NAMIC Wiki - User contributions [en]

2010 Summer Project Week Liver Ablation

2010-06-25T13:34:21Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:41:43Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:41:06Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:40:48Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:35:38Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:35:00Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:34:12Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:33:15Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:29:16Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:24:12Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:06:36Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T16:03:21Z

Hliu:

2010 Summer Project Week Liver Ablation

2010-06-17T15:52:06Z

Hliu:

2010 Summer Project Week Liver Ablation

2010-06-17T15:48:23Z

Hliu: /* Key Investigators */

2010 Summer Project Week Liver Ablation

2010-06-17T15:47:06Z

Hliu: /* Key Investigators */

File:Liver model.jpg

2010-06-17T15:46:13Z

Hliu:

File:Liver fiducial segmentation.jpg

2010-06-17T15:45:59Z

Hliu:

File:Liver fiducial.jpg

2010-06-17T15:45:33Z

Hliu:

2010 Summer Project Week Liver Ablation

2010-06-17T15:44:33Z

Hliu:

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:Liver_fiducial.jpg| Liver with fiducials
Image:Liver_fiducial_segmentation.jpg| Liver with fiducials and segmentation
Image:Liver_model.jpg| Liver model
</gallery>

==Key Investigators==
* BWH: Haiying Liu, Noby Hata, Sota Oguro
* Georgetown University: Ziv Yaniv

3D Ultrasound (US) is an emerging diagnostic technique that is non-invasive, fast and comparably cheap. It is commonly used for acquiring images of fetuses or anatomical regions and organs near the skin, for example the thyroid gland or other parenchymatous organs. 3D US has some advantages compared to 2D US, as it the diagnosis may become largely observer-independent and accurate volumetric measurements become possible. Compared to alternative imaging techniques, like CT or MRI, it features a much better spatial resolution and images can be acquired faster and a lot easier. It may, therefore, be combined with another imaging technique in order to enable ongoing screening during treatment or control studies. The combination of MR and US is desirable, as both techniques are very feasible for the analysis of soft tissue. However, this is a challenging task and quite a few problems have to be addressed.

[[Image:US_Thyroid_Bias.png‎|600px|Bias Field on Ultrasound Image and Segmentation of the Thyroid]]

The figure above shows a slice taken from a 3D ultrasound image of the human thyroid (upper left), together with the intensity profile along a line through the tyhroid (upper right, lower left) and a segmentation (lower right). US images suffer from speckle noise, sonic attenuation and also regions of sound shadows (insufficient gel layer). The sonic attenuation cannot be fully compensated by the imaging devices and the effect is clearly visible when examining the intensity profile along a line through the thyroid region (lower left image), which shows decreasing intensities with increasing distance to the surface.

In previous work, we have examined several pre-processing techniques for 3D US denoising, however, we did not find a satisfying solution for the bias field correction of the images. Since the intensity-based registration of MR with 3D US is a very hard problem and only few work has been done on the registration of 3D US with MR images, we will try to come up with some ideas for a combined approach for the bias field correction, segmentation and registration during the project weak.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objectives</h3>
* denoising and bias field correction of 3D US data
* model for the combined image correction, segmentation and registration between 3D US and MRI
* visualization of all processing steps within Slicer
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
The bias field on the 3D US data varies spatially with a very low frequency. It is similar to the bias field effects in MR caused by magnetic inhomogeneities. We will investigate whether an EM-based approach may be used for the correction, similar to the previous work by Wells et. al. and Pohl et. al., and try to adapt the already existing Slicer code to this problem.

For the registration, we may have to come up with a new formulation that uses not only the statistics of the intensities, but also some additional information about the tissue boundaries. The tissue boundaries are directly influencing the visible content of the 3D US images, however, they have a different appearance and structure within the MRI.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Fill this at the end of the week
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

The work will be provided as ITK modules and it intended to integrate them into a Slicer module.

==References==

* W.M. Wells, R. Kikinis, W.E.L. Grimson, F. Jolesz. Adaptive segmentation of MRI data. IEEE Transactions on Medical Imaging, 15, pp. 429-442, 1996
* K.M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian model for joint segmentation and registration. NeuroImage, 31(1), pp. 228-239, 2006
* E.N.K. Kollorz, D.A. Hahn, R. Linke, T.W. Goecke, J. Hornegger, and T. Kuwert. Quantification of Thyroid Volume using 3-D Ultrasound Imaging. IEEE Transactions on Medical Imaging, 27(4), pp. 457-466, 2008
* W. Wein, S. Brunke, A. Khamene, M.R. Callstrom, N. Navab. Automatic CT-Ultrasound Registration for Diagnostic Imaging and Image-guided Intervention. Medical Image Analysis, 12(5), pp. 577-585, 2008
</div>

2010 Summer Project Week Liver Ablation

2010-06-17T15:37:44Z

Hliu: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Haiying Liu, Noby Hata, Sota Oguro
* Georgetown University: Ziv Yaniv

3D Ultrasound (US) is an emerging diagnostic technique that is non-invasive, fast and comparably cheap. It is commonly used for acquiring images of fetuses or anatomical regions and organs near the skin, for example the thyroid gland or other parenchymatous organs. 3D US has some advantages compared to 2D US, as it the diagnosis may become largely observer-independent and accurate volumetric measurements become possible. Compared to alternative imaging techniques, like CT or MRI, it features a much better spatial resolution and images can be acquired faster and a lot easier. It may, therefore, be combined with another imaging technique in order to enable ongoing screening during treatment or control studies. The combination of MR and US is desirable, as both techniques are very feasible for the analysis of soft tissue. However, this is a challenging task and quite a few problems have to be addressed.

[[Image:US_Thyroid_Bias.png‎|600px|Bias Field on Ultrasound Image and Segmentation of the Thyroid]]

The figure above shows a slice taken from a 3D ultrasound image of the human thyroid (upper left), together with the intensity profile along a line through the tyhroid (upper right, lower left) and a segmentation (lower right). US images suffer from speckle noise, sonic attenuation and also regions of sound shadows (insufficient gel layer). The sonic attenuation cannot be fully compensated by the imaging devices and the effect is clearly visible when examining the intensity profile along a line through the thyroid region (lower left image), which shows decreasing intensities with increasing distance to the surface.

In previous work, we have examined several pre-processing techniques for 3D US denoising, however, we did not find a satisfying solution for the bias field correction of the images. Since the intensity-based registration of MR with 3D US is a very hard problem and only few work has been done on the registration of 3D US with MR images, we will try to come up with some ideas for a combined approach for the bias field correction, segmentation and registration during the project weak.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objectives</h3>
* denoising and bias field correction of 3D US data
* model for the combined image correction, segmentation and registration between 3D US and MRI
* visualization of all processing steps within Slicer
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
The bias field on the 3D US data varies spatially with a very low frequency. It is similar to the bias field effects in MR caused by magnetic inhomogeneities. We will investigate whether an EM-based approach may be used for the correction, similar to the previous work by Wells et. al. and Pohl et. al., and try to adapt the already existing Slicer code to this problem.

For the registration, we may have to come up with a new formulation that uses not only the statistics of the intensities, but also some additional information about the tissue boundaries. The tissue boundaries are directly influencing the visible content of the 3D US images, however, they have a different appearance and structure within the MRI.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Fill this at the end of the week
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

The work will be provided as ITK modules and it intended to integrate them into a Slicer module.

==References==

* W.M. Wells, R. Kikinis, W.E.L. Grimson, F. Jolesz. Adaptive segmentation of MRI data. IEEE Transactions on Medical Imaging, 15, pp. 429-442, 1996
* K.M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian model for joint segmentation and registration. NeuroImage, 31(1), pp. 228-239, 2006
* E.N.K. Kollorz, D.A. Hahn, R. Linke, T.W. Goecke, J. Hornegger, and T. Kuwert. Quantification of Thyroid Volume using 3-D Ultrasound Imaging. IEEE Transactions on Medical Imaging, 27(4), pp. 457-466, 2008
* W. Wein, S. Brunke, A. Khamene, M.R. Callstrom, N. Navab. Automatic CT-Ultrasound Registration for Diagnostic Imaging and Image-guided Intervention. Medical Image Analysis, 12(5), pp. 577-585, 2008
</div>

2010 Summer Project Week

2010-06-17T15:12:23Z

Hliu: /* IGT */

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="200px"|Monday, June 21
!width="200px"|Tuesday, June 22
!width="200px"|Wednesday, June 23
!width="200px"|Thursday, June 24
!width="200px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|8:30
|rowspan="5"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|9:00-9:45
|'''9am:''' NA-MIC Kit Update (Jim Miller)
|rowspan="4"|'''9am-12pm Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|rowspan="4"|'''9am-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|rowspan="4"|'''10am-12pm''' [[#Projects|Project Progress Updates]]
|-
|9:45-10:30
|bgcolor="#c1c2ec"|'''9:45am:''' 3D Slicer Update (Steve Pieper)
|-
|10:30-11:00
|'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)
|-
|11:00-12:00
|bgcolor="#c1c2ec"|'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|-
|12:00-1:00
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes
|-
|12:45-1:00
|
|
|bgcolor="#ccffcc"|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
|
|
|-
|1:00-1:30
|rowspan="5"|'''1-1:05pm''' Ron Kikinis: Welcome _____________________ '''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
|rowspan="4"|'''1-3pm: Breakout Session:''' QT/Slicer (Steve, JC, J2)
|rowspan="4"|'''1-3pm: Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
|rowspan="2"|'''1-2pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
|bgcolor="#f0e68b"|Adjourn by 1:30pm
|-
|1:30-2:00
|rowspan="9"|
|-
|2:00-2:30
|rowspan="2"|'''2-3pm''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
|-
|2:30-3:00
|rowspan="6"|
|-
|3:00-3:30
|rowspan="2" style="background: #ccffcc;"|'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
|rowspan="5"|'''3-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez) _____________________ '''3-4pm Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
|-
|3:30-4:00
|rowspan="4" style="background: #ccffcc;"|'''3:30-5:30pm Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|-
|4:00-4:30
|rowspan="2"|'''4-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)
|rowspan="2"|'''4-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|-
|4:30-5:00
|-
|5:00-5:30
|-
|5:30
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

Note:
***We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Lauren Chauvin, Junichi Tokuda, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnota, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesnyak, Charles Guttmann, Ron Kikinis)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

2010 Summer Project Week Liver Ablation

2010-06-17T15:07:52Z

Hliu: Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List </gallery> ==Key Investigators== * BWH: Haiying Liu, Noby Hata * Georgetown Universi…'

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Haiying Liu, Noby Hata
* Georgetown University: Ziv Yaniv

3D Ultrasound (US) is an emerging diagnostic technique that is non-invasive, fast and comparably cheap. It is commonly used for acquiring images of fetuses or anatomical regions and organs near the skin, for example the thyroid gland or other parenchymatous organs. 3D US has some advantages compared to 2D US, as it the diagnosis may become largely observer-independent and accurate volumetric measurements become possible. Compared to alternative imaging techniques, like CT or MRI, it features a much better spatial resolution and images can be acquired faster and a lot easier. It may, therefore, be combined with another imaging technique in order to enable ongoing screening during treatment or control studies. The combination of MR and US is desirable, as both techniques are very feasible for the analysis of soft tissue. However, this is a challenging task and quite a few problems have to be addressed.

[[Image:US_Thyroid_Bias.png‎|600px|Bias Field on Ultrasound Image and Segmentation of the Thyroid]]

The figure above shows a slice taken from a 3D ultrasound image of the human thyroid (upper left), together with the intensity profile along a line through the tyhroid (upper right, lower left) and a segmentation (lower right). US images suffer from speckle noise, sonic attenuation and also regions of sound shadows (insufficient gel layer). The sonic attenuation cannot be fully compensated by the imaging devices and the effect is clearly visible when examining the intensity profile along a line through the thyroid region (lower left image), which shows decreasing intensities with increasing distance to the surface.

In previous work, we have examined several pre-processing techniques for 3D US denoising, however, we did not find a satisfying solution for the bias field correction of the images. Since the intensity-based registration of MR with 3D US is a very hard problem and only few work has been done on the registration of 3D US with MR images, we will try to come up with some ideas for a combined approach for the bias field correction, segmentation and registration during the project weak.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objectives</h3>
* denoising and bias field correction of 3D US data
* model for the combined image correction, segmentation and registration between 3D US and MRI
* visualization of all processing steps within Slicer
</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
The bias field on the 3D US data varies spatially with a very low frequency. It is similar to the bias field effects in MR caused by magnetic inhomogeneities. We will investigate whether an EM-based approach may be used for the correction, similar to the previous work by Wells et. al. and Pohl et. al., and try to adapt the already existing Slicer code to this problem.

For the registration, we may have to come up with a new formulation that uses not only the statistics of the intensities, but also some additional information about the tissue boundaries. The tissue boundaries are directly influencing the visible content of the 3D US images, however, they have a different appearance and structure within the MRI.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
Fill this at the end of the week
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

The work will be provided as ITK modules and it intended to integrate them into a Slicer module.

==References==

* W.M. Wells, R. Kikinis, W.E.L. Grimson, F. Jolesz. Adaptive segmentation of MRI data. IEEE Transactions on Medical Imaging, 15, pp. 429-442, 1996
* K.M. Pohl, J. Fisher, W.E.L. Grimson, R. Kikinis, and W.M. Wells. A Bayesian model for joint segmentation and registration. NeuroImage, 31(1), pp. 228-239, 2006
* E.N.K. Kollorz, D.A. Hahn, R. Linke, T.W. Goecke, J. Hornegger, and T. Kuwert. Quantification of Thyroid Volume using 3-D Ultrasound Imaging. IEEE Transactions on Medical Imaging, 27(4), pp. 457-466, 2008
* W. Wein, S. Brunke, A. Khamene, M.R. Callstrom, N. Navab. Automatic CT-Ultrasound Registration for Diagnostic Imaging and Image-guided Intervention. Medical Image Analysis, 12(5), pp. 577-585, 2008
</div>

2010 Summer Project Week

2010-06-17T15:02:40Z

Hliu: /* IGT */

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|500px|right]]

__TOC__
==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==

{|border="1"
|-style="background: #b0d5e6; color: #02186f; font-size: 130%"
!Time
!width="200px"|Monday, June 21
!width="200px"|Tuesday, June 22
!width="200px"|Wednesday, June 23
!width="200px"|Thursday, June 24
!width="200px"|Friday, June 25
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|8:30
|rowspan="5"|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|9:00-9:45
|'''9am:''' NA-MIC Kit Update (Jim Miller)
|rowspan="4"|'''9am-12pm Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
|rowspan="4"|'''9am-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
|rowspan="4"|'''10am-12pm''' [[#Projects|Project Progress Updates]]
|-
|9:45-10:30
|bgcolor="#c1c2ec"|'''9:45am:''' 3D Slicer Update (Steve Pieper)
|-
|10:30-11:00
|'''10:30-11am:''' OpenIGTLink Update (Junichi Tokuda)
|-
|11:00-12:00
|bgcolor="#c1c2ec"|'''11am-12pm:''' Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
|-
|12:00-1:00
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes
|-
|12:45-1:00
|
|
|bgcolor="#ccffcc"|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
|
|
|-
|1:00-1:30
|rowspan="5"|'''1-1:05pm''' Ron Kikinis: Welcome _____________________ '''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
|rowspan="4"|'''1-3pm: Breakout Session:''' QT/Slicer (Steve, JC, J2)
|rowspan="4"|'''1-3pm: Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
|rowspan="2"|'''1-2pm: Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
|bgcolor="#f0e68b"|Adjourn by 1:30pm
|-
|1:30-2:00
|rowspan="9"|
|-
|2:00-2:30
|rowspan="2"|'''2-3pm''' Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
|-
|2:30-3:00
|rowspan="6"|
|-
|3:00-3:30
|rowspan="2" style="background: #ccffcc;"|'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
|rowspan="5"|'''3-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez) _____________________ '''3-4pm Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
|-
|3:30-4:00
|rowspan="4" style="background: #ccffcc;"|'''3:30-5:30pm Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
|-
|4:00-4:30
|rowspan="2"|'''4-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Dan Marcus, Stephen Aylward)
|rowspan="2"|'''4-5pm Breakout Session:''' [[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
|-
|4:30-5:00
|-
|5:00-5:30
|-
|5:30
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|}

Note:
***We need to empty room by 1:30pm on Friday. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah]]

==Projects==

=== Segmentation ===
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)

=== Registration ===
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

=== IGT ===
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
#[[2010_Summer_Project_Week_Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound|Intraoprative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda?, Pratik Patel?)
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi, Sam Song, Tamas Ungi)]]
#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation(Haiying Liu, Noby Hata)]]
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope Using EM Tracker and OpenIGTLink]] (Lauren Chauvin, Junichi Tokuda, Noby Hata)

=== Radiotherapy ===
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

=== Analysis ===
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnota, Peter Karasev, Curt Lisle, Ron Kikinis)
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse brain cortical thickness analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate image analysis using the standard Slicer pipeline]] (Yundi Shi, Martin Styner)
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)

===[[Microscopy Image Analysis]] ===
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)

=== Shape Analysis ===
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)

=== Diffusion ===
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
#[[Efficient Diffusion Connectivity via Multidirectional Fstar]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)

=== NA-MIC Kit Internals ===
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)

=== Workflows and Integration ===
# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesnyak, Charles Guttmann, Ron Kikinis)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Attendee List==

<big>'''NOTE:'''</big> THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]

# Anderson Peter , GE Navigation (Retired)
# Aucoin Nicole , BWH
# Audette Michel , Kitware
# Aylward Stephen , Kitware, Inc
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
# Bouix Sylvain , BWH
# Bowers Michael , Johns Hopkins University
# Budin Francois , UNC
# Burdette Everette , Acoustic MedSystems, Inc.
# CHAUVIN Laurent , Brigham and Women's Hospital
# Chen Min , Johns Hopkins University
# Crane Jason , UCSF
# Datar Manasi , SCI Institute
# Ding Liya , The Ohio State University
# Eckbo Ryan , BWH
# Ersoy Ilker , University of Missouri Columbia
# Fedorov Andriy , Surgical Planning Lab
# Fillion-Robin Jean-Christophe , Kitware Inc.
# Finet Julien , Kitware Inc
# Fishbaugh James , SCI Institute
# Fritscher Karl , UMIT
# Gao Yi , Gerogia Tech
# GELAS Arnaud , Harvard Medical School
# Gorgolewski Chris , SPL
# gouaillard alexandre , CoSMo Software
# Gouttard Sylvain , SCI Institute
# Grama Kedar , Rensselaer Polytechnic Institute
# Haehn Daniel , University of Pennsylvania
# Hafiane Adel , ENSI-Bourges
# Hageman Nathan , UCLA
# Hahn Dieter , University Erlangen
# Halle Michael , BWH/SPL
# Hamel Corentin , UNC Chapel Hill
# Hata Nobuhiko , Brigham and Women's Hospital
# Hayes Kathryn , Brigham and Women's Hospital
# Herlambang Nicholas , AZE, Ltd.
# Holton Leslie , Medtronic Navigation
# Ibanez Luis , KITWARE Inc.
# Jagadeesan Jayender , SPL
# Johnson Hans , University of Iowa
# Kapur Tina , Brigham and Women's Hospital
# Kikinis Ron , Brigham and Women's Hospital
# Kim Minjeong , UNC-Chapel Hill
# Kolesov Ivan , Georgia Institute of Technology
# Larson Garrett , UNC-CH
# Lee Joohwi , UNC Chapel Hill
# Li Rui , MGH
# Lienhard Stefan , LMI
# Lisle Curtis , KnowledgeVis, LLC
# Liu Felix , Beth Israel Deaconess Medical Center
# Liu Yanling , SAIC-Frederick, Inc.
# Liu Haiying , Brigham and Women's Hospital
# Lowekamp Bradley , Lockheed Martin
# machiraju raghu , The Ohio State University
# Magnotta Vincent , The University of Iowa
# malaterre mathieu , CoSMo Software
# Marcus Daniel , Washington University
# Marks William , Focused Ultrasound Lab, BWH, HMS
# Mastrogiacomo Katie , Brigham and Women's Hospital
# Matsui Joy , University of Iowa
# Megason Sean , Harvard Medical School
# Meier Dominik , BWH, Boston MA
# menze bjoern , CSAIL MIT
# menze bjoern , CSAIL MIT
# Milchenko Mikhail , WUSTL
# Miller James , GE Research
# Mosaliganti Kishore , Harvard Medical School
# Niethammer Marc , UNC Chapel Hill
# Norton Isaiah , BWH Neurosurgery
# Olson Beck , UCSF
# Onofrey John , Yale University
# Padmanabhan Raghav , RPI
# Palaniappan Kannappan , university of Missouri
# Paniagua Beatriz , University of North Caolina at Chapel Hill
# Papademetris Xenophon , Yale University
# Partyka David , Kitware Inc
# Patel Pratik , Brainlab Inc
# Pathak Sudhir , Univeristy Of Pittsburgh
# PECOT Thierry , Ohio State University
# Peroni Marta , Politecnico di Milano, MIT, MGH
# Perrot-Audet Antonin , Harvard Medical School
# Pieper Steve , Isomics, Inc.
# Plesniak Wendy , BWH
# Pohl Kilian , IBM
# Pujol Sonia , Brigham and Women's Hospital
# Rannou Nicolas , Harvard Medical School
# Riklin Raviv Tammy , MIT, CSAIL
# Ruiz Marco , UCSD
# Schroeder William , Kitware
# Scully Mark , The Mind Research Network
# Sharp Greg , MGH
# Shi Yundi , UNC Chapel Hill
# Shusharina Nadya , MGH
# Singh Shantanu , The Ohio State University
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
# Souhait Lydie , Harvard Medical School
# Spinczyk Dominik , Silesian University of Technology
# Srinivasan Padmapriya , BWH
# Tao Xiaodong , GE Research
# Tokuda Junichi , Brigham and Women's Hospital
# Ungi Tamas , Queen's University
# Vachet Clement , UNC Chapel Hill
# Veni Gopalkrishna , SCI Institute
# Wassermann Demian , SPL/LMI/PNL
# Weinrich Adam , Nokia
# Wells Sandy , BWH
# White Phillip , BWH/HMS
# Wu Guorong , University of North Carolina at Chapel Hill
# Yamada Atsushi , Nagoya Institute of Technology
# Yarmarkovich Alexander , ISOMICS
# Zaitsev Alexander , Brigham and Womens Hospital

2010 Summer Project Week

2010-05-13T19:45:41Z

Hliu: /* IGT */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

==Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm Breakout Session: Data Management (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**1-5pm: Breakout Session: Prostate Interventions (Junichi Tokuda)
**3-4pm: Breakout Session: VTK Widgets (Nicole, Kilian, JC)
**3-5pm: Breakout Session: QA Training (Luis Ibanesz)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
** noon lunch
** 1-2pm: GWE (Marco Ruiz)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===
*[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
*[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
*[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, ?)

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
*[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Greg Sharp, Nadya Shusharina)
*[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
*[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)

=== IGT ===
* Liver Ablation (Haiying Liu)

=== Radiotherapy ===
*[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp)
*[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
*Cortical thickness analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)

=== Informatics ===
* Computer Aided Photodynamic Therapy (Pietka, Spinczyk)

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)
*Viewer Manager Factory (Alex Y., Kilian, Steve, Nicole)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

2010 Summer Project Week

2010-05-07T16:31:06Z

Hliu: /* IGT */

__NOTOC__

Back to [[Project Events]], [[Events]]

[[Image:PW-MIT2010.png|300px]]

==Background==

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== Logistics ==
*'''Dates:''' June 21-25, 2010
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10 Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.

''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
''' $189/night/room (plus tax).'''
''' This rate is good only through June 1.'''

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

== TENTATIVE Agenda==

'''PLEASE NOTE THAT THIS IS A TENTATIVE AGENDA. IT WILL BE CONFIRMED IN MAY 2010.
'''
=== Monday, June 21, 2010 ===
** noon-1pm lunch
**1pm: Welcome (Ron Kikinis)
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)

=== Tuesday, June 22, 2010 ===
** 8:30am breakfast
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
**9:45-10:30am 3D Slicer Update (Steve Pieper)
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
** noon lunch
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
** 4-5pm Breakout Session: Data Management (Dan Marcus, Stephen Aylward)
** 5:30pm adjourn for day

=== Wednesday, June 23, 2010 ===
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
**1-5pm: Breakout Session: Prostate Interventions (Junichi Tokuda)
**3-4pm: Breakout Session: VTK Widgets (Nicole, Kilian, JC)
**3-5pm: Breakout Session: QA Training (Luis Ibanesz)
** 5:30pm adjourn for day

=== Thursday, June 24, 2010 ===
** 8:30am breakfast
** 11am: Breakout Session: TBD
** noon lunch
** 1-2pm: GWE (Marco Ruiz)
** 5:30pm adjourn for day

=== Friday, June 25, 2010 ===
** 8:30am breakfast
** 10am-noon: [[#Projects|Project Progress Updates]]
*** Noon: Lunch boxes and adjourn by 1:30pm.
***We need to empty room by 1:30. You are welcome to use wireless in Stata.
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
***Next Project Week [[AHM_2011|in Utah, Fill in Dates]]

==Projects==

=== Segmentation ===

=== Registration ===
*[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)

=== IGT ===
* Liver Ablation (Ziv Yaniv, Haiying Liu)

=== Radiotherapy ===

=== Analysis ===
*[[Microscopy Image Analysis]] (Arnaud Gelas)
*Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)

=== Informatics ===

=== Diffusion ===

=== Python ===

=== Slicer Internals ===
*Module Inventory (Steve, Jim)

=== Execution Model ===

===Other NA-MIC Kit Internals===
*VTKWidgets (JC, Nicole)
*Superbuild (Dave Partika)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on June 10, 2009: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 17, 2010: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

U-Tokyo-visit-03192010

2010-03-19T13:21:44Z

Hliu: /* Student / Fellow seminars */

=Univ Tokyo/NCIGT joint workshop on Image Guided Therapy=

==Date/Time==
9am-3pm, March 19, 2010

==Objective==
The objective of this workshop is discuss the mutual interest between the delegates from the University of Tokyo and NCIGT particular in Image Guided Therapy research.

==Faculty talks==
*at Abraham Conference Room, L1, BWH
9:30-10:00am: Welcome/Introduction, Nobuhiko Hata, PhD
* [[Media:hata-utokyo-ws.zip | Slides]]
*[http://www.spl.harvard.edu/pages/People/noby Speaker Bio]

10:00-10:30 Naohiko Sugita, PhD, the University of Tokyo
* Talk title: Machining process incorporating biomaterials effective for bone regeneration in arthroplasty
* [Abstract] The goal is to develop a machining process incorporating biomaterials effective for bone regeneration in arthroplasty. Temperature, mechanical stress, and form are critical parameters in regeneration of living tissues such as bone. The following investigations are under this theme: (1) investigation of the influence of cutting temperature and load on bone regeneration by the machining process, (2) development of a low power nanoscale machining process and tools, (3) investigation of effective cut shapes for bone regeneration, and (4) development of a biologically compatible machining system as a cutting tool.

* [[Media:sugita-utokyo-ws.zip | Slide with the movies]]
*[http://www.nml.t.u-tokyo.ac.jp/en/index-e.html Speaker Bio]

10:30-11:00 Yoshikazu Nakajima, PhD, the University of Tokyo
* Talk title: Three-dimensional shape measurement endoscope
*[Abstract] A three-dimensional shape measurement endoscope based on single-view imaging will be introduced in my talk. We propose a novel method integrating shape from focus and shading methods. Our prototype provides surfaces of organ's inner walls with 0.5 mm of accuracy and no lack of the surface in the experiments.
* [[Media:nakajima-utokyo-ws.zip | Slide with the movies]]
*[http://www.iml.u-tokyo.ac.jp/nl/index_e.html Speaker Bio]

11:00- 11:30 Ron Kikinis, MD, BWH
* Talk title: 3D Slicer as a Research Platform for Medical Image Computing
* [[Media:kikinis-utokyo-ws.ppt | Slide]]
*[http://www.spl.harvard.edu/pages/People/kikinis Speaker Bio]

==Student / Fellow seminars==
**Organized by Haytham Elhawary (BWH), TBD (Tokyo U)
**12:15-3:00pm
**Held at Room 4-002G, Ledge Building
**Talk format: 12 min talk/3 min questions

*12:15 - 12:30: Joonho SEO - Visual servoing system for non-invasive medical treatment using HIFU
** Visual servoing system for non-invasive medical treatment using high intensity focused ultrasound (HIFU). We aim to develop a medical treatment system for renal diseases such as renal calculi and renal cell carcinoma with HIFU's two well-known mechanism, cavitations and heat generation. Clinical use of HIFU system for renal diseases is immature because kidney is one of the moving organs by respirations, manual irradiation of HIFU focus into target in the body can cause a serious safety problem. Here, our research proposes a point/volumetric target tracking system based on ultrasound imaging. Specifically, we estimate the position of HIFU irradiations by registration of bi-plane ultrasound image and preoperative three-dimensional kidney model. The experiment is now conducted with phantom kidney model.
** [[Media:seo-utokyo-ws.zip | Slide with the movies]]

*12:30 - 12:45: Young Min BAEK - A surgical robot universally designed for several surgeries
** My research goal is to develop a surgical robot which can deal with variety of surgical operations. The problem of Computer Aided Surgery (CAS) is its high-cost which make it hard to be conducted in wide areas. Also, a burden of patients has become larger to get a benefit from CAS. General-purposed surgical robot faces to mainly two problems; 1) Mechanical Linkage, 2) Modular structure. To solve these problems, we've developed the surgical robot with easily changeable structure. Master and slave structure is employed with real-time operating systems as well. So far, experiments are conducted in two fields such as neurosurgery and eye surgery. We expect applications can be expanded to other fields in near future.
** [[Media:baek-utokyo-ws.zip | Slide with the movies]]

*12:45 - 1:00: Toki SAITO - Deformable-model-based 2-D/3-D registration for fracture surgeries
** My research topic is computer aided surgery. Especially, I focus on reconstruction of 3D shape and position estimation from 2D X-ray images. Its final goal is to reconstruct real-time computer tomography imaging using X-ray images, and it provides accurate and safe surgery. As a first step, we proposed an estimation method of fractured bone position and shape using statistical deformable models and X-ray images in a CT-less environment, and it provides fracture reduction path automatically and reduces surgeons' burden. In my presentation, I'll talk about it.
** [[Media:saito-utokyo-ws.zip | Slide with the movies]]

*1:00 - 1:15: Toshiyuki OYAMA - Numerical study of bubble motion in liquid
** My topic is a numerical study of bubble motion in liquid. The key of CFD simulation including bubbles is to capture interfaces of bubbles. By front-tracking method, that tracks explicitly positions of interfaces, bubble motion in liquid has been understood for these 15 years. Bubbles of 1 mm diameter rising in water bounce on a free surface between air and water. Applications of bubble motion are not only power plants or mixing towers but also medical treatment in vessels. Bubbles in vessels react on ultra sound. As a result, bubbles oscillate, produce heat and collapse stone in tissue or burn tumor. In my presentation I will speak mainly about bubble bouncing, this is my theme, but also introduce heating vessels with micro bubble and focused ultra sound.
** [[Media:oyama-utokyo-ws.zip | Slide with the movies]]

*1:15 - 1:30: Haytham Elhawary (Post-doctoral fellow, SNR (Hata) lab, BWH) - Intraoperative Visualization of White Matter Tracts During Brain Tumor Resection
** [[Media:Neurosurgery.zip | Slide]]
** [[Media:Video.wmv | Video]]

*1:30 - 1:45: Jayender Jagadeesan (Post-doctoral fellow, SNR (Hata) lab, BWH) - Image Guided Flexible Instrument Manipulation

*1:45 - 2:00: Panagiotis Vartholomeos (Post-doctoral fellow, SNR (Hata) lab, BWH) - Magnetic Guidance for Targeted Drug Delivery : Goal, Challenges and Clinical Applications

*2:00 - 2:15: Sota Oguro (Post-doctoral fellow, SNR (Hata) lab, BWH) - Non-rigid Registration of Pre-procedural MR Images and Intra-procedural CT Images for CT-guided Percutaneous Cryoablation of Renal Tumors

*2:15 - 2:30: Haiying Liu (Engineer for Image Guided Therapy, SNR (Hata) lab, BWH) - IGT Applications at BWH

2:30PM - 3:00PM
NCIGT tour/ Adjourn

==Confirmed Assistance==
Haytham Elhawary, Noby Hata, Jayender Jagadeesan, Haiying Liu, Panagiotis Vartholomeos, Sota Oguro

File:ImageGuidedTherapyPlanning.ppt

2010-01-15T19:54:31Z

Hliu: uploaded a new version of "File:ImageGuidedTherapyPlanning.ppt"

Powerpoint file for the IGT neuroplanning tutorial

File:ImageGuidedTherapyPlanning.pdf

2010-01-15T19:53:44Z

Hliu: uploaded a new version of "File:ImageGuidedTherapyPlanning.pdf"

Tutorial using neurosurgical planning as an example of Image Guided Therapy in Slicer3

Technical Information

2009-10-30T15:07:30Z

Hliu: /* Volume Rendering */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== Volume Rendering ===
Module '''VolumeRenderingCuda''' was used in Slicer for volume rendering. This module has been moved out of Slicer3 trunk and saved in NAMICSandBox/CUDAForVolumeRendering, and is not actively being developed. Now, we should use '''VolumeRendering''' module. Updated by Haiying Liu on Oct 30, 2009.


=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

Technical Information

2009-10-30T14:49:11Z

Hliu: /* Slicer */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== Volume Rendering ===
Module '''VolumeRenderingCuda''' was used in Slicer for volume rendering. This module has been moved out of Slicer3 trunk and saved in NAMICSandBox/CUDAForVolumeRendering, and is not actively being developed. Now, we should use '''VolumeRendering''' module.


=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

Technical Information

2009-10-30T14:40:36Z

Hliu: /* Slicer */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== Volume Rendering ===



=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

Technical Information

2009-10-30T14:39:30Z

Hliu: /* Slicer */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== Volume Rendering ===



=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===
Date: Sept. 26th 2008

Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. 
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:

==== Installation of Drivers ====

* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used
for the driver installation binary
~/Download/CUDA/Driver/
for the tool kit installation binary
~/Download/CUDA/Toolkit/
and for the SDK installation binary
~/Download/CUDA/SDK/
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press
a
Then type
Type 3
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.
* Login and change into root mode via:
su
* Then switch to the directory where you downloaded the driver. For me this means:
cd ~/Download/CUDA/Driver/
* Now we have to change the permissions for the driver-binary and make it executable. This works with
chmod +x BINARY-NAME
(Replace 'BINARY-NAME' with the name of the driver binary)
* Now start the installation with:
./BINARY-NAME
I changed none of the default values during the installation

* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt] If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'

* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values

Technical Information

2009-10-30T14:37:14Z

Hliu: /* Slicer */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== Volume Rendering ===



=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===
Date: Sept. 26th 2008

Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. 
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:

==== Installation of Drivers ====

* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used
for the driver installation binary
~/Download/CUDA/Driver/
for the tool kit installation binary
~/Download/CUDA/Toolkit/
and for the SDK installation binary
~/Download/CUDA/SDK/
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press
a
Then type
Type 3
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.
* Login and change into root mode via:
su
* Then switch to the directory where you downloaded the driver. For me this means:
cd ~/Download/CUDA/Driver/
* Now we have to change the permissions for the driver-binary and make it executable. This works with
chmod +x BINARY-NAME
(Replace 'BINARY-NAME' with the name of the driver binary)
* Now start the installation with:
./BINARY-NAME
I changed none of the default values during the installation

* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt] If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'

* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values

==== Enable CUDA in Slicer 3.3 Alpha ====

* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf] Below you find corrections to certains points that did not work for me the way it was explained in the manual

* In 1.1.2 Check out the following slicer branch instead and build it:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3
./Slicer3/Scripts/getbuildtest.tcl

* Before you can go on with step 1.2.2 you have to Uncomment:
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt

* In step 1.2.2
**you have to use your build directory (Slicer-build) as parameter for ccmake
**for CUDA_INSTALL_PREFIX use /usr/local/cuda
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc

* Step 1.2.3 was not necessary for me

* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available

This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).

Technical Information

2009-10-30T14:26:15Z

Hliu: /* Slicer */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== Volume Rendering ===
~ === 3D CUDA ===
~ I might not use Cuda acceleration since there is no real performance advantage at this point

~ ==== TO DO ====
~ * Nothing

~ ==== Contacts ====
~ * Ben Grauer: [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_With_Cuda Volume Rendering with CUDA]
~ * Nicholas Harlambang: CUDA Guru

~ ==== Documentation: VolumeRenderingCuda Module ====

~ * Adjust the '''threshold''' (scroll bar below 'Component Weights Scrollbars') to correct values. Especially the lower value. Normally > 0
~ * '''Scalar Opacity Mapping''': Shows a histogram of the used values an their transparence. Low transparent, high solid
~ * '''Scalar Color Mapping''': You can click into and than in the color circle above and select certain colors for a specific value
~ * '''Composite''': Here you can select different rendering modes
~ * '''Volume''': You can also select just to display a slice instead of the whole volume. You can transform the slice in the ''Transforms Module'' and than select the ~ transformation matrix in '''Slice Matrix'''
~ * '''Plus/Minus''': Select if you want to see everything or just the volume on one side of the slice and on the other

=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===
Date: Sept. 26th 2008

Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. 
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:

==== Installation of Drivers ====

* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used
for the driver installation binary
~/Download/CUDA/Driver/
for the tool kit installation binary
~/Download/CUDA/Toolkit/
and for the SDK installation binary
~/Download/CUDA/SDK/
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press
a
Then type
Type 3
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.
* Login and change into root mode via:
su
* Then switch to the directory where you downloaded the driver. For me this means:
cd ~/Download/CUDA/Driver/
* Now we have to change the permissions for the driver-binary and make it executable. This works with
chmod +x BINARY-NAME
(Replace 'BINARY-NAME' with the name of the driver binary)
* Now start the installation with:
./BINARY-NAME
I changed none of the default values during the installation

* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt] If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'

* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values

==== Enable CUDA in Slicer 3.3 Alpha ====

* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf] Below you find corrections to certains points that did not work for me the way it was explained in the manual

* In 1.1.2 Check out the following slicer branch instead and build it:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3
./Slicer3/Scripts/getbuildtest.tcl

* Before you can go on with step 1.2.2 you have to Uncomment:
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt

* In step 1.2.2
**you have to use your build directory (Slicer-build) as parameter for ccmake
**for CUDA_INSTALL_PREFIX use /usr/local/cuda
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc

* Step 1.2.3 was not necessary for me

* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available

This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).

Technical Information

2009-10-30T14:20:38Z

Hliu: /* Slicer */

=Technical information of 4D Ultrasound=

[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht <= Back to project page]

You have to understand the following steps to use 4DUltrasound

# Fullfill the requirements
# Check out code and build
# Prepare for use
# Understand how to use 4DUltrasound Tutorial

===Requirement===
In this section you will find requirements to run the software

==== Software ====
* Compiled version of Slicer 3 ''(You must compile Slicer on your own. Follow the build instructions [http://www.slicer.org/slicerWiki/index.php/Slicer3:Build_Instructions here] )''
* Compiled version of VTK ''(Provided by Slicer 3 in the "<code>Slicer-lib/VTK-build</code>" directory)''
* Source Code of OpenIGTLink ''(Provided by Slicer 3 in the "<code>Slicer-lib/OpenIGTLink</code>" directory)''
* Compiled version of OpenIGTLink ''(Provided by Slicer 3 in "<code>Slicer-lib/OpenIGTLink-build</code>" directory)''

===== Modifications =====
* OpenIGTLink Slicer Module:
# Open the file vtkIGTLToMRMLImage.cxx in the source directory of the OpenIGTLinkIF module
# Search for "crc" in this file -> You hit find the following lines <code> // If you want to skip CRC check, call Unpack() without argument. </code> <code> int c = imgMsg->Unpack(1); </code> 
# Change the last line to: <code> int c = imgMsg->Unpack(); </code>
# Recompile the OpenIGTLink Module
## Change to the <code> Slicer-build </code> directory and type <code> $make </code>

* OpenIGTLink:
# Open the file <code> igtlMessageBase.cxx </code> in the "Source" directory of OpenIGTLink
# Search for "crc" -> You will hit the following line <code> igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Comment out this line -> <code> // igtl_uint64 crc = crc64(0, 0, 0LL); // initial crc </code>
# Search for the next "crc" -> You will hit this line: <code> h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Comment out this line -> <code> // h->crc = crc64((unsigned char*)m_Body, GetBodyPackSize(), crc); </code>
# Recompile OpenIGTLink
## Change to the OpenIGTLink-build directory and type <code> $make </code>

==== Hardware ====

[[Image:Drawing-System_Design_Hardware.png |600px]]

''a) Conventional computer with GPGPU graphics card and video capture board b) S-Video connection from US machine to Computer to transfer video information c) US machine d) Tracked US (2D US transducer with attached tracking sensor) e) Tracked surgical instrument f) Magnetic field generator of the tracking system g) EM tracker base station to control and to connect each tracking component h) Serial connection between EM tracker and computer to transfer position and orientation information.''

* NDI Aurora Tracker [http://www.ndigital.com/medical/aurora.php]
** 2 * 6 DOF Sensors
*** 1 Sensor attached to the ultrasound probe
*** 1 Sensor can be used to simulate a tracked surgical instrument

* Ultrasound machine with Analog video output

* Frame Grabber Card
The System has successfully been test with the following 2 frame grabber cards:
** Hauppauge Impact VCB Model 558 [http://wiki.na-mic.org/Wiki/index.php/Technical_Information#Capture_Card_-_Hauppauge_WIN-TV_PCI_Board_ImpactVCB_Model_558]
** Kuroutoshikou KRDM-CX23883

* Optional: nVidia Cuda compatible graphics card

===== Hardware Setup =====

Tracker attached to ultrasound transducer

[[Image:Photo-Tracker_attached_to_Ultrasound.png | 400px ]]

===Build Instructions===

It is highly recommended to have a compiled version of Slicer and to have good knowledge about ''cmake''.

A video of the build process can be found [http://wiki.na-mic.org/Wiki/images/1/1f/BuildInstructions.swf here ] 

# '''Check out''' 4D Ultrasound from http://svn.na-mic.org/NAMICSandBox/trunk/4DUltrasound 
# '''Configure''' via ccmake (version > 2.6) in your build directory ''You need a compiled version of VTK + OpenIGTLink as well as the source code of OpentIGTLink'' If you know how to do this, skip the next steps and procede with ''Compile'' 
## Make a new directory in with the name "Build" in the 4DUltrasound dir: .../4DUltrasound$ mkdir Build 
## Change into the Build directory .../4DUltrasound$ cd Build 
## Execute ccmake in this directory with the parent directory as parameter .../4DUltrasound/Build$ ccmake ../ If ccmake (version > 2.6) is not installed in your system: the executable can as well be found in: .../Slicer3-lib/CMAKE-build/bin/ccmake 
## Type "c" to start the configuration -> You will receive an error message that VTK was not found -> Type "e" to exit the help message 
## Change the cursor to the variable with the name "VTK_DIR" and hit ENTER 
## Fill in your VTK-Build directory and hit ENTER (if you have a compiled version of Slicer you can use: .../Slicer3-lib/VTK-build ) ''(In Ubuntu you must provide the absolute path no relative path will work)'' 
## Hit "c" to start the configuration -> If you receive a warning, ignore it an hit "e" -> hit "c" again -> hit "e" to ignore the next warning -> Fill in the VTK-Build directory again -> hit "c" again -> Ignore the Integer-Type Error hit "e" again 
## Hit "c" 
## Enter the path to the directory of the compiled version of OpenIGTLink at the ''OpenIGTLink'' variable 
## Enter the path to the directory of the OpenIGTLink source code at the ''OPENIGTLINKSOURCE'' variable 
## Hit "c" 
## Set "BUILD_SHARED_LIBS" to OFF 
## Hit "g" to generate the Make files 
# '''Compile''' 4D Ultrasound: Type $ make in your build directory .../4DUltrasound/Build$ make 

=== Preparation to use 4D Ultrasound===

Tutorials how to prepare 4D Ultrasound for use can be found here: [[4DUltrasound_Preparation_to_use]]

===Running 4D Ultrasound===

Here you can see a video tutorial on how to use the software: [http://wiki.na-mic.org/Wiki/images/f/f9/Usage.swf]

You need a working version of Slicer with OpenIGTLink and you must
# Copy "CalibrationFile.txt" from <code> YOUR_SOURCE_DIR </code> to <code> YOUR_BUILD_DIR/bin </code>
# Run Slicer
# Add an "''activer Server Connector''" in the OpenIGTLink module which is waiting for data at port 18944
# Run 4DUltrasound on the same machine you run Slicer
$YOUR_BUILD_DIR/bin/4DUltrasound -c CalibrationFile.txt -gf -tu

====Commandline Options====
{|border="0", cellpadding="4"
|- bgcolor="silver"
! Command !! Alternative !! Description
|-
| --calibration-file xxx || -c xxx || Specify the calibration file (mandatory)
|-
| --grab-ultrasound-frames || -gf || Grab ultrasound frames from the capture board
|-

| --track-ultrasound || -tu || Enable ultrasound tracking
|-
| --track-instrument || -ti || Enable instrument tracking
|-
| --simulate-instrument || -si || Simulate instrument
|-

| --get-calibration-data || -gcd || Get calibration data
|-
| --grab-one-frame XXX || -gof XXX || Grab one frame and store as the specified bitmap file
|-
| --verbose || -v || Print more information
|-
|}

==== TO DO ====
{|border="0", cellpadding="5"
|- bgcolor="silver"
! Priority !! MUST
|-
| align="center" | ||
|-
| align="center" | ||
|- bgcolor="silver"
! Priority !! SHOULD
|-
| align="center", width="70px" | || width="600px"| Clean up Code and Make files (Remove unnecessary Koeniginen parts)
|-
| align="center", width="70px" | || width="600px"| Automatically copy Calibration file into binary directory
|-
| align="center", width="70px" | || width="600px"| Fix compiler checking in cmake
|-
| align="center", width="70px" | || width="600px"| Enable differnet video modes and channels in vtkVideo4Linux2
|-
| align="center", width="70px" bgcolor="#009900" | DONE || width="600px"| Outsource OpenIGTLink library
|-
|- bgcolor="silver"
! Priority !! COULD
|-
| align="center" bgcolor="#009900" width="70px" | DONE || width="600px"| Replace SonixGrabber with Ultrasound in source code
|-
| align="center", width="70px" | || width="600px"| OpenIGTLink test feature
|-
| align="center", width="70px" | || width="600px"| Tracker test feature
|-
| align="center", width="70px" | || width="600px"| Ultrasound test feature
|-
|}

=== Ultrasound device ===
The ultrasound images are received via a video capture card. Linux uses V4L2 to support the card.

==== Capture Card - Hauppauge WIN-TV PCI Board ImpactVCB Model 558====
* [http://www.haupauge.com/site/products/data_impactvcb.html Hauppauge Homepage]
* Incoming images are digitized using high quality 4:2:2 ([http://en.wikipedia.org/wiki/YUV Y:U:V]) video sampling
===== Linux (Ubuntu 8.10 , Fedora 5)=====
* The card is automatically correct detected. No further configuration needed.
* Linux Driver: Video4Linux2 bt878
** "bt" stands for Brooktree the original Manufacturer. Now bought by Conexant
* The Linux driver (bttv) for the WinTV card is now part of the Linux kernel (version 2.6.xxx and newer).
* [http://www.haupauge.com/site/support/support_pci_878.html Hauppage Linux Information]
* Linux installation hints [http://www.haupauge.com/site/support/linux.html]
* Modprobe option # for specific drivers: http://tldp.org/HOWTO/BTTV/cards.html
** The Impact VCB has # 10
** enable kernel module via: "''$ modprobe bttv card=10''" or add to /etc/modprobe.conf the following line "''options bttv card=10 ''"
** to switch to another card first remove the module via: "''$ modprobe -r bttv''"
* The card uses NTSC video interlacing per default
===== Hardware Information =====
* Channel 3 delivers the s-video signal
** To set the channel add the following at the end of void vtkV4L2VideoSource::InitDevice(void):
<code>
int channel = 3;
if (-1 == xioctl (fd,VIDIOC_S_INPUT , &channel))
errno_exit ("VIDIOC_S_INPUT");
</code>
* Specific Hardware information: [http://www.bttv-gallery.de/] !!be carefull huge page, takes a long time to load!!

==== Video4Linux2 ====
Video4Linux is part of the Linux kernel since version 2.6.xx
* V4L2 wiki [http://www.linuxtv.org/wiki/index.php/Main_Page]
* API Specificattion: [http://www.linuxtv.org/downloads/video4linux/API/V4L2_API/spec-single/v4l2.html]
* [http://linux.bytesex.org/xawtv/ xawtv] software for video preview from the guy who wrote the bt8xx driver
===== Old links may soon be dead =====
* [http://linuxtv.org/v4lwiki/index.php/Main_Page V4L Old wiki]
** [http://linuxtv.org/v4lwiki/index.php/Bttv_devices_%28bt848%2C_bt878%29 Driver for our Video Card]
* Link collection for V4L: [http://www.exploits.org/v4l]
* Homepage of the original developer of the bttv driver: [http://linux.bytesex.org/v4l2/] Is not up to date anymore
* [http://www.thedirks.org/v4l2/ Old Informaton] they might not be be up to date anymore

==== Contacts ====
* Christoph Ruetz
** [http://wiki.ncigt.org/index.php/User:Ruetz His Project Page]

=== Tracking device ===
We are using a NDI Aurora tracker. Synchrograb includes an NDI tracker class which works out of the box with the Aurora NDI tracker.

=====Contacts=====
* Haiying Liu

=== Calibration ===
Description: To get the correct information from the ultrasound device it has to be calibrated 
===== Contacts =====
* Raul San Jose
Information:
* I have serval links and information from Raul on which I have to go through

== Slicer ==
I am using the Slicer development version, i.e. Slicer trunk.

=== Python Synchrograb Module ===
I implemented a Pyhton module for Slicer to start Synchrograb. The module can be found in [http://svn.na-mic.org/NAMICSandBox/trunk/SynchroGrabJGumprecht/SlicerModule this] svn repository. Basically it starts a new shell and calls the Synchrograb binary within this shell. All Synchrograb commandline options are available in the module. So fare it is not part of the Slicer repository.

=== 3D CUDA ===
I might not use Cuda acceleration since there is no real performance advantage at this point

==== TO DO ====
* Nothing

==== Contacts ====
* Ben Grauer: [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_With_Cuda Volume Rendering with CUDA]
* Nicholas Harlambang: CUDA Guru

==== Documentation: VolumeRenderingCuda Module ====

* Adjust the '''threshold''' (scroll bar below 'Component Weights Scrollbars') to correct values. Especially the lower value. Normally > 0
* '''Scalar Opacity Mapping''': Shows a histogram of the used values an their transparence. Low transparent, high solid
* '''Scalar Color Mapping''': You can click into and than in the color circle above and select certain colors for a specific value
* '''Composite''': Here you can select different rendering modes
* '''Volume''': You can also select just to display a slice instead of the whole volume. You can transform the slice in the ''Transforms Module'' and than select the transformation matrix in '''Slice Matrix'''
* '''Plus/Minus''': Select if you want to see everything or just the volume on one side of the slice and on the other

=== Links ===

* Sandbox page [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox]
* [https://intweb/Sponsored_Staff_and_Volunteers SPL Intraweb web for incoming staff]

* [http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:DocumentationWink Wink - Software for Video Documentation]

* [http://bwhbri.partners.org/Editorial_Service/ BWH Editorial Service]

=== Infos on loadable Modules ===

[http://www.slicer.org/slicerWiki/index.php/Slicer3:Loadable_Modules:HOWTO HowTo Loadable Module] 

[http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:How_to_implement_an_Interactive_Module_GUI HowToLoadable Module GUI] 

[http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation Infos about Executable Modules inSlicer] 

=== Subscribe to different meetings ===

* Journal Club

* 1st Monday Seminar

* Office OPRC

* Radiology Grand Rounds

* Cimit Forum

=== How to "Enable CUDA 2.0 in Fedora 8 for use with Slicer 3.3 Alpha" ===
Date: Sept. 26th 2008

Fedora 8 is the newest Fedora version for which CUDA is available. The available CUDA Version is 2.0. 
To enable CUDA 2.0 in Fedora 8 for Slicer 3.3 Alpha follow the steps below:

==== Installation of Drivers ====

* Download the CUDA installation files (Driver, Toolkit, SDK) here [http://www.nvidia.com/object/cuda_get.html] and remember the directory in which you downloaded them. I used
for the driver installation binary
~/Download/CUDA/Driver/
for the tool kit installation binary
~/Download/CUDA/Toolkit/
and for the SDK installation binary
~/Download/CUDA/SDK/
* For the installation there must not run a X-Server. Therefore we have to restart the computer. When you see the GRUB Bootscreen after the reboot press any key to enter the GRUB menu. Highlight the Fedora Version you want to boot and press
a
Then type
Type 3
and hit the 'Enter' key. Fedora will boot up without X Server and drop you at Command Line Login prompt.
* Login and change into root mode via:
su
* Then switch to the directory where you downloaded the driver. For me this means:
cd ~/Download/CUDA/Driver/
* Now we have to change the permissions for the driver-binary and make it executable. This works with
chmod +x BINARY-NAME
(Replace 'BINARY-NAME' with the name of the driver binary)
* Now start the installation with:
./BINARY-NAME
I changed none of the default values during the installation

* For the sdk compilation follow this reference guide: [http://developer.download.nvidia.com/compute/cuda/2.0-Beta2/docs/SDK_Rel_Notes_Linux_2.0beta2.txt] If you get the error message: "ld: cannot find -lglut", like I did, have a look at the reference under 'IV. Known Issues'

* In the next step we do the same for the toolkit and for the sdk, e.g chance to the according directory, change the permissions and run the installation with the default values

==== Enable CUDA in Slicer 3.3 Alpha ====

* Start with the installation manual of Ben Grauer. You find it here [http://www.slicer.org/slicerWiki/images/a/ae/Cuda2slicer3.pdf] Below you find corrections to certains points that did not work for me the way it was explained in the manual

* In 1.1.2 Check out the following slicer branch instead and build it:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3
./Slicer3/Scripts/getbuildtest.tcl

* Before you can go on with step 1.2.2 you have to Uncomment:
**''CudaSupport'' in Slicer3/Libs/CMakeLists.txt
**''VolumeRenderingCuda'' in Slicer3/Modules/CMakeLists.txt

* In step 1.2.2
**you have to use your build directory (Slicer-build) as parameter for ccmake
**for CUDA_INSTALL_PREFIX use /usr/local/cuda
**for FOUND_CUT use $HOME/NVIDIA_CUDA_SDK/common/lib/linux/libcudpp.a
**for FOUND_CUT_INCLUDE use $HOME/NVIDIA_CUDA_SDK/common/inc

* Step 1.2.3 was not necessary for me

* Just do a rebuild (run Slicer3/Scripts/getbuildtest.tcl) and the VolumeRenderingCUDA module is available

This installation worked for me on a DELL machine with XEON Dual Core and a Nvidia G8800. For fast rendering make sure not enable compiz(Desktop Effects).

IGT:ToolKit/Neurosurgical-Planning

2009-08-26T00:22:53Z

Hliu: /* Software Installation Instructions */

[[Image:NeurosurgicalPlanningOverview.png|300px|thumb]]

Back to [[IGT:ToolKit|IGT:ToolKit]]

=Neurosurgical Planning for Image Guided Therapy using Slicer3=

==Overview==

This tutorial reviews Slicer3's Image Guided Therapy capabilities using the example of preoperative planning for neurosurgery. It covers how to perform multiple tasks in Slicer3, including:
* Image registration
* Segmentation and model making
* Diffusion Tensor Imaging and tractography
* Using an atlas

==Tutorial Materials==
* Tutorial slides for the neurosurgical planning tutorial: [[Media:ImageGuidedTherapyPlanning.pdf | pdf]] (recommended) or [[Media:ImageGuidedTherapyPlanning.ppt | ppt]]
* [[Media:NeurosurgicalPlanningTutorialData.zip | Neurosurgical planning tutorial dataset]] - contains:
** Patient dataset
** SPL-PNL brain atlas
** MRML scene registering the patient with the atlas
** MRML scene registering the patient's anatomical MRI with the patient's DTI
** MRML scene registering of precomputed tensor data for the patient's DTI

==Bonus Materials==
This is a subset of the data above, which demonstrates some of the capabilities of the tractography package in Slicer 3.4. Snapshots 1-4 demonstrate a progression of the analysis of the interrelation of the morphology and DTI.
#general view
#location of the precentral gyrus based the surface of the white matter
#peritumoral seeding of tractography: The general appearance is that of a "ball of spaghettis" with two tentacles,
#exploration of the "tentacles": fiducial based seeding in the cerebral peduncle and in the vicinity of Brocca's area reveal potential corticospinal tract and acuate fasciculus
*[[media:NeurosurgDTIdemo2008.zip|Original MRML scene and data in a zip file]]
*[[media:2009AprilExperiements.zip|Work in progress update]]
*[[media:MayExperiments.zip|Work in progress 2 update]]

==Software Installation Instructions==
Go to the [http://www.slicer.org/pages/Special:SlicerDownloads Slicer3 Install] site.

==People==
* [http://www.spl.harvard.edu/~dpace Danielle Pace]
* [http://www.spl.harvard.edu/~noby Nobuhiko Hata]

IGT:ToolKit/Neurosurgical-Planning

2009-08-26T00:20:32Z

Hliu: /* Bonus Materials */

[[Image:NeurosurgicalPlanningOverview.png|300px|thumb]]

Back to [[IGT:ToolKit|IGT:ToolKit]]

=Neurosurgical Planning for Image Guided Therapy using Slicer3=

==Overview==

This tutorial reviews Slicer3's Image Guided Therapy capabilities using the example of preoperative planning for neurosurgery. It covers how to perform multiple tasks in Slicer3, including:
* Image registration
* Segmentation and model making
* Diffusion Tensor Imaging and tractography
* Using an atlas

==Tutorial Materials==
* Tutorial slides for the neurosurgical planning tutorial: [[Media:ImageGuidedTherapyPlanning.pdf | pdf]] (recommended) or [[Media:ImageGuidedTherapyPlanning.ppt | ppt]]
* [[Media:NeurosurgicalPlanningTutorialData.zip | Neurosurgical planning tutorial dataset]] - contains:
** Patient dataset
** SPL-PNL brain atlas
** MRML scene registering the patient with the atlas
** MRML scene registering the patient's anatomical MRI with the patient's DTI
** MRML scene registering of precomputed tensor data for the patient's DTI

==Bonus Materials==
This is a subset of the data above, which demonstrates some of the capabilities of the tractography package in Slicer 3.4. Snapshots 1-4 demonstrate a progression of the analysis of the interrelation of the morphology and DTI.
#general view
#location of the precentral gyrus based the surface of the white matter
#peritumoral seeding of tractography: The general appearance is that of a "ball of spaghettis" with two tentacles,
#exploration of the "tentacles": fiducial based seeding in the cerebral peduncle and in the vicinity of Brocca's area reveal potential corticospinal tract and acuate fasciculus
*[[media:NeurosurgDTIdemo2008.zip|Original MRML scene and data in a zip file]]
*[[media:2009AprilExperiements.zip|Work in progress update]]
*[[media:MayExperiments.zip|Work in progress 2 update]]

==Software Installation Instructions==
Go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Slicer3 Install] site.

==People==
* [http://www.spl.harvard.edu/~dpace Danielle Pace]
* [http://www.spl.harvard.edu/~noby Nobuhiko Hata]

Events:Slicer Workshop August 2009

2009-08-26T00:12:07Z

Hliu: /* Afternoon: Introduction to Slicer IGT */

==Course Title==
[[Image:776px-Flyer SlicerWorkshop August2009.png|right|500 px]]
Introduction to Opensource Software Slicer and its Application to Image-Guided Therapy

== Course Syllabus ==
The purpose of this tutorial is to provide the members of the research community with a practical experience of the image processing, 3D visualization, and Image-Guided Therapy capabilities of the Open Source 3D Slicer software platform. The curriculum is '''hands-on''' which means that participants are required to attend the workshop with a suitable laptop, preloaded with the software and sample data as specified below. Attendance is limited in order to ensure quality interactions between the faculty and participants.

== Course Faculty ==
*Sonia Pujol, Ph.D., Instructor in Radiology, Harvard Medical School
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

*Lauren O'Donnell, Ph.D., Instructor in Radiology, Harvard Medical School
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

*Kathryn Hayes, M.S.E.
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

*Haiying Liu, M.Eng., M.Sc.
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

== Logistics ==
*Date: Tuesday, August 25, 2009
*Time: 9am - 4pm
*Location: 1249 Boylston Street, Boston MA ([http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street Directions])
*Participants are required to come with their own computer (PC, Linux or MacOS).
*'''Registration is on a first-come, first-served basis and space is limited to 15 participants'''.
 '''To register to this event, please send an e-mail to slicer-training at bwh.harvard.edu''' with your name, affiliation, contact information and the characteristics of the laptop you'll be bringing to the workshop.

== Agenda ==
===Morning: Introduction to Slicer===
* 9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
* 9:10 am - 9:30 am [[Media:Slicer3 Introduction IBMISPS2009 SoniaPujol.pdf | Slicer3 Overview and Applications ]](Sonia Pujol)
* 9:30 am - 10:30 am [[Media:Slicer3Course_DataLoadingAndVisualization_IBMISPS2009_SoniaPujol.pdf | Hands-on Session 1: Data Loading and 3D Visualization ]](Sonia Pujol)
* 10:30 am - 10:45 am Coffee-break
* 10:45 am - 11:30 am [[Media:Slicer3Course_DataLoadingAndVisualization_IBMISPS2009_SoniaPujol.pdf | Hands-on Session 2: Data Saving ]](Sonia Pujol)
* 11:30 am - 12:00 pm Discussion and Conclusion
* 12:00 -1pm Lunch Break

===Afternoon: Introduction to Slicer IGT===
*1:00 - 1:30 pm [[media:Slicer-IGT-Overview-IBMSPSAug2009.ppt|'''Introduction: Why Slicer3 for your IGT research? An overview of Slicer3 for IGT.''']] (15 min. O'Donnell)
* 1:30 - 4:00 pm [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning and Guidance by Slicer''']
**Module 1-3 (1:30-2:45 pm) (K. Hayes)
# Loading and visualizing anatomical MRI data
# Incorporating fMRI data using image registration and thresholding
# Creating a 3D model of the tumour volume
* 2:45 - 3:00 pm Coffee-break
**Module 4-6 (3:00-4:00 pm) (H. Liu)
# Predicting the locations of brain structures using image registration and a brain atlas
# Incorporating brain fiber tractography from diffusion weighted images
# Annotating the preoperative plan and saving the scene

== Preparation for the Workshop ==
Please complete the following items prior to the course. Support will be provided as requested
*Software Installation: Please install the newest [http://www.slicer.org/pages/Special:SlicerDownloads Slicer3.4 release ]appropriate to the computer you will be bringing to the workshop:
** Windows: Slicer3-3.4-2009-05-21-win32.exe
** Mac OSX Darwin PPC: Slicer3-3.4.2009-05-21-darwin-ppc.tar.gz
** Mac OSX Darwin Intel: Slicer3-3.4.2009-05-21-darwin-x86.tar.gz
** Linux x86: Slicer3-3.4.2009-05-21-linux-x86.tar.gz
** Linux x86-64: Slicer3-3.4.2009-05-21-linux-x86_64.tar.gz

The [http://www.slicer.org/slicerWiki/index.php/Slicer3:Downloads instructions for installing the Slicer3 program ] describe the different steps of the procedure on Mac OS, Linux and Windows.

Recommended configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory.

*Data to download: Please install the [http://www.slicer.org/slicerWiki/index.php/Image:Slicer3VisualizationDataset.zip Slicer3VisualizationDataset].

Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

File:ImageGuidedTherapyPlanning.ppt

2009-08-23T22:33:02Z

Hliu: uploaded a new version of "File:ImageGuidedTherapyPlanning.ppt"

Powerpoint file for the IGT neuroplanning tutorial

File:ImageGuidedTherapyPlanning.pdf

2009-08-23T22:30:01Z

Hliu: uploaded a new version of "File:ImageGuidedTherapyPlanning.pdf"

Tutorial using neurosurgical planning as an example of Image Guided Therapy in Slicer3

OpenCV Module in Slicer3

2009-08-19T02:55:05Z

Hliu: /* Future Work */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==
* To include OpenCV module into your Slicer3 build, open this file:
Slicer3/slicer_variables.tcl
 
and set ::USE_OPENCV to "ON"

* The compiling process will automatically download and build OpenCV 1.0 from http://sourceforge.net/projects/opencvlibrary/files/.

==Test the system==
[[Image:opencv_video_from_camera.png|300px|thumb|Video from a camera is displayed in the second window of OpenCV module in Slicer3.]]
#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=
# OpenCV 1.0 library is now built automatically as one of the external libraries in Slicer3 if we turn it on. OpenCV module in Slicer3 is then built on top of the OpenCV l.0 library. If we want to use OpenCV 1.1 in the future, we need figure out why our module fails to compile with OpenCV 1.1.
# More testing of the functionality in OpenCV module.

=Bug Fixes=

* There is a bug in OpenCV related to V4L2 devices:
** Here is the bugtrac with information: [[https://bugs.launchpad.net/ubuntu/+source/linux/+bug/260251]]
*** Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
** Here is the fix [[http://opencvlibrary.svn.sourceforge.net/viewvc/opencvlibrary/trunk/opencv/src/highgui/cvcap_v4l.cpp?r1=1604&r2=1609]]
*** Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp

OpenCV Module in Slicer3

2009-08-19T02:45:33Z

Hliu: /* Compile Slicer3 */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==
* To include OpenCV module into your Slicer3 build, open this file:
Slicer3/slicer_variables.tcl
 
and set ::USE_OPENCV to "ON"

* The compiling process will automatically download and build OpenCV 1.0 from http://sourceforge.net/projects/opencvlibrary/files/.

==Test the system==
[[Image:opencv_video_from_camera.png|300px|thumb|Video from a camera is displayed in the second window of OpenCV module in Slicer3.]]
#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=
# The latest OpenCV library supports svn and CMake. I have built it into the list of Slicer external libraries. When you compile Slicer3, you will automatically get OpenCV library compiled. However, the compilation of OpenCV module in Slicer trunk failed against the library. We need to figure out what caused the failure of that compilation in order to automate the build of OpenCV module.
# More testing of the functionality in OpenCV module.

=Bug Fixes=

* There is a bug in OpenCV related to V4L2 devices:
** Here is the bugtrac with information: [[https://bugs.launchpad.net/ubuntu/+source/linux/+bug/260251]]
*** Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
** Here is the fix [[http://opencvlibrary.svn.sourceforge.net/viewvc/opencvlibrary/trunk/opencv/src/highgui/cvcap_v4l.cpp?r1=1604&r2=1609]]
*** Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp

OpenCV Module in Slicer3

2009-08-19T02:44:34Z

Hliu:

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==
* To include OpenCV module into your Slicer3 build, open this file:
Slicer3/slicer_variables.tcl
 
and set ::USE_OPENCV to "ON"

* Then the compiling process will automatically download and build OpenCV 1.0 from http://sourceforge.net/projects/opencvlibrary/files/.

==Test the system==
[[Image:opencv_video_from_camera.png|300px|thumb|Video from a camera is displayed in the second window of OpenCV module in Slicer3.]]
#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=
# The latest OpenCV library supports svn and CMake. I have built it into the list of Slicer external libraries. When you compile Slicer3, you will automatically get OpenCV library compiled. However, the compilation of OpenCV module in Slicer trunk failed against the library. We need to figure out what caused the failure of that compilation in order to automate the build of OpenCV module.
# More testing of the functionality in OpenCV module.

=Bug Fixes=

* There is a bug in OpenCV related to V4L2 devices:
** Here is the bugtrac with information: [[https://bugs.launchpad.net/ubuntu/+source/linux/+bug/260251]]
*** Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
** Here is the fix [[http://opencvlibrary.svn.sourceforge.net/viewvc/opencvlibrary/trunk/opencv/src/highgui/cvcap_v4l.cpp?r1=1604&r2=1609]]
*** Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp

Events:Slicer Workshop August 2009

2009-08-17T13:55:56Z

Hliu:

==Course Title==
[[Image:776px-Flyer SlicerWorkshop August2009.png|right|500 px]]
Introduction to Opensource Software Slicer and its Application to Image-Guided Therapy

== Course Syllabus ==
The purpose of this tutorial is to provide the members of the research community with a practical experience of the image processing, 3D visualization, and Image-Guided Therapy capabilities of the Open Source 3D Slicer software platform. The curriculum is '''hands-on''' which means that participants are required to attend the workshop with a suitable laptop, preloaded with the software and sample data as specified below. Attendance is limited in order to ensure quality interactions between the faculty and participants.

== Course Faculty ==
*Sonia Pujol, Ph.D., Instructor in Radiology, Harvard Medical School
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

*Lauren O'Donnell, Instructor in Radiology, Harvard Medical School
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

*Kathryn Hayes, M.S.E.
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

*Haiying Liu, M.Eng., M.Sc.
Surgical Planning Laboratory, Brigham and Women's Hospital, Boston MA

== Logistics ==
*Date: Tuesday, August 25, 2009
*Time: 9am - 4pm
*Location: 1249 Boylston Street, Boston MA ([http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street Directions])
*Participants are required to come with their own computer (PC, Linux or MacOS).
*'''Registration is on a first-come, first-served basis and space is limited to 15 participants'''.
 '''To register to this event, please send an e-mail to slicer-training at bwh.harvard.edu''' with your name, affiliation, contact information and the characteristics of the laptop you'll be bringing to the workshop.

== Agenda ==
===Morning: Introduction to Slicer===
* 9:00 am - 9:10 am Preliminary session: Software and data installation trouble shooting
* 9:10 am - 9:30 am [[media:Slicer3_Introduction_SoniaPujol_NationalCancerInstitute_August15_2008.ppt| Slicer3 Overview and Applications]] (Sonia Pujol)
* 9:30 am - 10:30 am Hands-on Session 1: [[media:3DVisualization_SoniaPujol_NationalCancerInstitute_August15_2008.ppt‎| Data Loading and 3D Visualization]] (Sonia Pujol)
* 10:30 am - 10:45 am Coffee-break
* 10:45 am - 11:30 am Hands-on Session 2: [[media:3DVisualization_SoniaPujol_NationalCancerInstitute_August15_2008.ppt‎| Data Saving]] (Sonia Pujol)
* 11:30 am - 12:00 pm Discussion and Conclusion
* 12:00 -1pm Lunch Break

===Afternoon: Introduction to Slicer IGT===
*1:00 - 1:30 pm [[media:SlicerIGTOverview.ppt|'''Introduction: Why Slicer 3 for your IGT research? An example from BWH BrainLab collaboration''']] (15 min. Hata)
* 1:30 - 4:00 pm [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''Neurosurgical Planning and Guidance by Slicer"]
**Module 1-3 (1:30-2:45 pm)
# Loading and visualizing anatomical MRI data
# Incorporating fMRI data using image registration and thresholding
# Creating a 3D model of the tumour volume
* 2:45 - 3:00 pm Coffee-break
**Module 4-6 (3:00-4:00 pm)
# Predicting the locations of brain structures using image registration and a brain atlas
# Incorporating brain fiber tractography from diffusion weighted images
# Annotating the preoperative plan and saving the scene

== Preparation for the Workshop ==
Please complete the following items prior to the course. Support will be provided as requested
*Software Installation: Please install the newest [http://www.slicer.org/pages/Special:SlicerDownloads Slicer3.4 release ]appropriate to the computer you will be bringing to the workshop:
** Windows: Slicer3-3.4-2009-05-21-win32.exe
** Mac OSX Darwin PPC: Slicer3-3.4.2009-05-21-darwin-ppc.tar.gz
** Mac OSX Darwin Intel: Slicer3-3.4.2009-05-21-darwin-x86.tar.gz
** Linux x86: Slicer3-3.4.2009-05-21-linux-x86.tar.gz
** Linux x86-64: Slicer3-3.4.2009-05-21-linux-x86_64.tar.gz

The [http://www.slicer.org/slicerWiki/index.php/Slicer3:Downloads instructions for installing the Slicer3 program ] describe the different steps of the procedure on Mac OS, Linux and Windows.

Recommended configuration: Windows XP, Linux (x86 or x86_64), Mac OS (ppc or Intel), 2 GB of RAM and a dedicated graphic accelerator with 128 MB of on board graphic memory.

*Data to download: Please install the [http://www.slicer.org/slicerWiki/index.php/Image:Slicer3VisualizationDataset.zip Slicer3VisualizationDataset].

Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

OpenCV Module in Slicer3

2009-07-25T18:37:30Z

Hliu: /* Test the system */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Install OpenCV 1.0==

# Download OpeCV 1.0 at http://sourceforge.net/projects/opencvlibrary/files/. You get file "opencv-1.0.0.tar.gz"
# Move the file to any temporary folder and then unzip it using "tar xvfz opencv-1.0.0.tar.gz". You will get a directory called "opencv-1.0.0"
# cd to opencv-1.0.0 and run these commands:
./configure
make
sudo make install

 The above commands will configure, compile and install opencv 1.0 on your system.

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==

I have created a Slicer3 (in trunk) module named "OpenCV," whose name was suggested by Dr. Noby Hata.
It's basically the videoOpenIGTLink module plus a few bug fixes.
To include this module into your Slicer3 build, open this file:
Slicer3/Modules/CMakeLists.txt

and uncomment "OpenCV" (by default, it's commented for now because it depends on OpenCV library)

==Test the system==
[[Image:opencv_video_from_camera.png|300px|thumb|Video from a camera is displayed in the second window of OpenCV module in Slicer3.]]
#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=
# The latest OpenCV library supports svn and CMake. I have built it into the list of Slicer external libraries. When you compile Slicer3, you will automatically get OpenCV library compiled. However, the compilation of OpenCV module in Slicer trunk failed against the library. We need to figure out what caused the failure of that compilation in order to automate the build of OpenCV module.
# More testing of the functionality in OpenCV module.

File:Opencv video from camera.png

2009-07-25T18:36:29Z

Hliu:

OpenCV Module in Slicer3

2009-07-25T18:35:53Z

Hliu: /* Test the system */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Install OpenCV 1.0==

# Download OpeCV 1.0 at http://sourceforge.net/projects/opencvlibrary/files/. You get file "opencv-1.0.0.tar.gz"
# Move the file to any temporary folder and then unzip it using "tar xvfz opencv-1.0.0.tar.gz". You will get a directory called "opencv-1.0.0"
# cd to opencv-1.0.0 and run these commands:
./configure
make
sudo make install

 The above commands will configure, compile and install opencv 1.0 on your system.

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==

I have created a Slicer3 (in trunk) module named "OpenCV," whose name was suggested by Dr. Noby Hata.
It's basically the videoOpenIGTLink module plus a few bug fixes.
To include this module into your Slicer3 build, open this file:
Slicer3/Modules/CMakeLists.txt

and uncomment "OpenCV" (by default, it's commented for now because it depends on OpenCV library)

==Test the system==

#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.
[[Image:opencv_video_from_camera.png|300px|thumb|Video from a camera is displayed in the second window of OpenCV module in Slicer3.]]

=Future Work=
# The latest OpenCV library supports svn and CMake. I have built it into the list of Slicer external libraries. When you compile Slicer3, you will automatically get OpenCV library compiled. However, the compilation of OpenCV module in Slicer trunk failed against the library. We need to figure out what caused the failure of that compilation in order to automate the build of OpenCV module.
# More testing of the functionality in OpenCV module.

OpenCV Module in Slicer3

2009-07-25T18:30:38Z

Hliu: /* Future Work */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Install OpenCV 1.0==

# Download OpeCV 1.0 at http://sourceforge.net/projects/opencvlibrary/files/. You get file "opencv-1.0.0.tar.gz"
# Move the file to any temporary folder and then unzip it using "tar xvfz opencv-1.0.0.tar.gz". You will get a directory called "opencv-1.0.0"
# cd to opencv-1.0.0 and run these commands:
./configure
make
sudo make install

 The above commands will configure, compile and install opencv 1.0 on your system.

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==

I have created a Slicer3 (in trunk) module named "OpenCV," whose name was suggested by Dr. Noby Hata.
It's basically the videoOpenIGTLink module plus a few bug fixes.
To include this module into your Slicer3 build, open this file:
Slicer3/Modules/CMakeLists.txt

and uncomment "OpenCV" (by default, it's commented for now because it depends on OpenCV library)

==Test the system==

#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=
# The latest OpenCV library supports svn and CMake. I have built it into the list of Slicer external libraries. When you compile Slicer3, you will automatically get OpenCV library compiled. However, the compilation of OpenCV module in Slicer trunk failed against the library. We need to figure out what caused the failure of that compilation in order to automate the build of OpenCV module.
# More testing of the functionality in OpenCV module.

OpenCV Module in Slicer3

2009-07-25T18:28:29Z

Hliu: /* Future Work */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Install OpenCV 1.0==

# Download OpeCV 1.0 at http://sourceforge.net/projects/opencvlibrary/files/. You get file "opencv-1.0.0.tar.gz"
# Move the file to any temporary folder and then unzip it using "tar xvfz opencv-1.0.0.tar.gz". You will get a directory called "opencv-1.0.0"
# cd to opencv-1.0.0 and run these commands:
./configure
make
sudo make install

 The above commands will configure, compile and install opencv 1.0 on your system.

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==

I have created a Slicer3 (in trunk) module named "OpenCV," whose name was suggested by Dr. Noby Hata.
It's basically the videoOpenIGTLink module plus a few bug fixes.
To include this module into your Slicer3 build, open this file:
Slicer3/Modules/CMakeLists.txt

and uncomment "OpenCV" (by default, it's commented for now because it depends on OpenCV library)

==Test the system==

#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=
* The latest OpenCv library supports svn and CMake. I have built it into the list of Slicer external library. When you compile Slicer3, you will automatically get OpenCV library compiled. However, the compilation of OpenCV module in Slicer trunk failed against the library. We need to figure out what caused the failure of that compilation in order to automate the build of OpenCV modules.
* More testing of the functionality of OpenCV module.

OpenCV Module in Slicer3

2009-07-25T18:20:28Z

Hliu: /* Test the system */

=Steps to Build and Use OpenCV Module=

==My operating system==
The following Linux system is my desktop where this tutorial is based on: 
Ubuntu 8.04 - the Hardy Heron - released in April 2008. 
Linux brainlab-desktop 2.6.24-23-generic #1 SMP Mon Jan 26 00:13:11 UTC 2009 i686 GNU/Linux

==Install OpenCV 1.0==

# Download OpeCV 1.0 at http://sourceforge.net/projects/opencvlibrary/files/. You get file "opencv-1.0.0.tar.gz"
# Move the file to any temporary folder and then unzip it using "tar xvfz opencv-1.0.0.tar.gz". You will get a directory called "opencv-1.0.0"
# cd to opencv-1.0.0 and run these commands:
./configure
make
sudo make install

 The above commands will configure, compile and install opencv 1.0 on your system.

==Test camera==

#My camera is '''Logitech QuickCam Pro for Noteboks'''
#If you don't have a tool called "luvcview," you can get it using this command "sudo apt-get install luvcview"
#Plug in the camera to any usb port on your computer
#Run luvcview

 In a few seconds you should see video displayed in luvcview

==Compile Slicer3==

I have created a Slicer3 (in trunk) module named "OpenCV," whose name was suggested by Dr. Noby Hata.
It's basically the videoOpenIGTLink module plus a few bug fixes.
To include this module into your Slicer3 build, open this file:
Slicer3/Modules/CMakeLists.txt

and uncomment "OpenCV" (by default, it's commented for now because it depends on OpenCV library)

==Test the system==

#Plug in your camera into any usb port
#Bring Slicer up
#Go to the modules list in Slicer3 interface
#Pick OpenCV module
#Press the button "second window on"

You should see video from the camera in a few seconds.

=Future Work=