NAMIC Wiki - User contributions [en]

File:MMTest.tar.gz

2010-03-11T19:17:28Z

Talos:

2009 Summer Project Week Multimodal SPL Brain Atlas

2009-06-19T17:11:40Z

Talos:

__NOTOC__
<gallery>
Image:Thalamus.png
</gallery>

==Key Investigators==
* BWH: Ion-Florin Talos, Michael Halle, Wendy Plesniak
* GE: Jim Miller

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

<h3>Objective</h3>
To explore ways of linking the image data of the SPL multi-modal brain atlas (label maps, 3D-models) with ontological information on brain morphology and function

</div>

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

<h3>Approach, Plan</h3>

* continue work on XML-based intermediate data representation that supports anatomical hierarchies and can describe arbitrary overlapping image regions
* application integration of the new XML-based data representation (3D-Slicer)
* discussion of automated testing for atlas segmentation
* discussion of integration of FMA with atlas
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>

</div>
</div>
<div style="width: 970%; float: left;">
==References==
1. Talos IF, Rubin DL, Halle M, Musen MA, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.

2. Rubin DL, Talos IF, Halle M, Musen MA, Kikinis R. Computational neuroanatomy: ontology-based representation of neural components and connectivity. BMC Bioinformatics 2009; 10(Suppl 2):S3.
</div>

2009 Summer Project Week Multimodal SPL Brain Atlas

2009-06-19T15:54:15Z

Talos:

__NOTOC__
<gallery>
Image:Thalamus.png
</gallery>

==Key Investigators==
* BWH: Ion-Florin Talos, Michael Halle, Wendy Plesniak
* GE: Jim Miller

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

<h3>Objective</h3>
To explore ways of linking the image data of the SPL multi-modal brain atlas (label maps, 3D-models) with ontological information on brain morphology and function

</div>

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

<h3>Approach, Plan</h3>

* continue work on XML-based intermediate data representation that supports anatomical hierarchies and can describe arbitrary overlapping image regions (e.g. brain functional systems)
* application integration of the new XML-based data representation (3D-Slicer)

==References==
1. Talos IF, Rubin DL, Halle M, Musen MA, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263.
2. Rubin DL, Talos IF, Halle M, Musen MA, Kikinis R. Computational neuroanatomy: ontology-based representation of neural components and connectivity. BMC Bioinformatics 2009; 10(Suppl 2):S3.

2009 Summer Project Week Multimodal SPL Brain Atlas

2009-06-19T15:30:48Z

Talos:

__NOTOC__
<gallery>
Image:Thalamus.png
</gallery>

==Key Investigators==
* BWH: Ion-Florin Talos, Michael Halle, Wendy Plesniak
* GE: Jim Miller

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

<h3>Objective</h3>
To explore ways of linking the image data of the SPL multi-modal brain atlas (label maps, 3D-models) with ontological information on brain morphology and function

</div>

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

<h3>Approach, Plan</h3>

* continue work on XML-based intermediate data representation that supports anatomical hierarchies and can describe arbitrary overlapping image regions (e.g. brain functional systems)
* application integration of the new XML-based data representation (3D-Slicer)

==References==
1. Talos IF, Rubin DL, Halle M, Musen MA, Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform. 2008 Apr;41(2):251-263. PMID: 18164666. PMCID: PMC2376098.
2. Rubin DL, Talos IF, Halle M, Musen MA, Kikinis R. Computational neuroanatomy: ontology-based representation of neural components and connectivity. BMC Bioinformatics 2009; 10(Suppl 2):S3. PMID: 19208191. PMCID: PMC2646240.

2009 Summer Project Week

2009-06-19T14:53:37Z

Talos:

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

[[Image:PW2009-v3.png|300px]]

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** 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 Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-4pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 4:30pm CIMIT Forum (at BWH Shapiro Center) Open Source Software for Translational IGT Research and Commercial Use, Clif Burdette, Acoustic MedSystems, Inc. At BWH / Carl J. and Ruth Shapiro Cardiovascular Cente
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alexandre Gouaillard)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11am [[Events:TutorialContestJune2009|Tutorial Contest Presentations]]
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT for Programmers]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: [[Events:TutorialContestJune2009|Tutorial Contest Winner Announcement]] and [[#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_2010|in Utah, January 4-8, 2010]]

== Projects ==
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Ion-Florin Talos BWH)
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch BWH PNL)
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Marek Kubicki BWH)
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
#[[2009_Summer_Project_Week_Adaptive_RT| Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov,Vandana Mohan,Gregory Sharp, and Allen Tannenbaum)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
#[[2009_Summer_Project_Week_GWE_XNAT | GWE-XNAT Integration]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_GWE_Results_Browser | GWE Results Browser Improvements]] (Marco Ruiz UCSD)
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. the BIRN). 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-3-4/#dirlist Slicer-3-4 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].

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
==Attendee List==

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''
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|110
|- style=&#34height:50px&#34
|111
|- style=&#34height:50px&#34
|112
|- style=&#34height:50px&#34
|113
|- style=&#34height:50px&#34
|114
|- style=&#34height:50px&#34
|115
|- style=&#34height:50px&#34
|116
|- style=&#34height:50px&#34
|117
|- style=&#34height:50px&#34
|118
|- style=&#34height:50px&#34
|119
|- style=&#34height:50px&#34
|120
|- style=&#34height:50px&#34
|121
|- style=&#34height:50px&#34
|122
|- style=&#34height:50px&#34
|123
|- style=&#34height:50px&#34
|124
|- style=&#34height:50px&#34
|}
|
{| class="wikitable sortable"
!First
!Last
!Affiliation
|- style=&#34height:50px&#34
|John
|Melonakos
|AccelerEyes (Wed & Thu morning)
|- style=&#34height:50px&#34
|Jack
|Blevins
|Acoustic Med
|- style=&#34height:50px&#34
|Clif
|Burdette
|Acoustic Med (Mon-Wed)
|- style=&#34height:50px&#34
|Dana
|Peters
|Beth Israel Deaconess
|- style=&#34height:50px&#34
|Nicole
|Aucoin
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Giovanna
|Danagoulian
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haytham
|Elhawary
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Andriy
|Fedorov
|BWH (NAMIC Collaborator)
|- style=&#34height:50px&#34
|Daniel
|Haehn
|BWH (NAC)
|- style=&#34height:50px&#34
|Michael
|Halle
|BWH (NAC)
|- style=&#34height:50px&#34
|Nobuhiko
|Hata
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Katie
|Hayes
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Scott
|Hoge
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Tina
|Kapur
|BWH (NCIGT, NAMIC)
|- style=&#34height:50px&#34
|Ron
|Kikinis
|BWH (NAMIC, NAC, NCIGT)
|- style=&#34height:50px&#34
|Jayender
|Jagadeesan
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Haying
|Liu
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Lauren
|O'Donnell
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Wendy
|Plesniak
|BWH (NAC)
|- style=&#34height:50px&#34
|Megumi
|Nakao
|BWH (NAIST)
|- style=&#34height:50px&#34
|Sonia
|Pujol
|BWH (NAMIC)
|- style=&#34height:50px&#34
|Lei
|Qin
|BWH (NCIGT Collaborator)
|- style=&#34height:50px&#34
|Nicolas
|Rannou
|BWH (NAC)
|- style=&#34height:50px&#34
|Petter
|Risholm
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Florin
|Talos
|BWH (NAC)
|- style=&#34height:50px&#34
|Clare
|Tempany
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Junichi
|Tokuda
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Demian
|Wasserman
|BWH (INRIA)
|- style=&#34height:50px&#34
|Carl-Fredrik
|Westin
|BWH (NAC)
|- style=&#34height:50px&#34
|Sandy
|Wells
|BWH (NAC, NCIGT)
|- style=&#34height:50px&#34
|Lilla
|Zollei
|MGH (NAC)
|- style=&#34height:50px&#34
|Padma
|Akella
|BWH (NCIGT)
|- style=&#34height:50px&#34
|Sylvain
|Bouix
|BWH (PNL)
|- style=&#34height:50px&#34
|Julien
|de Siebenthal
|BWH (PNL)
|- style=&#34height:50px&#34
|Marek
|Kubicki
|BWH (NAMIC DBP PNL)
|- style=&#34height:50px&#34
|Juhana
|Frosen
|BWH Tues only
|- style=&#34height:50px&#34
|Sun Woo
|Lee
|BWH (PNL)
|- style=&#34height:50px&#34
|Jimi
|Malcolm
|BWH (PNL)
|- style=&#34height:50px&#34
|Eric
|Melonakos
|BWH (PNL)
|- style=&#34height:50px&#34
|Yogesh
|Rathi
|BWH (PNL)
|- style=&#34height:50px&#34
|Peter
|Savadjiev
|BWH (PNL)
|- style=&#34height:50px&#34
|Doug
|Terry
|BWH (PNL)
|- style=&#34height:50px&#34
|Andrew
|Rausch
|BWH (Mon only)
|- style=&#34height:50px&#34
|Cal
|Hisley
|Des Moines Unive
|- style=&#34height:50px&#34
|Jim
|Miller
|GE
|- style=&#34height:50px&#34
|Xiaodong
|Tao
|GE
|- style=&#34height:50px&#34
|Vandana
|Mohan
|GA Tech
|- style=&#34height:50px&#34
|Yi
|Gao
|GA Tech
|- style=&#34height:50px&#34
|Ivan
|Kolosev
|GA Tech
|- style=&#34height:50px&#34
|Behnood
|Gholami
|GA Tech
|- style=&#34height:50px&#34
|Ziv
|Yaniv
|Georgetown
|- style=&#34height:50px&#34
|Alex
|Gouaillard
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Arnaud
|Gelas
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Sean
|Megason
|Harvard Systems Biology (Wed only)
|- style=&#34height:50px&#34
|Lydie
|Souhait
|Harvard Systems Biology
|- style=&#34height:50px&#34
|Moti
|Freiman
|Hebrew University of Jerusalem
|- style=&#34height:50px&#34
|Amanda
|Peters
|Harvard SEAS
|- style=&#34height:50px&#34
|Maria Francesca
|Spadea
|Italy
|- style=&#34height:50px&#34
|Curtis
|Lisle
|KnowledgeVis
|- style=&#34height:50px&#34
|Steve
|Pieper
|Isomics
|- style=&#34height:50px&#34
|Alex
|Yarmarkovich
|Isomics
|- style=&#34height:50px&#34
|Nathan
|Cho
|JHU
|- style=&#34height:50px&#34
|Bennett
|Landman
|JHU
|- style=&#34height:50px&#34
|Snehashis
|Roy
|JHU
|- style=&#34height:50px&#34
|Sam
|Song
|JHU
|- style=&#34height:50px&#34
|Sebastien
|Barre
|Kitware
|- style=&#34height:50px&#34
|Luis
|Ibanez
|Kitware
|- style=&#34height:50px&#34
|Daniel
|Blezek
|Mayo
|- style=&#34height:50px&#34
|Yong
|Gao
|MGH
|- style=&#34height:50px&#34
|Randy
|Gollub
|MGH
|- style=&#34height:50px&#34
|Rui
|Li
|MGH
|- style=&#34height:50px&#34
|Greg
|Sharp
|MGH
|- style=&#34height:50px&#34
|Robert
|Yaffe
|MGH - Mon
|- style=&#34height:50px&#34
|Sylvain
|Jaume
|MIT
|- style=&#34height:50px&#34
|Bjoern
|Menze
|MIT
|- style=&#34height:50px&#34
|Jeremy
|Bockholt
|MRN (NAMIC Lupus DBP)
|- style=&#34height:50px&#34
|Mark
|Scully
|MRN (NAMIC Lupus DBP) Tue-Th
|- style=&#34height:50px&#34
|Joe
|Stam
|NVIDIA (Wed & Thurs)
|- style=&#34height:50px&#34
|Kimberly
|Powell
|NVIDIA (Wed)
|- style=&#34height:50px&#34
|Marta
|Peroni
|Politecnico di Milano
|- style=&#34height:50px&#34
|Andras
|Lasso
|Queen's (NAMIC DBP)
|- style=&#34height:50px&#34
|Yanling
|Liu
|SAIC/NCI-Frederick
|- style=&#34height:50px&#34
|Melanie
|Grebe
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Lining
|Yang
|Siemens Corporate Research
|- style=&#34height:50px&#34
|Harish
|Doddi
|Stanford University
|- style=&#34height:50px&#34
|Marco
|Ruiz
|UCSD
|- style=&#34height:50px&#34
|Nathan
|Hageman
|UCLA (Mon-Thurs)
|- style=&#34height:50px&#34
|Hans
|Johnson
|U Iowa
|- style=&#34height:50px&#34
|Vincent
|Magnotta
|U Iowa
|- style=&#34height:50px&#34
|Jeffrey
|Yager
|U Iowa
|- style=&#34height:50px&#34
|Manasi
|Ramachandran
|U Iowa
|- style=&#34height:50px&#34
|Dave
|Welch
|U Iowa
|- style=&#34height:50px&#34
|Andrzej
|Przybyszewski
|UMass Med (Mon)
|- style=&#34height:50px&#34
|James
|Balter
|U Michigan
|- style=&#34height:50px&#34
|Dan
|McShan
|U Michigan
|- style=&#34height:50px&#34
|Zhou
|Shen
|U Michigan
|- style=&#34height:50px&#34
|Beatriz
|Paniagua
|UNC
|- style=&#34height:50px&#34
|Minjeong
|Kim
|UNC
|- style=&#34height:50px&#34
|Zhexing
|Liu
|UNC
|- style=&#34height:50px&#34
|Clement
|Vachet
|UNC (NAMIC DBP)
|- style=&#34height:50px&#34
|Guorong
|Wu
|UNC
|- style=&#34height:50px&#34
|Samuel
|Gerber
|SCI, Utah
|- style=&#34height:50px&#34
|Ran
|Tao
|SCI, Utah
|- style=&#34height:50px&#34
|Marcel
|Prastawa
|SCI, Utah
|- style=&#34height:50px&#34
|Ross
|Whitaker
|SCI, Utah
|- style=&#34height:50px&#34
|Curtis
|Rueden
|UW-Madison
|- style=&#34height:50px&#34
|Dan
|Marcus
|WUSTL
|- style=&#34height:50px&#34
|Misha
|Milchenko
|WUSTL
|- style=&#34height:50px&#34
|Kevin
|Archie
|WUSTL
|- style=&#34height:50px&#34
|Tim
|Olsen
|WUSTL
|- style=&#34height:50px&#34
|Mehdi
|Esteghamatian
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Diego
|Cantor
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Danielle
|Pace
|Robarts Research Inst. / Western Ontario
|- style=&#34height:50px&#34
|Vidya
|Rajagopalan
|VA Tech
|- style=&#34height:50px&#34
|Gregory
|Fischer
|WPI
|- style=&#34height:50px&#34
|Dominique
|Belhachemi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Alark
|Joshi
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Xenios
|Papademetris
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Dustin
|Scheinost
|Yale U (Tu & Wed)
|- style=&#34height:50px&#34
|Michelle
|Borkin
|Harvard SEAS (Mon only)
|- style=&#34height:50px&#34
|Renxin
|Chu
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Ben
|Schwartz
|BWH (NCIGT) (Mon, Tue)
|- style=&#34height:50px&#34
|Marianna
|Jakab
|BWH (NCIGT, NAC) (Mon, Tue)
|- style=&#34height:50px&#34
|Viswanath
|Avasarala
|GE (Wed, Thurs)
|- style=&#34height:50px&#34
|}
|}

'''Please do not add any more names here. If you need to register, please send an email to tkapur at bwh.harvard.edu and we will accommodate you if we can.'''

The following was used to convert from excel to mediawiki markup: http://area23.brightbyte.de/csv2wp.php

2009 Summer Project Week

2009-06-08T19:30:40Z

Talos: /* Collaboration Projects */

2009 Summer Project Week Multimodal SPL Brain Atlas

2009-06-08T19:26:07Z

Talos:

__NOTOC__
<gallery>
Image:Thalamus.png
</gallery>

==Key Investigators==
* BWH: Ion-Florin Talos
* Utah:
* UNC:
* Georgia Tech:

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

<h3>Objective</h3>
To create a segmentation pipeline for thalamic nuclei

</div>

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

<h3>Approach, Plan</h3>
apply the spectral clustering approach to delineating the major thalamic nuclei in a high-resolution, volumetric DTI-dataset (voxel size 1 mm, 120 gradients)

==References==
*Zyian U, Tuch D, Westin CF, Segmentation of Thalamic Nuclei from DTI Using Spectral Clustering, Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv. 2006;9(Pt 2):807-14.

2009 Summer Project Week Multimodal SPL Brain Atlas

2009-06-08T19:08:20Z

Talos: Created page with '__NOTOC__ <gallery> Image:Thalamus.png </gallery> ==Key Investigators== * BWH: Ion-Florin Talos * Utah: * UNC: * Georgia Tech: <div style="margin: 20px;"> <div style="width: 27...'

File:Thalamus.png

2009-06-08T18:51:19Z

Talos:

2009 Summer Project Week

2009-06-08T18:41:57Z

Talos:

2009 Summer Project Week

2009-06-01T18:26:43Z

Talos:

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

*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].

==Introduction to the FIRST JOINT PROJECT WEEK==

We are pleased to announce the FIRST JOINT PROJECT WEEK of hands-on research and development activity for Image-Guided Therapy and Neuroscience applications. 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 will begin on''' Thursday, April 16th 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 that this FIRST JOINT EVENT is based on is available [[Project_Events#Past|here]].

== Agenda==
* Monday
** 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 Start project work
* Tuesday
** 8:30am breakfast
**9:30-10am: NA-MIC Kit Overview (Jim Miller)
** 10-10:30am Slicer 3.4 Update (Steve Pieper)
** 10:30-11am Slicer IGT and Imaging Kit Update Update (Noby Hata, Scott Hoge)
** 11am-12:00pm Breakout Session: [[2009 Project Week Breakout Session: Slicer-Python]] (Demian W)
** noon lunch
** 2:30pm-5pm: [[2009 Project Week Data Clinic|Data Clinic]] (Ron Kikinis)
** 5:30pm adjourn for day
* Wednesday
** 8:30am breakfast
** 9am-12pm Breakout Session: [[2009 Project Week Breakout Session: ITK]] (Luis Ibanez)
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: 3D+T Microscopy Cell Dataset Segmentation]] (Alex G.)
** 5:30pm adjourn for day
* Thursday
** 8:30am breakfast
** 9-11pm Tutorial Contest Presentations
** noon lunch
** 2:30pm: Breakout Session: [[2009 Project Week Breakout Session: XNAT]] (Dan M.)
** 5:30pm adjourn for day
* Friday
** 8:30am breakfast
** 10am-noon: Tutorial Contest Winner Announcement and Project Progress using update [[#Projects|Project Wiki pages]]
*** 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_2010|in Utah, January 4-8, 2010]]

== Projects ==

The list of projects for this week will go here.
=== Collaboration Projects ===
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images]]
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi, Dan Blezek?, Steve, Alex G?)
#Liver Ablation in Slicer (Haiying, Ziv)
#SLicer3 and Brainlab - introduction to UCLA (Haiying, Xenios, Pratik, Nathan Hageman)
#Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp, Steve, Wendy)
#Brain DTI Atlas? (Florin, Utah, UNC, GeorgiaTech)
#Xnat user interface improvements for NA-MIC (Dan M, Florin, Ron, Wendy)
#xnat and DICOMRT (Greg Sharp, Dan M) - might be done?
#Grid Wizard+xnat clinic (Clement Vachet)
#?Fluid Mechanincs Module (Nathan Hageman)
#?DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman)
#Cortical Thickness Pipeline (Clement Vachet, Ipek Oguz)
#Demo Brainlab/Slicer in BWH OR (Haiying, Nathan Hageman)
#Skull Stripping (Xiaodong, Snehashis Roy)
#FastMarching for brain tumor segmentation (Fedorov, GeorgiaTech)
#Meningioma growth simulation for validation (Fedorov, Marcel, Ron)
#Automatic brain MRI processing pipeline (Marcel, Hans)
#XNAT integration into Harvard Catalyst i2b2 framework(Gao, Yong)
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez,Thomas Yeo, Polina Goland), - (Mon, Tue, Wed)
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze, Jeff Yager, Vince Magnotta)
#Drunk Monkey Contd (Vidya Rajgopalan, Andrey Fedorov)

===IGT Projects:===
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi, Sam, Nathan Cho, Jack), - Mon, Tue, Thursday 7pm-midnight)
#port 4d gated ultrasound code to Slicer - (Danielle)
#integration of stereo video into Slicer (Mehdi)
#multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego, sylvain jaume, nicholas, noby)
#neuroendoscope workflow presentation (sebastien barre)
#breakout session on Dynamic Patient Models (James Balter)
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Sandy Wells, Jim Balter, and others)

===NA-MIC Engineering Projects===
# DICOM Validation and Cleanup Tool (Luis, Sid, Steve, Greg)
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve, Demian, Jim)
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole, Karthik, Sebastien, Wendy)
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole)
# EM Segmenter (Sylvain, Nicolas)
# Plug-in 3D Viewer based on XIP (Lining)
# IAFE Mesh Modules - improvements and testing (Curt, Steve, Vince)
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wen, Steve, Dan M, Dan B)
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber,Jim Miller, Ross Whitaker)
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao, Jim Miller, Sylvain Bouix, Tom Fletcher, Ross Whitaker, Julien Siebenthal)
# Fix [http://www.na-mic.org/Bug/view.php?id=416 bug 416] in registration (Andriy, Luis, Bill, Jim, Steve)
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn)

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# Join the kickoff TCON on April 16, 3pm ET.
# [[Engineering:TCON_2009|June 18 TCON]] at 3pm ET to tie loose ends. Anyone with un-addressed questions should call.
# By 3pm ET on June 11, 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 18, 2009: 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. the BIRN). 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-3-4/#dirlist Slicer-3-4 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==
If you plan to attend, please add your name here.

#Ron Kikinis, BWH
#Ferenc Jolesz, BWH
#Clare Tempany, BWH
#Tina Kapur, BWH
#Steve Pieper, Isomics Inc
#Jim Miller, GE Research
#Xiaodong Tao, GE Research
#Bill Lorensen, EAB
#Randy Gollub, MGH
#Nicole Aucoin, BWH
#Dan Marcus, WUSTL
#Junichi Tokuda, BWH
#Alex Gouaillard, Harvard Systems Biology
#Arnaud Gelas, Harvard Systems Biology
#Kishore Mosanliganti, Harvard Systems Biology
#Lydie Souhait, Harvard Systems Biology
#Luis Ibanez, Kitware Inc
#Vincent Magnotta, UIowa
#Hans Johnson, UIowa
#Xenios Papademetris, Yale
#Gregory S. Fischer, WPI (Mon, Tue, Wed)
#Daniel Blezek, Mayo (Tue-Fri)
#Danielle Pace, Robarts Research Institute / UWO
#Clement Vachet, UNC-Chapel Hill
#Dave Welch, UIowa
#Demian Wassermann, Odyssée lab, INRIA, France
#Manasi Ramachandran, UIowa
#Greg Sharp, MGH
#Rui Li, MGH
#Mehdi Esteghamatian, Robarts Research Institute / UWO
#Misha Milchenko, WUSTL
#Kevin Archie, WUSTL
#Tim Olsen, WUSTL
#Wendy Plesniak BWH
#Haiying Liu BWH
#Curtis Lisle, KnowledgeVis / Isomics
#Diego Cantor, Robarts Research Institute / UWO
#Daniel Haehn, BWH
#Nicolas Rannou, BWH
#Sylvain Jaume, MIT
#Alex Yarmarkovich, Isomics
#Marco Ruiz, UCSD
#Andriy Fedorov, BWH
#Harish Doddi, Stanford University
#Saikat Pal, Stanford University
#Scott Hoge, BWH
#Vandana Mohan, Georgia Tech
#Ivan Kolosev, Georgia Tech
#Behnood Gholami, Georgia Tech
#James Balter, U Michigan
#Dan McShan, U Michigan
#Zhou Shen, U Michigan
#Maria Francesca Spadea, Italy
#Lining Yang, Siemens Corporate Research
#Beatriz Paniagua, UNC-Chapel Hill
#Bennett Landman, Johns Hopkins University
#Snehashis Roy, Johns Hopkins University
#Marta Peroni, Politecnico di Milano
#Sebastien Barre, Kitware, Inc.
#Samuel Gerber, SCI University of Utah
#Ran Tao, SCI University of Utah
#Marcel Prastawa, SCI University of Utah
#Katie Hayes, BWH
#Sonia Pujol, BWH
#Andras Lasso, Queen's University
#Yong Gao, MGH
#Minjeong Kim, UNC-Chapel Hill
#Guorong Wu, UNC-Chapel Hill
#Jeffrey Yager, UIowa
#Yanling Liu, SAIC/NCI-Frederick
#Ziv Yaniv, Georgetown
#Bjoern Menze, MIT
#Vidya Rajagopalan, Virginia Tech
#Sandy Wells, BWH
#Lilla Zollei, MGH
#Lauren O'Donnell, BWH
#Florin Talos, BWH

== Logistics ==
*'''Dates:''' June 22-26, 2009
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week). Due by Friday, June 12th, 2009. Please make checks out to "Massachusetts Institute of Technology" and mail to: Donna Kaufman, MIT, 77 Massachusetts Ave., 38-409a, Cambridge, MA 02139. Receipts will be provided by email as checks are received. Please send questions to dkauf at mit.edu. '''If this is your first event and you are attending for only one day, the registration fee is waived.''' Please let us know, so that we can cover the costs with one of our grants.
*'''Registration Method''' Add your name to the Attendee List section of this page
*'''Hotel:''' We have a group rate of $189/night (plus tax) at the Le Meridien (which used to be the Hotel at MIT). [http://www.starwoodmeeting.com/Book/MITDECSE Please click here to reserve.] This rate is good only through June 1.
*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.
*2009 Summer Project Week [[NA-MIC/Projects/Theme/Template|'''Template''']]
*[[2008_Summer_Project_Week#Projects|Last Year's Projects as a reference]]
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]

2008 IGT Project Week

2008-12-12T01:25:40Z

Talos:

=Introduction=
<gallery perrow="4" widths="200px">
Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
Image:Nac.png|[http://nac.spl.harvard.edu/ Neuroimage Analysis Center]
Image:Cimit_logo.gif|[http://www.cimit.org CIMIT]
</gallery>
'''Dates: Monday, December 8th to Friday, December 12th'''

Location: Monday's activities will take place in Room BC-4-004 F at the Ledge Building, located at 1 Brigham Circle, Boston MA. (Directions to this room from the entrance of 1 Brigham Circle: to get to the 4th floor conference Room BC4-004 F, take the elevator to the 4th floor. Take a right off the elevator. Go through 2 sets of doors, once you go through the second set, take a right, it is the 3rd door down on your left hand side.) Rest of the week will be at the SPL facility at 1249 Boylston Street, Boston MA ([http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. Directions]) (See here for information about area [[Boston_Hotels|hotels]].)

IGT Project Week is a hands-on event that will involve various scientific, clinical, and engineering activities that are part of building image-guided therapy systems. Please note that is '''not''' a week long session of lectures and/or slide presentations. Instead, active researchers in the field will gather for a week to get actual work done on projects that they have identified ahead of time. A fair amount of effort will be put into phone calls between the hosts and the participants in the month leading upto the event to ensure that every participant belongs to a project that makes sense to be pursued in such a collaborative setting. Depending on the needs of the projects, the hosts, NCIGT at Brigham and Women's Hospital, will reserve time at appropriate research imaging and therapy equipment.

Before the event, individual phone calls/meetings will be held with confirmed participants to review the scope of the work that they will collaboratively pursue during this week. The event itself will start with short presentation by each project team to allows all participants to be acquainted with others who are doing similar work. In the rest of the week, most of the time will be spent doing hands-on programming, imaging, algorithm design, phantom or animal experiments or other validation in small project teams. Given that this is the first stand-alone IGT event of this kind, we expect to have about 5-10 teams of size 3-4 each. To facilitate this work, a conference room will be setup with several tables, with internet and power access, to allow teams to either work on their own laptops. Based on the project requirements, times will also be reserved on the research imaging equipment and therapy equipment at Brigham and Women's Hospital. 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 modeled after the [http://www.na-mic.org/Wiki/index.php/Project_Events NA-MIC Project Week] and its main goal is to foster a hand-on image-guided therapy systems community. The first event is being organized by NCIGT and several other NIH funded grants, and the outcome at this meeting will determine the format and frequency of future events. Unfortunately, no travel support is available from NCIGT for this event; it must be sponsored by their host institution/grant.

If you are interested in joining this event, please send an email to Tina Kapur: tkapur at bwh.harvard.edu

=Agenda=

==Monday==
Please note that Monday's session will be held at The Ledge Building located at One Brigham Circle Room BC-4-004 F

*1:30-3:30pm: Presentation of all Projects by Project Leaders Using the descriptions below ([[#Projects]])
*3:30pm - 430pm: [[2008 IGT Project Week Prostate Breakout Session|Prostate breakout session]]
*3:30-5pm: Start Project Work

==Tuesday==
Please note that the rest of the week will be held at the 2nd floor conference room, 1249 Boylston Street.

*9am: Breakfast
*9am-noon: Work
*noon: lunch
*1-5pm: Work
*3pm: coffee

==Wednesday==
*9am: Breakfast
*9am-noon: Work
*10-noon: Radiation Therapy Collaboration Discussion with James Balter
*noon: lunch
*1pm: Journal Club Talk: James Balter, University of Michigan: "Finding the truth: Surrogates and Sampling for Setup and monitoring of treatment" [[2008 December 10 Balter talk|Abstract]]
*2-5pm: Work
*3pm: coffee

==Thursday==
*9am: Breakfast
*9am-noon: Work
*noon: lunch
*1-5pm: Work
*3pm: coffee
*720pm: Mockup MR-guided Prostate Biopsy (221 Longwood)

==Friday==
*9am: Breakfast
*10am: Review of Progress
*12pm: adjourn

=Projects=

This is a working list of projects for this week.

#[[2008 IGT Project Week Fast Imaging Library|Fast Imaging Library]] (Scott Hoge,Bob Kraft)
#[[2008 IGT Project Week Nonrigid MR-ULS Registration Algorithms for Neurosurgery, Prostate MRgFUS and Brachytherapy|Nonrigid MR-ULS Registration Algorithms for Neurosurgery, Prostate MRgFUS and Brachytherapy]] (Matt Toews, Sandy Wells, Michel Audette, Tina Kapur, Nathan McDannold, Ben Schwartz, Steve Haker)
#[[2008 IGT Project Week Dynamic control of the MRI acquisition|Dynamic control of the MRI acquisition]] (Ben Schwartz, Nathan McDannold, Scott Hoge)
#[[2008 IGT Project Week RF Ablation System|RF Ablation System]] (Ziv Yaniv Georgetown, Noby Hata, Paul Morrison)
#[[2008 IGT Project Week Volume Rendering for IGT using CUDA|Volume Rendering for IGT using CUDA]] (Xenios Papademeteris, John Onofrey, Noby Hata, Steve Pieper, Isaiah Norton)
#[[2008 IGT Project Week Realtime Tractography for Neurosurgery VVLINK| Realtime Tractography for Neurosurgery:VVLINK]](Xenios Papademeteris, Noby Hata, Haiying Liu, Isaiah Norton, Jean-Jacques Lemaire, Madeline, Steve Pieper )
#[[2008 IGT Project Week Tractography for Neurosurgery: Workflow feedback| Tractography for Neurosurgery: Workflow feedback]](Isaiah Norton, Jean-Jacques Lemaire, Haiying Liu, Steve Pieper )
#[[2008 IGT Project Week Prostate Robotics|Prostate Robotics]] (Junichi Tokuda, Noby Hata, Clif Burdette, Jack Blevins, Clare Tempany,Sam Song, Bong Joon Cho, Greg Fisher, Roland Goerlitz)
#[[2008 IGT Project Week Work-flow based Slicer Module for IGT application|Work-flow based Slicer Module for IGT application]] (Andinet Enquobahrie, Noby Hata, Steve Pieper)
#[[2008 IGT Project Week Optimal Transseptal Puncture Location for RF ablation|Optimal Transseptal Puncture Location for RF cardiac ablation]] (Jayender Jagadeesan, Raul San Jose, Noby Hata, Greg Michaud)
#[[2008 IGT Project Week Neurosurgical Planning and Simulation|Neurosurgical Planning and Simulation]] (Michel Audette, Andinet Enquobahrie)

=Confirmed Attendees=
#Ziv Yaniv, Georgetown - Monday 11:00pm-Wednesday 3pm
#Andinet Enquobahrie, Kitware- Monday 1:30pm-Tuesday 5pm
#Michel Audette, Kitware - Monday 1:30pm-Friday noon
#Xenios Papademetris, Yale- Monday 1:30pm-Tuesday 5pm.
#John Onofrey, Yale-Monday 1:30pm-Tuesday 5pm
#Sandy Wells, BWH- Monday 1:30pm-Friday noon
#Tina Kapur, BWH - Monday 1:30pm-Friday noon
#Matt Toews, BWH - Monday 1:30pm-Friday noon
#Noby Hata, BWH - Monday 1:30pm-Friday noon
#Steve Pieper, BWH - Monday 1:30pm-Friday noon
#Katie Hayes, BWH - Monday 1:30pm-Friday noon
#Scott Hoge, BWH - Monday 1:30pm-Friday noon
#Nathan McDannold, BWH - Mon, Fri
#Ben Schwartz, BWH - Mon, Tue, Thurs, Fri
#Ron Kikinis, BWH- Monday 1:30pm-Friday noon
#Clare Tempany, BWH- Monday 1:30pm-3:30pm, Friday 10am-noon
#Ferenc Jolesz, BWH- Monday 1:30pm-3:30pm, Friday 10am-noon
#Junichi Tokuda, BWH - Monday 1:30pm-Friday noon
#Haiying Liu, BWH- Monday 1:30pm-Friday noon
#Greg Fischer, WPI- Monday-Thursday (only late afternoons and evening)
#Clif Burdette, AcousticMed Systems- Monday 1:30pm-Friday noon
#Jack Blevins, AcousticMed Systems- Monday 1:30pm-Thursday 5pm
#Bong Joon Cho (Nathan), JHU- Monday 1:30pm-Friday noon
#Sam Song, JHU- Monday 1:30pm-Friday noon
#Andriy Fedorov, BWH/W&M- Monday 1:30pm-Wednesday
#Haytham Elhawary, BWH- Monday 1:30pm-Friday noon
#Bob Kraft, Wake Forest Univ- Monday 1:30pm-Friday noon
#James Balter, U Michigan- Wednesday 9am-Thursday 4pm
#Paul Morrison, BWH - Monday, Tuesday afternoon, Wed morning
#Jayender, BWH - Monday 1:30pm-Friday noon
#Madeline Seeland, BWH - Monday 1:30pm-Friday noon
#Raul San Jose Estepar, BWH - Mon, Tue, Thursday
#Yanmei Tei, BWH - Mon
#Wentao Wu, BWH - Mon
#Jean-Jacques Lemaire, BWH - Mon, Tue
#Nikos Chrisochoides, W&M - Monday 1:30pm-Wednesday
#Isaiah Norton, Mon, Tue&Thur: most of the day; Wed. afternoon
#Ehud Schmidt, Mon, Fri
#Roland Goerlitz, Mon 1:30pm-Friday noon
#Nicu Archip, Monday
#Florin Talos, Monday
#* We are at capacity for this event.

File:MPRAGE 0p75mm iso 16min 17.zip

2008-07-15T19:15:54Z

Talos:

Slicer3.2:Training

2008-07-01T19:55:24Z

Talos:

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category/#'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.3'''
| style="background:#D1FFF9; color:black"| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|100px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.4'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3 ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]<br>
This tutorial takes the trainee through the slicer3 diffusion display and processing options.
See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|100px|Glyphs and tracts]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.2'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3722 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for more background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|100px|Brain Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.3'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3731 SPL Abdominal Atlas]
This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3729 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 '''here'''] for more background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3731 SPL Abdominal Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Abdominal-Atlas-3Dsnapshot.png|100px|Abdominal Atlas]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

Slicer3.2:Training

2008-07-01T19:26:20Z

Talos:

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category/#'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.3'''
| style="background:#D1FFF9; color:black"| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|100px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.4'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3 ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]<br>
This tutorial takes the trainee through the slicer3 diffusion display and processing options.
See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|100px|Glyphs and tracts]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.2'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
This three-dimensional brain atlas derived from a volumetric, whole-head MRI scan contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3722 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for more background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|100px|Brain Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.3'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3731 SPL Abdominal Atlas]
This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3729 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 '''here'''] for more background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3731 SPL Abdominal Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Abdominal-Atlas-3Dsnapshot.png|100px|Abdominal Atlas]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

Slicer3.2:Training

2008-07-01T19:18:55Z

Talos:

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category/#'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.3'''
| style="background:#D1FFF9; color:black"| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|100px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.4'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3 ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]<br>
This tutorial takes the trainee through the slicer3 diffusion display and processing options.
See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|100px|Glyphs and tracts]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.2'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
This three-dimensional brain atlas derived from a volumetric, whole-head MRI scan contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3722 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|100px|Brain Atlas]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.3'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3731 SPL Abdominal Atlas]
This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3729 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3731 SPL Abdominal Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Abdominal-Atlas-3Dsnapshot.png|100px|Abdominal Atlas]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

File:Abdominal-Atlas-3Dsnapshot.png

2008-07-01T19:15:56Z

Talos:

Slicer3.2:Training

2008-07-01T19:03:58Z

Talos:

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category/#'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.3'''
| style="background:#D1FFF9; color:black"| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|100px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.4'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3 ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]<br>
This tutorial takes the trainee through the slicer3 diffusion display and processing options.
See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|100px|Glyphs and tracts]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.2'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
This three-dimensional brain atlas derived from a volumetric, whole-head MRI scan contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3722 tutorial]. See [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1265 '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|100px|Brain Atlas]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

Slicer3.2:Training

2008-07-01T18:38:39Z

Talos:

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Category/#'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.1'''
| style="background:#D1FFF9; color:black"| [[Media:3DVisualization_SoniaPujol_Munich2008.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.2'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegmentation2008.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.3'''
| style="background:#D1FFF9; color:black"| Affine and deformable [[Media:Na-MIC-Slicer-Registration.ppt|registration in Slicer 3]]
| style="background:#D1FFF9; color:black"| [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Na-MIC-Slicer-Registration.png|100px|SlicerRegistration]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1.4'''
| style="background:#D1FFF9; color:black"| [[Media:slicer3diffusionTutorial6.ppt| Processing of DWI and DTI data in Slicer3 ]] [[Media:Slicer3 dti tutorial4.ppt|earlier version]]<br>
This tutorial takes the trainee through the slicer3 diffusion display and processing options.
See [http://slicer.org/slicerWiki/index.php/Slicer3:DTMRI '''here'''] for background info.
| style="background:#D1FFF9; color:black"|[[Media:Slicer3-diffusion-Tutorial material.zip|Slicer3-diffusion-Tutorial material.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Line-glyph-tracts.jpg|100px|Glyphs and tracts]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.1'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Plug-ins for Slicer3: Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2.2'''
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|Image Guided Therapy Planning Tutorial]]<br>
See [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning '''here'''] for background info.
This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping
| style="background:#D1FFF9; color:black"|[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.1'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|-
| style="background:#72b291; color:black" align="Center"| '''3.2'''
| style="background:#D1FFF9; color:black"| [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
This three-dimensional brain atlas derived from a volumetric, whole-head MRI scan contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a [http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3722 tutorial].
| style="background:#D1FFF9; color:black"|[http://www.spl.harvard.edu/extensions/PubDB/publications/download_bitstream.php?bitstreamid=3732 SPL-PNL Brain Atlas]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Atlas.png|100px|Brain Atlas]]
|}

* Category 1 = Basic functionality
* Category 2 = Advanced functionality
* Category 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

File:Atlas.png

2008-07-01T18:15:29Z

Talos:

BrainAtlas

2008-03-13T15:42:47Z

Talos:

[[Image:Nac.png|right|thumb|96px|[http://nac.spl.harvard.edu Link] to the NAC website]]

* this page is under construction

= Introduction =

* The Surgical Planning Laboratory, in conjunction with the Neuroscience Laboratory, created a three-dimensional digitized atlas of the human brain that has been used for surgical planning, model-driven segmentation, research, and teaching, and can be found on the World Wide Web at http://www.spl.harvard.edu

The atlas was created initially as a joint effort between the Laboratory of Neuroscience of the Harvard Medical School at the Brockton VA Medical Center, Brockton, MA and the Surgical Planning Laboratory, Department of Radiology at the Brigham and Women's Hospital, Boston, MA. Dr. Shenton, one of the original people involved at the Laboratory of Neuroscience at Brockton VA Medical Center, is now Director of the Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School.

* We are pleased to make this brain atlas available to our colleagues with the following stipulations:

The data is being distributed under the [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl '''Slicer license''']. By dowloading these data you also agree to '''acknowledge our contribution in any of your publications''' that result from the use of this atlas. Please acknowledge the following grants: P41RR013218, R01MH050740

* For your reference, here are the inital publications discussing this atlas:
** Shenton et al. [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=349 Harvard brain atlas: A teaching and visualization tool.] Proceedings of Biomedical Visualization 10-17, 1995.
** Kikinis et al. [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=347 A Digital Brain Atlas for Surgical Planning, Model Driven Segmentation and Teaching.] IEEE Transactions on Visualization and Computer Graphics 1996; 2(3):232-241.

= Directions =

* The atlas consists of
** a brain mri of a normal subject (T1W SPGR) acquired on a 1.5T system,
** a data set containing labels for different anatomical structures
** 3d surface models of these structures
** a mrml file that allows loading all of the data into 3d Slicer for visualization (see [[Slicer:Workshops:User_Training_101|the '''Slicer 101''' page]] for a link to the 3D Slicer download site and for information on how to load data and mrml files)
** a list of label values for the segmented structures
** inside slicer there are several pre-defined views for the motor, visual and limbic systems, diencephalon, brain stem, left cerebral hemisphere
* The [[Media:Brain_Atlas_Tutorial07.ppt| <big>'''tutorial'''</big>]] explains how to view the data.
* '''Get the [[Media:Spl_pnl_brain_atlas_2007b.zip|SPL-PNL-Brain_Atlas_2007]] here'''.
* '''Get the [[Media:Spl_pnl_brain_atlas_2007_slicer3.zip|SPL-PNL-Brain_Atlas_2007 for Slicer3]] here''' (you need a version of Slicer that is dated 05-15-2007 or later).
* [[media:SPL-BrainAtlas-label_list.txt| A list of the labels is available]].

Slicer:Workshops:User Training 101

2008-02-21T17:58:20Z

Talos:

<div class="thumb tright"><div style="width: 90px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div
class="thumbcaption">[http://www.spl.harvard.edu/nac Link to the NAC website]</div></div></div>

= Introduction =
This is a training compendium for using 3DSlicer. This work is jointly sponsored by NA-MIC, NAC and NCIGT.

This series of courses will teach you how to
* load and view data
* segment data and create 3D models
* perform Diffusion Tensor Imaging and fMRI analysis
For an overview of Slicer, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]

= Software =
<div class="floatleft"><span>[[Image:3DSlicer.png|80px|[[Image:3DSlicer.png| 3D Slicer Logo]]]]</span></div>

The current version of Slicer that is fully supported is Slicer 2.6.

Please follow the [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started]] instructions to install the version of the Slicer program appropriate to your platform.

= Training Compendium =

For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).

[[Image:101.png|thumb|right|450px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).]]

{| border="2"
|- bgcolor="white"
|
| '''Course'''
| '''Dataset'''
|- bgcolor="white"
||[[Image:Training1 LoadingViewing.PNG|50px]]
|
[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training7Save.PNG|50px]]
|
[[Media:SlicerTraining7SavingData.ppt| Data Saving ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial-with-dicom.zip]]
|- bgcolor="white"
|[[Image:Training2Segmentation.PNG|50px]]
|
[[Media:Slicer_Segmentation_Tutorial.ppt| Manual Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
|[[Image:Training3LevelSets.PNG|50px]]
|
[[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training10EM.png|50px]]
|
[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| Automatic Brain Segmentation ]]
|
[[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip ]]
|- bgcolor="white"
| [[Image:Training11Registration.PNG|55px]]
|
[[Media:SlicerAdvancedTraining11_Registration.ppt| Registration]]
|
[[Media:RegistrationSample.zip| RegistrationSample.zip]]
|- bgcolor="white"
|[[Image:Training4DTI.PNG|50px]]
|
[[Media:Slicer_DTMRI_Training4.ppt| Diffusion Tensor Imaging Analysis ]]
|
[[Media:SlicerSampleDTI.zip| SlicerSampleDTI.zip]] [[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training8Nrrd.PNG|50px]]
|
[[Media:SlicerTraining8-NrrdFileFormat.ppt| Nrrd File Format]]
|
[[Media:Tensor_data.zip|Tensor_data.zip]]
|- bgcolor="white"
| [[Image:Training9DicomToNrrd.PNG|50px]]
|
[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Dicom to Nrrd Conversion ]]
|
[[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training5fMRI.PNG|50px]]
|
[[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonace Imaging Analysis ]]
|
[[Media:FMRIData1_short.zip|FMRIData1_short.zip]] [[Media:FMRIData2_long.zip|FMRIData2_long.zip]]
|- bgcolor="white"
| [[Image:Training6FreeSurfer.PNG|50px]]
|
[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurfer Reader ]]
|
[[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
|}

= Slicer Additional Resources =
[[Image:Limbic-2007.jpg|thumb|right|330px| A rendering of the Limbic System from the SPL PNL brain atlas]]

* [[BrainAtlas|SPL PNL Brain Atlas]]
* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel [[Media:EMSegmentTutorial.zip|data]] and white matter hyperintensities
* [[DataFusion|Data Fusion and Registration]]
* [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
* [[SlicerOnBIRN|How to use Slicer with BIRN]]
* [[media:Abdomen-v2.zip|CT based atlas of the abdomen]]. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.
* [[media:AbdominalAtlas.tar.gz|CT based atlas of the abdomen for Slicer 3]]; [[media:Abdominal_Atlas_Tutorial08.ppt|tutorial]] describing how to load and display the data in Slicer 3
* [http://www.airwayinspector.org/ Airway inspector]: 3D Slicer based tool for morphometry analysis of the lung airways and emphysema.

= Feedback =

* [[Slicer:Feedback|Feedback about Slicer]]
* [http://www.na-mic.org/Bug/ Bug reports]

= Acknowledgements =
*Slicer is being developed by a community of contributors. For more information see the [http://www.slicer.org Slicer] website.

<br /> Back to [[Training:Main|Training:Main]]

Slicer:Workshops:User Training 101

2008-02-21T16:18:00Z

Talos:

<div class="thumb tright"><div style="width: 90px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div
class="thumbcaption">[http://www.spl.harvard.edu/nac Link to the NAC website]</div></div></div>

= Introduction =
This is a training compendium for using 3DSlicer. This work is jointly sponsored by NA-MIC, NAC and NCIGT.

This series of courses will teach you how to
* load and view data
* segment data and create 3D models
* perform Diffusion Tensor Imaging and fMRI analysis
For an overview of Slicer, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]

= Software =
<div class="floatleft"><span>[[Image:3DSlicer.png|80px|[[Image:3DSlicer.png| 3D Slicer Logo]]]]</span></div>

The current version of Slicer that is fully supported is Slicer 2.6.

Please follow the [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started]] instructions to install the version of the Slicer program appropriate to your platform.

= Training Compendium =

For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).

[[Image:101.png|thumb|right|450px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).]]

{| border="2"
|- bgcolor="white"
|
| '''Course'''
| '''Dataset'''
|- bgcolor="white"
||[[Image:Training1 LoadingViewing.PNG|50px]]
|
[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training7Save.PNG|50px]]
|
[[Media:SlicerTraining7SavingData.ppt| Data Saving ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial-with-dicom.zip]]
|- bgcolor="white"
|[[Image:Training2Segmentation.PNG|50px]]
|
[[Media:Slicer_Segmentation_Tutorial.ppt| Manual Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
|[[Image:Training3LevelSets.PNG|50px]]
|
[[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training10EM.png|50px]]
|
[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| Automatic Brain Segmentation ]]
|
[[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip ]]
|- bgcolor="white"
| [[Image:Training11Registration.PNG|55px]]
|
[[Media:SlicerAdvancedTraining11_Registration.ppt| Registration]]
|
[[Media:RegistrationSample.zip| RegistrationSample.zip]]
|- bgcolor="white"
|[[Image:Training4DTI.PNG|50px]]
|
[[Media:Slicer_DTMRI_Training4.ppt| Diffusion Tensor Imaging Analysis ]]
|
[[Media:SlicerSampleDTI.zip| SlicerSampleDTI.zip]] [[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training8Nrrd.PNG|50px]]
|
[[Media:SlicerTraining8-NrrdFileFormat.ppt| Nrrd File Format]]
|
[[Media:Tensor_data.zip|Tensor_data.zip]]
|- bgcolor="white"
| [[Image:Training9DicomToNrrd.PNG|50px]]
|
[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Dicom to Nrrd Conversion ]]
|
[[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training5fMRI.PNG|50px]]
|
[[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonace Imaging Analysis ]]
|
[[Media:FMRIData1_short.zip|FMRIData1_short.zip]] [[Media:FMRIData2_long.zip|FMRIData2_long.zip]]
|- bgcolor="white"
| [[Image:Training6FreeSurfer.PNG|50px]]
|
[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurfer Reader ]]
|
[[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
|}

= Slicer Additional Resources =
[[Image:Limbic-2007.jpg|thumb|right|330px| A rendering of the Limbic System from the SPL PNL brain atlas]]

* [[BrainAtlas|SPL PNL Brain Atlas]]
* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel [[Media:EMSegmentTutorial.zip|data]] and white matter hyperintensities
* [[DataFusion|Data Fusion and Registration]]
* [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
* [[SlicerOnBIRN|How to use Slicer with BIRN]]
* [[media:Abdomen-v2.zip|CT based atlas of the abdomen]]. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.
* [[media:AbdominalAtlas.tar.gz|CT based atlas of the abdomen for Slicer 3]]; [[media:Abdominal_Atlas_Tutorial08.ppt|tuorial]] describing how to load and display the data in Slicer 3
* [http://www.airwayinspector.org/ Airway inspector]: 3D Slicer based tool for morphometry analysis of the lung airways and emphysema.

= Feedback =

* [[Slicer:Feedback|Feedback about Slicer]]
* [http://www.na-mic.org/Bug/ Bug reports]

= Acknowledgements =
*Slicer is being developed by a community of contributors. For more information see the [http://www.slicer.org Slicer] website.

<br /> Back to [[Training:Main|Training:Main]]

Slicer:Workshops:User Training 101

2008-02-21T16:14:30Z

Talos:

<div class="thumb tright"><div style="width: 90px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div
class="thumbcaption">[http://www.spl.harvard.edu/nac Link to the NAC website]</div></div></div>

= Introduction =
This is a training compendium for using 3DSlicer. This work is jointly sponsored by NA-MIC, NAC and NCIGT.

This series of courses will teach you how to
* load and view data
* segment data and create 3D models
* perform Diffusion Tensor Imaging and fMRI analysis
For an overview of Slicer, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]

= Software =
<div class="floatleft"><span>[[Image:3DSlicer.png|80px|[[Image:3DSlicer.png| 3D Slicer Logo]]]]</span></div>

The current version of Slicer that is fully supported is Slicer 2.6.

Please follow the [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started]] instructions to install the version of the Slicer program appropriate to your platform.

= Training Compendium =

For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).

[[Image:101.png|thumb|right|450px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).]]

{| border="2"
|- bgcolor="white"
|
| '''Course'''
| '''Dataset'''
|- bgcolor="white"
||[[Image:Training1 LoadingViewing.PNG|50px]]
|
[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training7Save.PNG|50px]]
|
[[Media:SlicerTraining7SavingData.ppt| Data Saving ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial-with-dicom.zip]]
|- bgcolor="white"
|[[Image:Training2Segmentation.PNG|50px]]
|
[[Media:Slicer_Segmentation_Tutorial.ppt| Manual Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
|[[Image:Training3LevelSets.PNG|50px]]
|
[[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training10EM.png|50px]]
|
[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| Automatic Brain Segmentation ]]
|
[[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip ]]
|- bgcolor="white"
| [[Image:Training11Registration.PNG|55px]]
|
[[Media:SlicerAdvancedTraining11_Registration.ppt| Registration]]
|
[[Media:RegistrationSample.zip| RegistrationSample.zip]]
|- bgcolor="white"
|[[Image:Training4DTI.PNG|50px]]
|
[[Media:Slicer_DTMRI_Training4.ppt| Diffusion Tensor Imaging Analysis ]]
|
[[Media:SlicerSampleDTI.zip| SlicerSampleDTI.zip]] [[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training8Nrrd.PNG|50px]]
|
[[Media:SlicerTraining8-NrrdFileFormat.ppt| Nrrd File Format]]
|
[[Media:Tensor_data.zip|Tensor_data.zip]]
|- bgcolor="white"
| [[Image:Training9DicomToNrrd.PNG|50px]]
|
[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Dicom to Nrrd Conversion ]]
|
[[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training5fMRI.PNG|50px]]
|
[[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonace Imaging Analysis ]]
|
[[Media:FMRIData1_short.zip|FMRIData1_short.zip]] [[Media:FMRIData2_long.zip|FMRIData2_long.zip]]
|- bgcolor="white"
| [[Image:Training6FreeSurfer.PNG|50px]]
|
[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurfer Reader ]]
|
[[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
|}

= Slicer Additional Resources =
[[Image:Limbic-2007.jpg|thumb|right|330px| A rendering of the Limbic System from the SPL PNL brain atlas]]

* [[BrainAtlas|SPL PNL Brain Atlas]]
* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel [[Media:EMSegmentTutorial.zip|data]] and white matter hyperintensities
* [[DataFusion|Data Fusion and Registration]]
* [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
* [[SlicerOnBIRN|How to use Slicer with BIRN]]
* [[media:Abdomen-v2.zip|CT based atlas of the abdomen]]. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.
* [[media:AbdominalAtlas.tar.gz|CT based atlas of the abdomen for Slicer 3]]
* [http://www.airwayinspector.org/ Airway inspector]: 3D Slicer based tool for morphometry analysis of the lung airways and emphysema.

= Feedback =

* [[Slicer:Feedback|Feedback about Slicer]]
* [http://www.na-mic.org/Bug/ Bug reports]

= Acknowledgements =
*Slicer is being developed by a community of contributors. For more information see the [http://www.slicer.org Slicer] website.

<br /> Back to [[Training:Main|Training:Main]]

File:Abdominal Atlas Tutorial08.ppt

2008-02-21T16:09:57Z

Talos: SPL Abdominal Atlas Tutorial for Slicer 3

SPL Abdominal Atlas Tutorial for Slicer 3

File:AbdominalAtlas.tar.gz

2008-02-21T16:06:07Z

Talos: SPL Abdominal Atlas for Slicer 3

SPL Abdominal Atlas for Slicer 3

File:Atlas demo.zip

2007-11-21T20:55:10Z

Talos: atlas demo files

atlas demo files

BrainAtlas

2007-05-11T13:29:32Z

Talos:

[[Image:Nac.png|right|thumb|96px|[http://www.spl.harvard.edu/nac Link to the NAC website]]

* this page is under construction

= Introduction =

* The Surgical Planning Laboratory, in conjunction with the Neuroscience Laboratory, created a three-dimensional digitized atlas of the human brain that has been used for surgical planning, model-driven segmentation, research, and teaching, and can be found on the World Wide Web at http://www.spl.harvard.edu

The atlas was created initially as a joint effort between the Laboratory of Neuroscience of the Harvard Medical School at the Brockton VA Medical Center, Brockton, MA and the Surgical Planning Laboratory, Department of Radiology at the Brigham and Women's Hospital, Boston, MA. Dr. Shenton, one of the original people involved at the Laboratory of Neuroscience at Brockton VA Medical Center, is now Director of the Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School.

* We are pleased to make this brain atlas available to our colleagues with the following stipulations:

The data is being distributed under the [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl '''Slicer license''']. By dowloading this data you also agree to '''acknowledge our contribution in any of your publications''' that result from the use of this atlas. Please acknowledge the following grants: P41RR013218, R01MH050740

* For your reference, here are the inital publication discussing this atlas:
** [http://splweb.bwh.harvard.edu:8000/pages/papers/ieee_95/ieee7.html Shenton et al. Harvard brain atlas: A teaching and visualization tool. Proceedings:Biomedical Visualization 10-17, 1995.]
** [http://splweb.bwh.harvard.edu:8000/pages/papers/atlas/text.html Kikinis et al. A Digital Brain Atlas for Surgical Planning, Model Driven Segmentation and Teaching. IEEE Transactions on Visualization and Computer Graphics, Vol.2, No.3, September 1996.]

= Directions =

* The atlas consists of
** a brain mri of a normal subject (T1W SPGR) acquired on a 1.5T system,
** a data set containing labels for different anatomical structures
** 3d surface models of these structures
** a mrml file that allows loading all of the data into 3d Slicer for visualization (see [[Slicer:Workshops:User_Training_101|the '''Slicer 101''' page]] for a link to the 3D Slicer download site and for information on how to load data and mrml files)
** a list of label values for the segmented structures
** inside slicer there are several pre-defined views for the motor, visual and limbic systems, diencephalon, brain stem, left cerebral hemisphere
* The [[Media:Brain_Atlas_Tutorial07.ppt| <big>'''tutorial'''</big>]] explains how to view the data.
* '''Get the [[Media:Spl_pnl_brain_atlas_2007a.zip|SPL-PNL-Brain_Atlas_2007]] here'''.
* [[media:SPL-BrainAtlas-label_list.txt| A list of the labels is available]].

File:SPL-BrainAtlas-label list.txt

2007-05-11T13:19:23Z

Talos:

File:Spl pnl brain atlas 2007a.zip

2007-05-11T13:18:49Z

Talos:

BrainAtlas

2007-05-10T22:10:29Z

Talos:

[[Image:Nac.png|right|thumb|96px|[http://www.spl.harvard.edu/nac Link to the NAC website]]

* this page is under construction

= Introduction =

* The Surgical Planning Laboratory, in conjunction with the Neuroscience Laboratory, created a three-dimensional digitized atlas of the human brain that has been used for surgical planning, model-driven segmentation, research, and teaching, and can be found on the World Wide Web at http://www.spl.harvard.edu

The atlas was created initially as a joint effort between the Laboratory of Neuroscience of the Harvard Medical School at the Brockton VA Medical Center, Brockton, MA and the Surgical Planning Laboratory, Department of Radiology at the Brigham and Women's Hospital, Boston, MA. Dr. Shenton, one of the original people involved at the Laboratory of Neuroscience at Brockton VA Medical Center, is now Director of the Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School.

* We are pleased to make this brain atlas available to our colleagues with the following stipulations:

The data is being distributed under the [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl '''Slicer license''']. By dowloading this data you also agree to '''acknowledge our contribution in any of your publications''' that result from the use of this atlas. Please acknowledge the following grants: P41RR013218, R01MH050740

* For your reference, here are the inital publication discussing this atlas:
** [http://splweb.bwh.harvard.edu:8000/pages/papers/ieee_95/ieee7.html Shenton et al. Harvard brain atlas: A teaching and visualization tool. Proceedings:Biomedical Visualization 10-17, 1995.]
** [http://splweb.bwh.harvard.edu:8000/pages/papers/atlas/text.html Kikinis et al. A Digital Brain Atlas for Surgical Planning, Model Driven Segmentation and Teaching. IEEE Transactions on Visualization and Computer Graphics, Vol.2, No.3, September 1996.]

= Directions =

* The atlas consists of
** a brain mri of a normal subject (T1W SPGR) acquired on a 1.5T system,
** a data set containing labels for different anatomical structures
** 3d surface models of these structures
** a mrml file that allows loading all of the data into 3d Slicer for visualization (see [[Slicer:Workshops:User_Training_101|the '''Slicer 101''' page]] for a link to the 3D Slicer download site and for information on how to load data and mrml files)
** inside slicer there are several pre-defined views for the motor, visual and limbic systems, diencephalon, brain stem, left cerebral hemisphere
* The [[Media:Brain_Atlas_Tutorial07.ppt| <big>'''tutorial'''</big>]] explains how to view the data.
* '''Get the [[Media:Spl_pnl_brain_atlas_2007.zip|SPL-PNL-Brain_Atlas_2007]] here'''.
* [[media:SPL-BrainAtlas-label_list.doc | A list of the labels is available]].

P41-2007-Joint-Retreat

2007-01-26T19:05:38Z

Talos: /* 01.10-02.30 BWH */

=Joint Retreat =
* What is the objective
**To familiarize the others with the ongoing activties in the respective cores
**To identify opportunities for leverage and augmentation
* Who:
**The MGH Center for Functional Imaging Technologies
**The BWH Neuroimage Analysis Center
**Core PI's for the two centers plus not more than 2 people per core
* Where:
**MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)
* When:
**Monday, Jan. 29, 11am-5pm

=Agenda=
==11.00-12.30 MGH==
**Bruce Rosen, Overview
**Bruce Fischl, High resolution anatomical modeling
**David Boas, Optical Imaging
**Larry Wald, High resolution structural and functional MRI
**Matti Hamalainen, MEG and mulit-modal inverse problems.
*12.30-01.00 pm Break

==01.10-02.30 BWH==
**Ron Kikinis, Overview
**CF Westin, Diffusion MRI
**Sandy Wells
**Andrea Mewes, Neonate Imaging
**Florin Talos, Computational Neuroanatomy
**Mike Halle
**Domink Meier: confirmed- Time Series Analysis PI
**Steve Pieper

==02.30-03.00 Break==
*03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)
*04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)

=Participants=
#Ron Kikinis, PI, NAC
#Steve Pieper
#Bruce Fischl
#David Boas
#Larry Wald
#Matti Hamalainen
#Bruce Rosen
#Carl-Fredrik Westin
#Juliette Selb
#Lilla Zollei
#Jean Augustinack
#Kinh Tieu
#Anna Custo
#Thomas Witzel
#Wanmei Ou
#Florin Talos
#Michael Halle
#Andrea Mewes

P41-2007-Joint-Retreat

2007-01-26T14:03:54Z

Talos: /* Participants */

=Joint Retreat =
* What is the objective
**To familiarize the others with the ongoing activties in the respective cores
**To identify opportunities for leverage and augmentation
* Who:
**The MGH Center for Functional Imaging Technologies
**The BWH Neuroimage Analysis Center
**Core PI's for the two centers plus not more than 2 people per core
* Where:
**MIT Stata CEnter, Seminar Room G449 (Patil Conference Room / Kiva)
* When:
**Monday, Jan. 29, 11am-5pm

=Agenda=
==11.00-12.30 MGH==
**Bruce Rosen, Overview
**Bruce Fischl, High resolution anatomical modeling
**David Boas, Optical Imaging
**Larry Wald, High resolution structural and functional MRI
**Matti Hamalainen, MEG and mulit-modal inverse problems.
*12.30-01.00 pm Break

==01.10-02.30 BWH==
**Ron Kikinis
**Sandy Wells
**CF Westin, Diffusion MRI
**Andrea Mewes
**Mike Halle
**Domink Meier
**Steve Pieper
**Florin Talos

==02.30-03.00 Break==
*03.00-04.00 General Discussion (Sandy Wells, Bruce Fischl)
*04.00-05.00 DTI discussion (Bruce Rosen, Ron Kikinis)

=Participants=
#Ron Kikinis, PI, NAC
#Steve Pieper
#Bruce Fischl
#David Boas
#Larry Wald
#Matti Hamalainen
#Bruce Rosen
#Carl-Fredrik Westin
#Juliette Selb
#Lilla Zollei
#Jean Augustinack
#Kinh Tieu
#Anna Custo
#Thomas Witzel
#Wanmei Ou
#Florin Talos