public.kitware.com/VTK/doc/release/4.0/html/classvtkVolumeProperty.html vtkVolumeProperty]
|-
| - || Animation || 100% || Partial Memory Update || 4D Animated Image Data
|-
| + || No more static Symbols || 80% || || Remove the need of all c-style static Symbols in the CUDA code
|-
| --- || Multicore/GPU implementation || 0% || Everything else || Multicore implementation of the Cuda Rendering
|-
| -- || Gradients || ?% || ||
|}

= VTK Cuda Runtime API support =
The c-interface to the CUDA objects and functions will be wrapped in a safe object oriented VTK-C++ class hierarchy.
*[[VTK Cuda Wrapper Classes]]
*[[VTK Cuda Memory Management Classes]]

== Cuda Memory ==
Cuda memory comes in different shapes and forms:
*'''Host Memory''': Non-Paged Memory on the host side for fast interaction with the CUDA devices. see ''vtkCudaHostMemory.h''
*'''Linear Memory''': Linerely arranged memory on the CUDA device. see ''vtkCudaMemory.h''
*'''Pitch Memory''': 2D memory arrays that are aligned in the correct fashion for a fast interaction on the cuda devices. (Arranged over the memory banks for quick access). see ''vtkCudaMemoryPitch.h''
*'''Array Memory''': Arrays allocated over the CUDA API. see ''vtkCudaMemoryArray.h''
*'''Texture Memory''': Not discussed here. see [[VTK Cuda Wrapper Classes]]
All these memories are derived from a base class (see ''vtkCudaMemoryBase.h'') as shown in the following picture:

[[Image:vtkCudaMemoryManagementClassDiagram.png|frame|none|Cuda Memory Class Diagram]]

= VTK Modules and Pipeline =
These are the modules that will be created in order to integrate a Cuda based Volume Rendering into the Slicer3 pipeline
# '''A [http://www.vtk.org/doc/release/5.0/html/a01572.html vtkImageReader]:''' to read Volume data as any kind of Volume Data
# '''A [[vtkCudaImageFilter]]:''' A Filter to convert from the reader output to a cuda-able DataSet
# '''A [[vtkCudaDataSet]]:''' A new vtkDataSet where that holds and handles the data transfer from and to one or multiple CUDA devices.
# '''A [[vtkCudaVolumeMapper]]:''' A new vtkVolumeMapper that renders the scene using the
## lighting model
## a prepared Z buffer
## a camera position
## A [[http://www.vtk.org/doc/release/5.0/html/a02096.html vtkTexture]] and a Plane to render the result to
# '''An actor''' that places the volume into the scene
# Chain this '''pipeline''' together and attach it to a rendering window.

In the following image the pipeline is displayed together with the connections from the VTK, Slicer3 and CUDA frameworks.
[[Image:VtkCudaVolumeRenderingPipeline.png|frame|none|500px|CUDA Volume Rendering Pipeline]]

Description:
* The '''Fat''' line displays the pipeline flow.
* Green colored fields are classes from the Slicer3 or vtk implementation
* Red colored fields are CUDA and hardware specific parts
* Blue colored fields are specially implemented parts for the communication of cuda and vtk and the volume rendering algorithms.

= A Slicer3 User Interface =
The GUI will be designed using KWWidgets. With this the user will be able to change the rendering resolution, step size, control the color sceme and load and store further information.

= Tasks and Timeline =
== Tasks and Completion ==
{| border=1 cellspacing
|- bgcolor="#9badcf"
! Task
! colspan=3 | Status
|- bgcolor="#bbddff"
|colspan=3 | Overall Status
| rowspan=20 valign="top" | 75%
|-

|- bgcolor="#ddffff"
|colspan=2 | Integrate into VTK
| rowspan=4 valign="top" | 85%
|-
|VTK Memory Class Definitions || 90%
|-
|VTK Access Classes || 80%
|-
|VTK Algorithm || 90%
|-

|-bgcolor="#ddffff"
|colspan=2 bgcolor="#ddffff" | CUDA Volume Rendering Algorithm
| rowspan=4 valign="top" bgcolor="#ddffff" | 80%
|-
|Adapt to Z-buffer || 70%
|-
|Adapt lighting model || 0%
|-
|Adapt to input Image || 100%
|-

|- bgcolor="#ddffff"
|colspan=2 | Integration into Slicer
| rowspan=4 valign="top" | 80%
|-
|Integrate as a Module || 100%
|-
| GUI || 90%
|}

== Timeline ==
{| border="1"
|- bgcolor="#abcdef"
! From !! To !! Task
|-
| 12/14/07 || 05/31/08 || Master Thesis Duration
|-
| 12/14/07 || 12/31/07 || Reading into the Project, Defining Basic Classes
|-
| 01/01/08 || 01/06/08 || Basic Class Definition Ready for Hands on Meeting
|-
| 01/07/08 || 01/12/08 || Hands on meeting in Salt Lake City
|-
| 01/14/08 || 02/01/08 || Further Implementation
|-
| 05/01/08 || 29/05/08 || Write Master Thesis
|-
| 06/14/08 || || Hand in Masters Thesis in Zurich
|}

== Progress ==
See the daily progress [http://www.google.com/notebook/public/08097279861700679221/BDQdBIgoQ1czeruoi?hl=en here].
* (01/03/08): Successfully proved that CUDA runs inside of Slicer3 with the code from Nicholas Harlambang
* (02/01/08): Cuda inside of Slicer3 and external Application, 4D imaging
* (02/05/08): Integration Rendering with Cuda Code and Transfer Functions
* (02/11/08): Integration with Network Module [[OpenIGTLink]] See [http://people.ee.ethz.ch/~grauerb/Slicer3/openIGTLinkCuda02_02.htm here]
* (03/06/08): Model is aligned correctly in Slicer RAS space.

=Resources=
#For testing purposes: [[Image:Heart256.raw]] Store this file in Slicer3/Modules/VolumeRenderingCuda/Testing/heart256.raw
#Also checkout the main project page at [[Slicer-IGT/GPU-IGT]]
#Currently I am working in this branche: http://www.na-mic.org/svn/Slicer3/branches/cuda
##on CudaSupport: [http://www.na-mic.org/svn/Slicer3/branches/cuda/Modules/VolumeRenderingCuda Libs/CudaSupport]
##and CudaVolumeRendering: [http://www.na-mic.org/svn/Slicer3/branches/cuda/Modules/VolumeRenderingCuda Modules/VolumeRenderingCuda]

==People Involved==
* Nobuhiko Hata: SuperVisor
* Nicholas Harlambang: Implementer of the Cuda Code and Algorithms
* Benjamin Grauer: Implementer of the VTK/Cuda integration and CudaSupport Library
* Andreas Freudling: First Implementation of Volume Rendering in Slicer3 and great supporter

==Screen Captures==
<gallery>
Image:FirstCudaVolumeRenderInSlicer3.png|The First Volume Render using CUDA within the Slicer Window
Image:First4DVolumeRenderInSlicer3.png|The First 4D Volume Rendering in CUDA using VTK
Image:CudaIntegrationMethodHead.png|The First Volume Render using CUDA within the Slicer Window
Image:CudaIntegrationMethodInterpolationHead.png|Volume Rendered Head with a Interpolation Smoother
</gallery>

Slicer3:4DUltrasound 4D US

2008-04-18T19:09:53Z

Bensch: /* Video */

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the '''Ultrasound Server''' is retrieving images based on the position of the scanner.
The '''computer's server software''' supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the '''OpenIGTLink''', the network protocol of 3D Slicer.

Finally '''3D Slicer''' visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

= Media =
== Video ==
Check out the [http://people.ee.ethz.ch/~grauerb/Slicer3/ROD/US_Data_with_Tool_FULL.htm Screen Capture Video] of the Ultrasound Module or [[Media:US_ScreenCaptureUsingZBuffer.zip|download as ZIP file]].

== Images ==
[[Image:US_Photoseries_1.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_2.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_3.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_4.png|thumb|200px|left|Scanner working with Slicer3]]

File:US ScreenCaptureUsingZBuffer.zip

2008-04-18T19:07:58Z

Bensch:

Slicer3:4DUltrasound 4D US

2008-04-18T19:03:01Z

Bensch: /* Video */

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the '''Ultrasound Server''' is retrieving images based on the position of the scanner.
The '''computer's server software''' supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the '''OpenIGTLink''', the network protocol of 3D Slicer.

Finally '''3D Slicer''' visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

= Media =
== Video ==
Check out the [http://people.ee.ethz.ch/~grauerb/ROD/US_Data_with_Tool_FULL.htm Screen Capture Video] of the Ultrasound Module or [[Media:US_Data.rar|download as RAR file]].

== Images ==
[[Image:US_Photoseries_1.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_2.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_3.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_4.png|thumb|200px|left|Scanner working with Slicer3]]

Slicer3:4DUltrasound 4D US

2008-04-18T18:59:53Z

Bensch: /* Media */

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the '''Ultrasound Server''' is retrieving images based on the position of the scanner.
The '''computer's server software''' supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the '''OpenIGTLink''', the network protocol of 3D Slicer.

Finally '''3D Slicer''' visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

= Media =
== Video ==
Check out the [http://people.ee.ethz.ch/~grauerb/ROD/US_Data_with_Tool_FULL.htm Screen Capture Video] of the Ultrasound Module
== Images ==
[[Image:US_Photoseries_1.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_2.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_3.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_4.png|thumb|200px|left|Scanner working with Slicer3]]

Slicer3:4DUltrasound 4D US

2008-04-18T18:57:54Z

Bensch: /* Media */

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the '''Ultrasound Server''' is retrieving images based on the position of the scanner.
The '''computer's server software''' supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the '''OpenIGTLink''', the network protocol of 3D Slicer.

Finally '''3D Slicer''' visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

= Media =
[[Image:US_Photoseries_1.png|thumb|200px|none|Scanner working with Slicer3]]
[[Image:US_Photoseries_2.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_3.png|thumb|200px|left|Scanner working with Slicer3]]
[[Image:US_Photoseries_4.png|thumb|200px|left|Scanner working with Slicer3]]

File:US Photoseries 4.png

2008-04-18T15:06:56Z

Bensch:

File:US Photoseries 3.png

2008-04-18T15:06:45Z

Bensch:

File:US Photoseries 2.png

2008-04-18T15:06:32Z

Bensch:

File:US Photoseries 1.png

2008-04-18T15:06:19Z

Bensch:

Slicer3:4DUltrasound 4D US

2008-04-18T15:05:38Z

Bensch:

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the '''Ultrasound Server''' is retrieving images based on the position of the scanner.
The '''computer's server software''' supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the '''OpenIGTLink''', the network protocol of 3D Slicer.

Finally '''3D Slicer''' visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

= Media =
[[Image:US_Photoseries_1.png|frame|none|Scanner working with Slicer3]]
[[Image:US_Photoseries_2.png|frame|none|Scanner working with Slicer3]]
[[Image:US_Photoseries_3.png|frame|none|Scanner working with Slicer3]]
[[Image:US_Photoseries_4.png|frame|none|Scanner working with Slicer3]]

Slicer Training Volume Rendering

2008-03-27T18:53:38Z

Bensch: /* More Information */

Slicer Training Volume Rendering

2008-03-27T17:42:29Z

Bensch: /* More Information */

= Volume Rendering =
== Get It Running ==
#To get volume rendering to work within '''3D Slicer''' we have to make sure that a '''MRML node''' with '''Volumetric Data''' exists.
#If not a new set of volume data must be loaded. For this demo we will load the tutorial data found [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip here].
##'''Download and Uncompress''' this folder
##In 3D Slicer go to '''File -> Load Scene'''
##Select the ''tutorial.xml''
#Now select the '''VolumeRendering Module'''.
#Select a valid volume as the '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

The Volume Rendering will be initialized. Have patience....

== Parameters ==
=== Performance Triggers ===
[[Image:Slicer3_VolRen_Performance.png|thumb|right|Volume Rendering - Performance]]
You can adjust the performance of volume rendering by enabling and disabling quality improvements.
The Volume Rendering Module has '''three performance levels'''
#Low Resolution Hardware Rendering (worst - fastest)
#Full Resolution Hardware Rendering
#Software Rendering (best - slowest)
When all of them are selected slicer uses the low resolution when the camera is moving or nodes in the scene are changing and when nothing is changing anymore the high resolution volume is performed.

The FPS tag lets slicer decide what resolution should be used to produce an interactive experience.

=== Cropping ===
With cropping the volume can be limited to a certain area.
This is useful if a surgeon only wants to see a certain part of the volume or cut at an exact plane.
[[Image:Slicer3_VolRen_Crop.png|thumb|left|Volume Rendering - Cropping]]
This feature also comes with a integrated 3 dimensional widget to adjust the handlers on the visualization screen.

Try it out!

=== Advanced Options and the Transfer Function ===
The advanced tab lets more experienced doctors do the fine tuning on the '''Transfer Functions'''.
[[Image:Slicer3_VolRen_Advanced.png|thumb|right|Volume Rendering - Advanced]]

'''Transfer Functions''' are the basic building block of volume rendering.
They define the final rendering color for each voxel in the 3D grey scale data.
This can be used to give all tissue with the density of bone a solid white color and paint the skin tissue in a translucent pink above it.

== More Information ==
*Slicer3 Volume Rendering Module: [[Slicer3:Volume_Rendering]]
*Slicer3 Volume Rendering Module using [http://www.nvidia.com/cuda CUDA]: [[Slicer3:Volume Rendering With Cuda]]
R. A. Drebin, L. Carpenter, and P. Hanrahan. Volume rendering. pp. 6574,
1988. 3.1
[2] K. Engel, M. Kraus, and T. Ertl. High-quality pre-integrated volume rendering
using hardwareaccelerated pixel shading, 2001, citeseer.ist.psu.edu/
engel01highquality.html. 3.1.2

[3] D. T. Gering, A. Nabavi, R. Kikinis, N. Hata, J. ODonnell, W. E. L. Grimson,
F. A. Jolesz, P. M. Black, and W. M. W. III. An integrated visualization system
for surgical planning and guidance using image fusion and an open MR. J Magn
Reson Imag 13(6):967975, 2001. 3.4

[4] H.-R. Ke and R.-C. Chang. Ray-cast volume rendering accelerated by incremental
trilinear interpolation and cell templates. The Visual Computer 11:297308,
June 2005, http://www.springerlink.com/content/u177877621757257/. 1

[5] J. Kniss, J. Kniss, G. Kindlmann, and C. Hansen. Multidimensional transfer
functions for interactive volume rendering. 8(3):270285, 2002. 3.1.3

[6] J. Kniss, J. Kniss, S. Premoze, C. Hansen, P. Shirley, and A. McPherson. A
model for volume lighting and modeling. 9(2):150162, 2003. 3.1.4

[7] E. B. Lum, B. Wilson, and K.-L. Ma. High-quality lighting and efficient preintegration
for volume rendering. Joint EUROGRAPHICS - IEEE TCVG Symposium

on Visualization, 2004. 3.1.2
[8] K. Martin, W. Schroeder, and B. Lorensen. vtkvolumeraycastcompositefunction
from the vtk framework. opensource, freebsd license, http://www.vtk.org.
3.2.1.3
15
Bibliography

[9] N. Max, P. Hanrahan, and R. Crawfis. Area and volume coherence for efficient
visualization of 3d scalar functions. SIGGRAPH Comput. Graph. 24(5):2733,
1990. 3.1.2

[10] P. M. Novotny, S. K. Jacobsen, N. V. Vasilyev, D. T. Kettler, I. S. Salgo, P. E.
Dupont, P. J. D. Nido, and R. D. Howe. 3d ultrasound in robotic surgery:
performance evaluation with stereo displays. Int J Med Robot 2(3):279285,
Sep 2006, http://dx.doi.org/10.1002/rcs.102. 4

[11] P. M. Novotny, D. T. Kettler, P. Jordan, P. E. Dupont, P. J. del Nido, and
R. D. Howe. Stereo display of 3d ultrasound images for surgical robot guidance.
Conf Proc IEEE Eng Med Biol Soc 1:15091512, 2006, http://dx.doi.org/
10.1109/IEMBS.2006.259486. 4

[12] P. M. Novotny, J. A. Stoll, N. V. Vasilyev, P. J. del Nido, P. E. Dupont,
T. E. Zickler, and R. D. Howe. Gpu based real-time instrument tracking with
three-dimensional ultrasound. Med Image Anal 11(5):458464, Oct 2007, http:
//dx.doi.org/10.1016/j.media.2007.06.009. 4

[13] NVidia. NVIDIA CUDA Compute Unified Device Architecture - Programming
Guide. NVidia Corporation, 1.1 edition, Nov 2007, http://www.nvidia.com/
cuda. 1
16

Slicer Training Volume Rendering

2008-03-27T17:41:53Z

Bensch: /* More Information */

= Volume Rendering =
== Get It Running ==
#To get volume rendering to work within '''3D Slicer''' we have to make sure that a '''MRML node''' with '''Volumetric Data''' exists.
#If not a new set of volume data must be loaded. For this demo we will load the tutorial data found [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip here].
##'''Download and Uncompress''' this folder
##In 3D Slicer go to '''File -> Load Scene'''
##Select the ''tutorial.xml''
#Now select the '''VolumeRendering Module'''.
#Select a valid volume as the '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

The Volume Rendering will be initialized. Have patience....

== Parameters ==
=== Performance Triggers ===
[[Image:Slicer3_VolRen_Performance.png|thumb|right|Volume Rendering - Performance]]
You can adjust the performance of volume rendering by enabling and disabling quality improvements.
The Volume Rendering Module has '''three performance levels'''
#Low Resolution Hardware Rendering (worst - fastest)
#Full Resolution Hardware Rendering
#Software Rendering (best - slowest)
When all of them are selected slicer uses the low resolution when the camera is moving or nodes in the scene are changing and when nothing is changing anymore the high resolution volume is performed.

The FPS tag lets slicer decide what resolution should be used to produce an interactive experience.

=== Cropping ===
With cropping the volume can be limited to a certain area.
This is useful if a surgeon only wants to see a certain part of the volume or cut at an exact plane.
[[Image:Slicer3_VolRen_Crop.png|thumb|left|Volume Rendering - Cropping]]
This feature also comes with a integrated 3 dimensional widget to adjust the handlers on the visualization screen.

Try it out!

=== Advanced Options and the Transfer Function ===
The advanced tab lets more experienced doctors do the fine tuning on the '''Transfer Functions'''.
[[Image:Slicer3_VolRen_Advanced.png|thumb|right|Volume Rendering - Advanced]]

'''Transfer Functions''' are the basic building block of volume rendering.
They define the final rendering color for each voxel in the 3D grey scale data.
This can be used to give all tissue with the density of bone a solid white color and paint the skin tissue in a translucent pink above it.

== More Information ==
*Slicer3 Volume Rendering Module: [[Slicer3:Volume_Rendering]]
*Slicer3 Volume Rendering Module using [http://www.nvidia.com/cuda CUDA]: [[Slicer3:Volume Rendering With Cuda]]
R. A. Drebin, L. Carpenter, and P. Hanrahan. Volume rendering. pp. 6574,
1988. 3.1
[2] K. Engel, M. Kraus, and T. Ertl. High-quality pre-integrated volume rendering
using hardwareaccelerated pixel shading, 2001, citeseer.ist.psu.edu/
engel01highquality.html. 3.1.2
[3] D. T. Gering, A. Nabavi, R. Kikinis, N. Hata, J. ODonnell, W. E. L. Grimson,
F. A. Jolesz, P. M. Black, and W. M. W. III. An integrated visualization system
for surgical planning and guidance using image fusion and an open MR. J Magn
Reson Imag 13(6):967975, 2001. 3.4
[4] H.-R. Ke and R.-C. Chang. Ray-cast volume rendering accelerated by incremental
trilinear interpolation and cell templates. The Visual Computer 11:297308,
June 2005, http://www.springerlink.com/content/u177877621757257/. 1
[5] J. Kniss, J. Kniss, G. Kindlmann, and C. Hansen. Multidimensional transfer
functions for interactive volume rendering. 8(3):270285, 2002. 3.1.3
[6] J. Kniss, J. Kniss, S. Premoze, C. Hansen, P. Shirley, and A. McPherson. A
model for volume lighting and modeling. 9(2):150162, 2003. 3.1.4
[7] E. B. Lum, B. Wilson, and K.-L. Ma. High-quality lighting and efficient preintegration
for volume rendering. Joint EUROGRAPHICS - IEEE TCVG Symposium
on Visualization, 2004. 3.1.2
[8] K. Martin, W. Schroeder, and B. Lorensen. vtkvolumeraycastcompositefunction
from the vtk framework. opensource, freebsd license, http://www.vtk.org.
3.2.1.3
15
Bibliography
[9] N. Max, P. Hanrahan, and R. Crawfis. Area and volume coherence for efficient
visualization of 3d scalar functions. SIGGRAPH Comput. Graph. 24(5):2733,
1990. 3.1.2
[10] P. M. Novotny, S. K. Jacobsen, N. V. Vasilyev, D. T. Kettler, I. S. Salgo, P. E.
Dupont, P. J. D. Nido, and R. D. Howe. 3d ultrasound in robotic surgery:
performance evaluation with stereo displays. Int J Med Robot 2(3):279285,
Sep 2006, http://dx.doi.org/10.1002/rcs.102. 4
[11] P. M. Novotny, D. T. Kettler, P. Jordan, P. E. Dupont, P. J. del Nido, and
R. D. Howe. Stereo display of 3d ultrasound images for surgical robot guidance.
Conf Proc IEEE Eng Med Biol Soc 1:15091512, 2006, http://dx.doi.org/
10.1109/IEMBS.2006.259486. 4
[12] P. M. Novotny, J. A. Stoll, N. V. Vasilyev, P. J. del Nido, P. E. Dupont,
T. E. Zickler, and R. D. Howe. Gpu based real-time instrument tracking with
three-dimensional ultrasound. Med Image Anal 11(5):458464, Oct 2007, http:
//dx.doi.org/10.1016/j.media.2007.06.009. 4
[13] NVidia. NVIDIA CUDA Compute Unified Device Architecture - Programming
Guide. NVidia Corporation, 1.1 edition, Nov 2007, http://www.nvidia.com/
cuda. 1
16

Slicer Training Volume Rendering

2008-03-27T17:40:23Z

Bensch: /* More Information */

Slicer Training Volume Rendering

2008-03-27T17:40:14Z

Bensch: /* More Information */

Slicer Training Volume Rendering

2008-03-27T17:39:07Z

Bensch: /* Transfer Functions */

Slicer Training Volume Rendering

2008-03-27T17:36:36Z

Bensch: /* Advanced Options and the Transfer Function */

Slicer Training Volume Rendering

2008-03-27T17:30:53Z

Bensch: /* Advanced Options and the Transfer Function */

Slicer Training Volume Rendering

2008-03-27T17:28:36Z

Bensch: /* Advanced Options and the Transfer Function */

Slicer Training Volume Rendering

2008-03-27T17:28:23Z

Bensch: /* Cropping */

Slicer Training Volume Rendering

2008-03-27T17:26:16Z

Bensch: /* Performance Triggers */

Slicer Training Volume Rendering

2008-03-27T17:25:27Z

Bensch: /* Performance Triggers */

Slicer Training Volume Rendering

2008-03-27T17:24:47Z

Bensch: /* Performance Triggers */

Slicer Training Volume Rendering

2008-03-27T17:21:37Z

Bensch: /* Performance Triggers */

Slicer Training Volume Rendering

2008-03-27T17:21:20Z

Bensch: /* = Performance Triggers */

Slicer Training Volume Rendering

2008-03-27T17:21:09Z

Bensch: /* Parameters */

Slicer Training Volume Rendering

2008-03-27T17:20:26Z

Bensch: /* Volume Rendering */

Slicer Training Volume Rendering

2008-03-27T17:19:25Z

Bensch: /* Volume Rendering */

= Volume Rendering =
#To get volume rendering to work within '''3D Slicer''' we have to make sure that a '''MRML node''' with '''Volumetric Data''' exists.
#If not a new set of volume data must be loaded. For this demo we will load the tutorial data found [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip here].
##'''Download and Uncompress''' this folder
##In 3D Slicer go to '''File -> Load Scene'''
##Select the ''tutorial.xml''
#Now select the '''VolumeRendering Module'''.
#Select a valid volume as the '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]
#The preprocessing should now be starting and Volume Rendering will be initialized

[[Image:Slicer3_VolRen_Performance.png|thumb|none|Volume Rendering - Performance]]
[[Image:Slicer3_VolRen_Crop.png|thumb|none|Volume Rendering - Cropping]]
[[Image:Slicer3_VolRen_Advanced.png|thumb|none|Volume Rendering - Advanced]]

== Transfer Functions ==

File:Slicer3 VolRen Advanced.png

2008-03-27T16:49:05Z

Bensch:

File:Slicer3 VolRen Performance.png

2008-03-27T16:48:49Z

Bensch:

Slicer Training Volume Rendering

2008-03-27T16:48:26Z

Bensch: /* Volume Rendering */

File:Slicer3 VolRen Crop.png

2008-03-27T16:47:24Z

Bensch:

Slicer Training Volume Rendering

2008-03-27T16:47:04Z

Bensch: /* Volume Rendering */

= Volume Rendering =

[[Image:Slicer3_VolRen_Crop.png|thumb|none|Volume Rendering Cropping]]

== Transfer Functions ==

Slicer Training Volume Rendering

2008-03-27T16:21:19Z

Bensch: New page: = Volume Rendering = == Transfer Functions ==

= Volume Rendering =

== Transfer Functions ==

Slicer3:4DUltrasound 4D US

2008-03-27T14:55:25Z

Bensch: /* Introduction */

Slicer3:4DUltrasound 4D US

2008-03-27T14:55:01Z

Bensch: /* Introduction */

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the '''Ultrasound Server''' is retrieving images based on the position of the scanner.
The '''computer's server software''' supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the '''OpenIGTLink''', the network protocol of 3D Slicer.

Finally 3D Slicer visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

Slicer3:4DUltrasound 4D US

2008-03-26T20:42:01Z

Bensch: /* Image Acquisition */

= Introduction =
The following graph shows how the Ultrasound scanner will be connected with 3D Slicer using the IGT Link
[[Image:US_openIGTLink.png|frame|none|Transfer Image from Ultrasound]]

To the right the Ultrasound Server is retrieving images based on the position of the scanner.
The computer's server software supports an interface to translate the scanning planes and to retrieve and send images from the scanner.

Then the data is transferred over the network using the openIGT link, the network protocol of Slicer.

Finally 3D Slicer visualizes the data and sends tracking commands back over the link to update the viewing plane.

= Detailed Process =
== Image Acquisition ==
This is the region that has to be designed by the developers of the scanner.

== Data Transfer ==
There are two data transfers involved in this process, ''Image Transfers'' from the scanner to slicer and ''command transfers'' into the revers direction.

=== Image Transfers ===
To transfer an image from a server to 3D Slicer the following objects have to considered:
#Open connection to 3D Slicer
#Data Creation
##Create ImageData buffer on server
##Create MRML Node holding a ImageData in Slicer connected to the ImageData on the server
#Data Transfer
##Fill ImageData buffer on Server with US Data
##Send Data over Link

By now the MRML node's image data is updated and ready to visualize.

=== Command Transfer ===
Tracking commands are sent using the command structure supported by slicer's openIGT Link

== Data Visualization ==
To Transfer 3D images from the scanner to Slicer we make use of openIGT Link

= Interfaces =

= Misc =
A tutorial to get openIGT Link running with 3D Slicer and 4D volume rendering can be found [[Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data|here]].

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:41:15Z

Bensch: /* Check Connection */

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data. The theory is described on [[Slicer3:4DUltrasound 4D US]]

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*'''Download and compile''' a copy of Slicer3 as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the '''OpenIGTLink Module''' from the Modules Tab. [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the '''Connector Browser''' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the '''Data''' Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3_OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''VolumeRendering'''.
#You can now choose ''Scanner'' as '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:32:34Z

Bensch:

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data. The theory is described on [[Slicer3:4DUltrasound 4D US]]

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*'''Download and compile''' a copy of Slicer3 as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the '''OpenIGTLink Module''' from the Modules Tab. [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the '''Connector Browser''' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3_OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''VolumeRendering'''.
#You can now choose ''Scanner'' as '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:26:24Z

Bensch: /* Setting up the 3D Slicer */

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data.

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*'''Download and compile''' a copy of Slicer3 as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the '''OpenIGTLink Module''' from the Modules Tab. [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the '''Connector Browser''' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3_OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''VolumeRendering'''.
#You can now choose ''Scanner'' as '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:26:00Z

Bensch: /* Prepare Slicer3 */

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data.

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*'''Download and compile''' a copy of Slicer3 as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the '''OpenIGTLink Module''' from the Modules Tab. [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the 'Connector Browser' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3_OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''VolumeRendering'''.
#You can now choose ''Scanner'' as '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

File:Slicer3 OpenIGT VolumeRendering SelectScanner.png

2008-03-26T20:24:40Z

Bensch:

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:24:27Z

Bensch: /* Check Connection */

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data.

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*Download and Compile a copy of Slicer as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the OpenIGTLink Module from the Modules Tab [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the 'Connector Browser' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3_OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''VolumeRendering'''.
#You can now choose ''Scanner'' as '''Source Volume''' [[Image:Slicer3_OpenIGT_VolumeRendering_SelectScanner.png|thumb|none|Select Scanner in Volume Rendering Module]]

File:Slicer3 OpenIGT Data Shows Scanner Node.png

2008-03-26T20:16:46Z

Bensch:

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:16:40Z

Bensch: /* Check Connection */

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data.

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*Download and Compile a copy of Slicer as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the OpenIGTLink Module from the Modules Tab [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the 'Connector Browser' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3_OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''Volume Rendering'''.
#You can now choose ''Scanner'' as '''Source Volume'''.

File:Slicer3-OpenIGT Data Shows Scanner Node.png

2008-03-26T20:15:47Z

Bensch:

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:15:33Z

Bensch: /* Check Connection */

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data.

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*Download and Compile a copy of Slicer as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the OpenIGTLink Module from the Modules Tab [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the 'Connector Browser' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''. [[Image:Slicer3:OpenIGT_Data_Shows_Scanner_Node.png|thumb|none|Scanner Visible]]
#Select the module '''Volume Rendering'''.
#You can now choose ''Scanner'' as '''Source Volume'''.

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:14:47Z

Bensch:

This tutorial will teach you how to setup Slicer3 and an image provider to send and display 4D image data.

= Prepare Slicer3 =

== Downloading and Compiling the source ==
*Download and Compile a copy of Slicer as described in [[Slicer3:Build_Instructions]].
** !! use http://www.na-mic.org/svn/Slicer3/branches/igt_cuda_merge as the source !!

== Setting up the 3D Slicer ==
#Start up Slicer3
#Select the OpenIGTLink Module from the Modules Tab [[Image:Slicer3_Select_OpenIGTLinkModule.png|thumb|none|Select the OpenIGTLink Module]]
#Start the server, by clicking on the 'Connector Browser' Tab. [[Image:Slicer3_Enable_OpenIGT_Server.png|thumb|none|Enable OpenIGT Server]]
##Add a Server
##Select a Name (optional)
##Set the type to server
##Enable the server by setting the status to 'Enabled'.

== Get IP-Address of the Slicer Computer ==
Store the IP-Address of the computer. This is done by 'ipconfig' on Windows and 'ifconfig' on UNIX.

= Prepare the Image Provider =
== Downloading and Compilation ==
*Check out the Server code from http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
svn co http://www.na-mic.org/svn/NAMICSandBox/trunk/BRPTools/ScannerIO
*Compile the Code
cmake .
make
*Download the data package with ct-scans of a human heart [[Media:heart256.zip]] and unzip it into the source directory
== Start the Scanner-Simulator ==
*start the scanner with the Arguments:
Usage: ./bin/ScannerSim <x> <y> <z> <type> <rx> <ry> <rz> <fname_temp> <bindex> <eindex> <fps> <hostname>
<x>, <y>, <z> : Number of pixels in x, y and z direction.
<type> : Type (2:int8 3:uint8 4:int16 5:uint16 6:int32 7:uint32
<rx>, <ry>, <rz>: resolution (pixel size) in x, y and z direction
<fname_temp> : File name template (e.g. "RawImage_%04d.raw").
<bindex> : Begin index.
<eindex> : End index.
<fps> : Frame rate (frames per second).
<hostname> : hostname (port# is fixed to 18944)
*For the heart dataset the following will do:
./bin/ScannerSim 256 256 256 3 1 1 1 heart256-%d.raw 1 5 10 [Slicer-IP-Address]

= Check Connection =
#The Provider should now transfer images to Slicer3 (should be running)
#In Slicer3 go to the Data Module
#In the '''Display & Modify Scene''' section should now be a new node called ''Scanner(vtkMRMLScalarVolumeNode1)''.
#Select the module '''Volume Rendering'''.
#You can now choose ''Scanner'' as '''Source Volume'''.

Slicer3:openIGT Tutorial For 4D Volume Rendering Data

2008-03-26T20:08:40Z

Bensch: /* Downloading and Compilation */