NAMIC Wiki - User contributions [en]

PREDICT-HD Longitudinal Shape Analysis

2015-01-09T16:26:48Z

Reginakim: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
Image:Left_right_putamen_50406.gif|Evolution of left/right putamen
Image:Putamen_volume_estimated_from_shape_regression.png|Volume of left/right putamen extracted from continuous shape model
</gallery>

==Key Investigators==
Regina EY Kim,
James Fishbaugh,
Hans Johnson

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Share development code
** Test on a few longidutidal data set
** Identify any immediate improvement requirement
** Identify long-term improvement requirement
** Make sure the implementation is applicable on large-scale dataset.

* See differences of Shape analysis between current and old version of segmentation
** Estimate time efficiency
** Estimate what is improved
* Identify 6 month goals/plans for Shape Analysis Project
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Sharing code: github
* Testing: 8 subjects with longitudinal data has been identified.
** Sampled from control(2), low(2), medium(2), and high(2) CAP group.
** Also sampled from 6 different sites

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Deformetrica built locally with VTK5.
* Shape modeling looks good with improved labeling approach
* Code Sharing Plan
** Source code sharing on a shared point for effective collaboration
** VTK6 Compatibility (Deformetrica)
** ITK3/4 Compatibility (ShapeWork)
* Focus area in Statistical Modeling

</div>
</div>

<h3> Shape Analysis Pipeline Installation </h3>
Shape analysis pipeline requires installation of two main tools:
# Deformetrica (James Fishbaugh)
# ShapeWork (Prasanna Muralidharan)

<h4> Deformetrica (http://www.deformetrica.org) installation </h4>
# Download 'Deformatrica 2.1' from http://www.deformetrica.org/?page_id=15
# Go to "Installation Instructions" and follow the instructions
:* FFT download & installation:
<pre>
$ mkdir FFTW
[eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools ]
$ cd FFTW/
[eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools/FFTW ]
$ wget http://www.fftw.org/fftw-3.3.4.tar.gz
--2015-01-06 14:27:58-- http://www.fftw.org/fftw-3.3.4.tar.gz
Resolving www.fftw.org... 216.119.142.145
Connecting to www.fftw.org|216.119.142.145|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3940427 (3.8M) [application/octet-stream]
Saving to: 'fftw-3.3.4.tar.gz'

100%[==================================================================================================================================================>]
3,940,427 4.44MB/s in 0.8s

2015-01-06 14:27:59 (4.44 MB/s) - 'fftw-3.3.4.tar.gz' saved [3940427/3940427]

$ tar -zxvf fftw-3.3.4.tar.g
</pre>

:* Install FFTW: http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix
<pre>

$ mkdir /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
$ ./fftw-3.3.4/configure --prefix /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
$ make
$ make install
</pre>
:* Build deformetrica
<pre>
$ cmake -D ITK_DIR=/Shared/sinapse/sharedopt/UtahShapeTools/ITK4/build/ -D VTK_DIR=/Shared/sinapse/scratch/eunyokim/src/NamicExternal/build_Mac_201410/VTK-build/ ../app
VTK 6.2 is used.
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
CUDA was not found.
Deformetrica will be compiled without Cuda
-- Configuring done
-- Generating done
-- Build files have been written to: /Shared/sinapse/sharedopt/UtahShapeTools/deformetrica-2.1/deformetrica/bin
</pre>
:* build
<pre>
$ make
... ...
Linking CXX executable sparseMatching2
Linking CXX executable sparseMatching3
[100%] [100%] Built target sparseMatching3
Built target sparseMatching2
</pre>

<h4> ShapeWork Installation </h4>

PREDICT-HD Longitudinal Shape Analysis

2015-01-07T17:31:52Z

Reginakim: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Regina EY Kim,
James Fishbaugh,
Hans Johnson

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Share development code
** Test on a few longidutidal data set
** Identify any immediate improvement requirement
** Identify long-term improvement requirement
** Make sure the implementation is applicable on large-scale dataset.

* See differences of Shape analysis between current and old version of segmentation
** Estimate time efficiency
** Estimate what is improved
* Identify 6 month goals/plans for Shape Analysis Project
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Sharing code: github
* Testing: 8 subjects with longitudinal data has been identified.
** Sampled from control(2), low(2), medium(2), and high(2) CAP group.
** Also sampled from 6 different sites

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

<h3> Shape Analysis Pipeline Installation </h3>
Shape analysis pipeline requires installation of two main tools:
# Deformetrica (James Fishbaugh)
# ShapeWork (Prasanna Muralidharan)

<h4> Deformetrica (http://www.deformetrica.org) installation </h4>
# Download 'Deformatrica 2.1' from http://www.deformetrica.org/?page_id=15
# Go to "Installation Instructions" and follow the instructions
:* FFT download & installation:
<pre>
$ mkdir FFTW
[eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools ]
$ cd FFTW/
[eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools/FFTW ]
$ wget http://www.fftw.org/fftw-3.3.4.tar.gz
--2015-01-06 14:27:58-- http://www.fftw.org/fftw-3.3.4.tar.gz
Resolving www.fftw.org... 216.119.142.145
Connecting to www.fftw.org|216.119.142.145|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3940427 (3.8M) [application/octet-stream]
Saving to: 'fftw-3.3.4.tar.gz'

100%[==================================================================================================================================================>]
3,940,427 4.44MB/s in 0.8s

2015-01-06 14:27:59 (4.44 MB/s) - 'fftw-3.3.4.tar.gz' saved [3940427/3940427]

$ tar -zxvf fftw-3.3.4.tar.g
</pre>

:* Install FFTW: http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix
<pre>

$ mkdir /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
$ ./fftw-3.3.4/configure --prefix /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
$ make
$ make install
</pre>
:* Build deformetrica
<pre>
$ cmake -D ITK_DIR=/Shared/sinapse/sharedopt/UtahShapeTools/ITK4/build/ -D VTK_DIR=/Shared/sinapse/scratch/eunyokim/src/NamicExternal/build_Mac_201410/VTK-build/ ../app
VTK 6.2 is used.
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
CUDA was not found.
Deformetrica will be compiled without Cuda
-- Configuring done
-- Generating done
-- Build files have been written to: /Shared/sinapse/sharedopt/UtahShapeTools/deformetrica-2.1/deformetrica/bin
</pre>
:* build
<pre>
$ make
... ...
Linking CXX executable sparseMatching2
Linking CXX executable sparseMatching3
[100%] [100%] Built target sparseMatching3
Built target sparseMatching2
</pre>

<h4> ShapeWork Installation </h4>

PREDICT-HD Longitudinal Shape Analysis

2015-01-07T00:48:57Z

Reginakim: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Regina EY Kim,
James Fishbaugh,
Hans Johnson

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Share development code
** Test on a few longidutidal data set
** Identify any immediate improvement requirement
** Identify long-term improvement requirement
** Make sure the implementation is applicable on large-scale dataset.

* See differences of Shape analysis between current and old version of segmentation
** Estimate time efficiency
** Estimate what is improved
* Identify 6 month goals/plans for Shape Analysis Project
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Sharing code: github
* Testing: 8 subjects with longitudinal data has been identified.
** Sampled from control(2), low(2), medium(2), and high(2) CAP group.
** Also sampled from 6 different sites

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

<h3> Shape Analysis Pipeline Installation </h3>
Shape analysis pipeline requires installation of two main tools:
# Deformetrica (James Fishbaugh)
# ShapeWork (Prasanna Muralidharan)

<h4> Deformetrica (http://www.deformetrica.org) installation </h4>
# Download 'Deformatrica 2.1' from http://www.deformetrica.org/?page_id=15
# Go to "Installation Instructions" and follow the instructions
:* FFT download & installation:
<pre>
$ mkdir FFTW
[eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools ]
$ cd FFTW/
[eunyokim@wundt /Shared/sinapse/sharedopt/UtahShapeTools/FFTW ]
$ wget http://www.fftw.org/fftw-3.3.4.tar.gz
--2015-01-06 14:27:58-- http://www.fftw.org/fftw-3.3.4.tar.gz
Resolving www.fftw.org... 216.119.142.145
Connecting to www.fftw.org|216.119.142.145|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3940427 (3.8M) [application/octet-stream]
Saving to: 'fftw-3.3.4.tar.gz'

100%[==================================================================================================================================================>] 3,940,427 4.44MB/s in 0.8s

2015-01-06 14:27:59 (4.44 MB/s) - 'fftw-3.3.4.tar.gz' saved [3940427/3940427]

$ tar -zxvf fftw-3.3.4.tar.g
</pre>

:* Install FFTW: http://www.fftw.org/fftw3_doc/Installation-on-Unix.html#Installation-on-Unix
<pre>

$ mkdir /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
$ ./fftw-3.3.4/configure --prefix /Shared/sinapse/sharedopt/UtahShapeTools/FFTW/bin/
$ make
$ make install
</pre>

<h4> ShapeWork Installation </h4>

PREDICT-HD Longitudinal Shape Analysis

2014-12-30T20:41:33Z

Reginakim: /* Project Description */

PREDICT-HD Longitudinal Shape Analysis

2014-12-30T20:38:51Z

Reginakim: /* Key Investigators */

PREDICT-HD Longitudinal Shape Analysis

2014-12-30T20:38:34Z

Reginakim: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Regina EY Kim
James Fishbaugh
Hans Johnson

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Share development code
** Test on a few longidutidal data set
** Identify any immediate improvement requirement
** Identify long-term improvement requirement

* See differences of Shape analysis between current and old version of segmentation
** Estimate time efficiency
** Estimate what is improved
* Identify 6 month goals/plans for Shape Analysis Project
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Sharing code: github
* Testing: 8 subjects with longitudinal data has been identified.
** Sampled from control(2), low(2), medium(2), and high(2) CAP group.
** Also sampled from 6 different sites

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

PREDICT-HD Longitudinal Shape Analysis

2014-12-30T20:30:59Z

Reginakim: /* Project Description */

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
Regina EY Kim
James Fishbaugh
Hans Johnson

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Share development code
* Test on a few longidutidal data set
* See differences of Shape analysis between current and old version of segmentation
** Estimate time efficiency
** Estimate what is improved
* Identify 6 month goals/plans for Shape Analysis Project
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

PREDICT-HD Longitudinal Shape Analysis

2014-12-30T20:29:45Z

Reginakim: /* Key Investigators */

PREDICT-HD Longitudinal Shape Analysis

2014-12-30T20:28:33Z

Reginakim: Created page with '__NOTOC__ <gallery> Image:PW-2015SLC.png|Projects List </gallery> ==Key Investigators== ==Project Description== <div style="margin: 20px;…'

__NOTOC__
<gallery>
Image:PW-2015SLC.png|[[2015_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
*
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Winter Project Week

2014-12-30T20:27:29Z

Reginakim: /* Huntington's Disease */

__NOTOC__

[[image:PW-2015SLC.png|300px]]

Welcome to the 20th Project week page!

== Introduction ==
Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws 80-120 researchers. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. The next events in this ongoing series will occur in [http://wiki.na-mic.org/Wiki/index.php/2015_Winter_Project_Week Salt Lake City, Utah in January of 2015], followed by one in Boston, MA in June of 2015.

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

Please make sure that you are on the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

== '''Logistics''' ==
*'''Dates:''' January 5-9, 2015.
*'''Location:''' Salt Lake City, Utah
*'''REGISTRATION:''' Please click [http://umarket.utah.edu/ecom/checkout.tpl?App_Type=0046&Item_Num=WPW2015 '''here'''] to register online before December 24, 2014. All participants must pay a registration fee 550 USD, which covers our catering and facilities costs.
*'''Venue:''' The venue for the meeting is the Marriott City Center, Salt Lake City, Utah. You can book online, by clicking [http://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=2015%20Winter%20Project%20Week^slccc%60namnama%60149%60USD%60false%601/4/15%601/10/15%6012/05/14&app=resvlink&stop_mobi=yes here.] The room rate for the meeting is 149 USD per night.

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:19%" | '''Monday, January 5'''
| style="width:19%" | '''Tuesday, January 6'''
| style="width:19%" | '''Wednesday, January 7'''
| style="width:19%" | '''Thursday, January 8'''
| style="width:19%" | '''Friday, January 9'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
| <br><font color="#9966cc"></font>
|9-10am: [[2015 Winter Project Week COPD Breakout|Breakout Session:COPD]] (Raul San Jose) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
|9-10am: [[2015 Winter Project Week QIICR and DICOM Breakout|Breakout Session:QIICR and DICOM]] (Andrey Fedorov, Steve Pieper) <br><font color="#44AA88">''(Amethyst 1)''</font> <br>
| '''[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|9am: Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
|
|
|
| [[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''l
| style="background:#dbf3ff; color:#522200"|[[2015_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#dbf3ff; color:#522200"|[[2015_SLC_Training_Workshop|Slicer Workshop (Ron Kikinis)]]
| <font color="#44AA88">''(Olympus B)''</font>
|
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|
|3:15-4pm: [[2015_Winter_Project_Week_Segmentations_Breakout|Breakout Session: Segmentations]] <br><font color="#44AA88">''(Amethyst 2)'' <br> 
| style="background:#ffffff; color:black"|
|[[2015_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Olympus B)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

=Projects=
* [[2015_Project_Week:_Template | Template for project pages]]

==Image-Guided Therapy==
* [[NeedleFinder | Image-based Needle Detection from MRI]] (Andre Mastmeyer, Guillaume Pernelle, Tina Kapur, Steve Pieper, Ron Kikinis)
* [[2015_Winter_Project_Week:_Neurosurgery_Case_Review| Review of data from recent AMIGO US/MR neurosurgery]] (Steve Pieper, Jim Miller, Alireza Mehrtash, Sandy Wells, Tina Kapur, Ron Kikinis)
* [[2015_Winter_Project_Week:_Benchtop_Nuerosurgery|Tracked ultrasound benchtop experimental system for neurosurgery]] (Steve Pieper, Jim Miller)
*[[NeedlePlace | Workflow for percutaneous needle place]] (Bamshad Azizi, Li Ming, Li Ye, Kevin Cleary)
*Registration of pre-op and intra-op DTI to correlate parameters with post-op prognosis(Li Ye, Steve Pieper, Alireza Mehrtash, Lauren O'Donnell)
* [[ProstateSegmentation | Prostate segmentation and biopsy]] (Peter Behringer, Andriy Fedorov)
* [[Needle Detection Tutorial | Needle Detection Tutorial]] (Gao Yang, Andre Mastmeyer, Guillaume Pernelle, Tina Kapur)

==Huntington's Disease==
* [[PREDICT-HD Longitudinal Shape Analysis | PREDICT-HD Longitudinal Shape Analysis]] (Regina EY Kim, James Fishbaugh, Hans Johnson)

==TBI==

==Stroke==

==Cardiac==

== Lung ==

*Small lung nodule differential diagnosis using 3D Slicer (Li Ming, Jay Jagadeesan, Jim Miller)

== COPD ==
* [[Slicer CIP | SlicerCIP Extension]] (Alex Yarmakovich, Jorge Onieva, Raul San Jose)
* [[Nodule Sizing | Lung nodule sizing tool]] (Raul San Jose)
* [[Density Inspector | Density Inspector]] (Alex Yarmakovich, Raul San Jose, Jorge Onieva)
* [[PA/A Tool | Pulmonary Artery/Aorta measuring tool]] (Jorge Onieva, Rola Harmouche, German Gonzalez)
* [[Picassa Snap | Picasa Snap: tagging your favorite slicer snapshots]] (Jorge Onieva)
* [[Feature Extraction with Particles | Feature Extraction on ROIs based on Particles]] (Raul San Jose, James Ross)
* [[ CIP and Nipype | CIP analysis pipelines in Nipype]] (Rola Harmouche, James Ross, Alex Yarmakovich)
* [[Supervised Feature Enhancement | Supervised feature enhancement]] (James Ross, German Gonzalez, Rola Harmouche)
* [[Organ Detection | Organ detection with OpenCV]] (German Gonzalez, James Ross, Raul San Jose)

==Head and Neck Cancer / Radiotherapy ==

==[http://qiicr.org QIICR]==
* Mechanism to pull related DICOM series on derived modality load (Andrey, Csaba)
* [[2015_Winter_Project_Week:_Multiframe_DICOM | Segmentation object and enhanced multiframe object IO in DCMTK and Slicer]] (Steve, Andrey, Michael)
* [[T1 mapping for variable flip angle | T1 mapping for variable flip angle]] (Artem, Xiao, Andrey)
* Representation of Iowa QIN data using DICOM (Andrey, Christian Bauer)

==Feature Extraction==

==Additional Brain Image Analysis==

==Slicer4 Extensions==
* PET Tumor Segmentation (Christian Bauer)

==TMJOA RO1 - Collaboration with NAMIC==
* Improved model display (Francois Boudin, Steve Pieper)

==Infrastructure==

* Micro and Macro Scale in Slicer (Nicole Aucoin, Bradley Lowekamp)
* Rulers in Markups module (Nicole Aucoin)
* [[2015_Winter_Project_Week:Segmentations|Segmentations]] (Csaba Pinter, ?)
* [[2015_Winter_Project_Week:DICOM_References|DICOM references]] (Andrey Fedorov, Csaba Pinter, Steve Pieper)
* [[2015_Winter_Project_Week:OpenAtlas|Open Atlas]] (Bill Lorensen)
* automatic indexing of CLI modules in Slicer's extension store for nice dashboards based on the [https://github.com/commontk/ctk-cli-indexer ctk-cli-indexer] (JC, maybe Hans Meine remotely)

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration.

# Nicole Aucoin ; Brigham and Women's Hospital
# Bamshad Azizi Koutenaei ; Children's National Health System
# Christian Bauer ; University of Iowa
# Peter Behringer ; Brigham and Women's Hospital
# Francois Budin ; UNC
# Byunghyun Cho; Koh Young Technology Inc.
# Xiao Da ; Athinoula A. Martinos Center for Biomedical Imaging
# Andriy Fedorov ; Brigham and Women's Hospital
# JC Fillion-Robin; Kitware, Inc.
# James Fishbaugh; University of Utah
# Yang Gao ; Brigham and Women's Hospital
# German Gonzalez ; Brigham and Women's Hospital
# Rola Harmouche ; Brigham and Women's Hospital
# Hans Johnson ; University of Iowa
# Tina Kapur ; Brigham and Women's Hospital
# Ron Kikinis ; Brigham and Women's Hospital
# Eun Young Regina Kim ; University of Iowa
# Sangyong Kim, Kohyoung Techonology
# Franklin King, Queen's University and Brigham and Women's Hospital
# Ming Li ; Brigham and Women's Hospital
# Ye Li ; Brigham and Women's Hospital
# Ruizhi Liao; Brigham and Women's Hospital
# Julia Lopinto ; The University of Michigan
# Bill Lorensen; Noware
# Bradley Lowenkamp; Medical Science Computing
# Lucie Macron ; The University of Michigan
# Artem Mamonov ; MGH Martinos
# Andre Mastmeyer ; University of Keil and Brigham and Women's Hospital
# Alireza Mehrtash ; Brigham and Women's Hospital
# James Miller ; GE Global Research
# Lauren O'Donnell; Brigham and Women's Hospital and Harvard Medical School
# Jorge Onieva ; Brigham and Women's Hospital
# Guillaume Pernelle; Imperial College London
# Steve Pieper ; Isomics Inc.
# Csaba Pinter ; Queens University
# Adam Rankin ; Robarts Research Institute
# James Ross ; Brigham and Women's Hospital
# Raul San Jose ; Brigham and Women's Hospital
# Anuja Sharma; University of Utah
# Matthew Toews; Brigham and Women's Hospital
# Junichi Tokuda ; Brigham and Women's Hospital
# Bo Wang ; SCI Institute University of Utah
# William Wells; Brigham and Women's Hospital
# Alexander Yarmarkovich; Brigham and Women's Hospital

2014 Summer Project Week:LongitudinalSeg

2014-06-27T12:23:53Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Longseg_hdsubcorts.png
Image:OuterView.gif|[[2014_Summer_Project_Week#Projects|Left caudate & putamen View 1. Segmentation from BRAINSCut. Coloring is velocity of fast (red) to slow(green)]]
Image:InnerView.gif|[[2014_Summer_Project_Week#Projects|Left caudate & putamen View 2. Segmentation from BRAINSCut. Coloring is velocity of fast (red) to slow(green)]]
Image:OuterView malf.gif|[[2014_Summer_Project_Week#Projects|Left caudate & putamen View 1. Segmentation from ANTs MALF Tool. Coloring is velocity of fast (red) to slow(green)]]
Image:InnerView Malf.gif|[[2014_Summer_Project_Week#Projects|Left caudate & putamen View 2. Segmentation from ANTs MALF Tool. Coloring is velocity of fast (red) to slow(green)]]
</gallery>

==Key Investigators==
* Iowa: Regina Kim
* Iowa: Hans Johnson
* Utah: James Fishbaugh
* Utah: Guido Gerig

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Longitudinal imaging studies involve tracking changes in individuals by repeated image acquisition over time. The goal of these studies is to quantify biological shape variability within and across individuals, and also to distinguish between normal and disease populations. However, data variability is influenced by outside sources such as image acquisition, image calibration, human expert judgement, and limited robustness of segmentation and registration algorithms.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Deploy a shape analysis tool for large-scale multi center data processing
* Apply & validate the tool on longitudinal data sample (BRAINSCut Segmentation)
** extension of tests to MABMIS results
** extension of tests to MALF (ANTs) results
* Visual comparison of shape analysis.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Tool has been migrated into University of Iowa cite.
* Shape changes are detected using both MALF and BRAINSCut segmentation
** One subjects of five time points data in the course of 8 years period.
** Putamen and caudate tested
** About 10 hours for 50 iterations.
* A new tool experience: Multi-atlas Slicer extension module from JHU
* Future Work:
** Shape smoothing parameter determination
** Investigation of Pros & Cons using different segmentation tool
</div>
</div>

2014 Summer Project Week:LongitudinalSeg

2014-06-27T11:59:36Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Longseg_hdsubcorts.png
Image:OuterView.gif
Image:InnerView.gif
Image:OuterView malf.gif
Image:InnerView Malf.gif
</gallery>

==Key Investigators==
* Iowa: Regina Kim
* Iowa: Hans Johnson
* Utah: James Fishbaugh
* Utah: Guido Gerig

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Longitudinal imaging studies involve tracking changes in individuals by repeated image acquisition over time. The goal of these studies is to quantify biological shape variability within and across individuals, and also to distinguish between normal and disease populations. However, data variability is influenced by outside sources such as image acquisition, image calibration, human expert judgement, and limited robustness of segmentation and registration algorithms.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Deploy a shape analysis tool for large-scale multi center data processing
* Apply & validate the tool on longitudinal data sample (BRAINSCut Segmentation)
** extension of tests to MABMIS results
** extension of tests to MALF (ANTs) results
* Visual comparison of shape analysis.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

File:InnerView Malf.gif

2014-06-27T11:57:09Z

Reginakim:

File:OuterView malf.gif

2014-06-27T11:52:06Z

Reginakim:

File:OuterView.gif

2014-06-27T11:46:54Z

Reginakim:

File:InnerView.gif

2014-06-27T11:43:20Z

Reginakim:

File:Animated l caudate View2.gif

2014-06-27T11:34:47Z

Reginakim:

2014 Summer Project Week:LongitudinalSeg

2014-06-27T11:33:44Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Longseg_hdsubcorts.png
Image:L caudate putamen BCut.avi
</gallery>

==Key Investigators==
* Iowa: Regina Kim
* Iowa: Hans Johnson
* Utah: James Fishbaugh
* Utah: Guido Gerig

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Longitudinal imaging studies involve tracking changes in individuals by repeated image acquisition over time. The goal of these studies is to quantify biological shape variability within and across individuals, and also to distinguish between normal and disease populations. However, data variability is influenced by outside sources such as image acquisition, image calibration, human expert judgement, and limited robustness of segmentation and registration algorithms.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Deploy a shape analysis tool for large-scale multi center data processing
* Apply & validate the tool on longitudinal data sample (BRAINSCut Segmentation)
** extension of tests to MABMIS results
** extension of tests to MALF (ANTs) results
* Visual comparison of shape analysis.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

File:L caudate putamen BCut.avi

2014-06-27T11:32:43Z

Reginakim: Velocity display of two time points of HD subject with two time points.

Velocity display of two time points of HD subject with two time points.

2014 Summer Project Week:LongitudinalSeg

2014-06-23T19:04:10Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Longseg_hdsubcorts.png
</gallery>

==Key Investigators==
* Iowa: Regina Kim
* Iowa: Hans Johnson
* Utah: James Fishbaugh
* Utah: Guido Gerig

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
Longitudinal imaging studies involve tracking changes in individuals by repeated image acquisition over time. The goal of these studies is to quantify biological shape variability within and across individuals, and also to distinguish between normal and disease populations. However, data variability is influenced by outside sources such as image acquisition, image calibration, human expert judgement, and limited robustness of segmentation and registration algorithms.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Deploy a shape analysis tool for large-scale multi center data processing
* Apply & validate the tool on longitudinal data sample (BRAINSCut Segmentation)
** extension of tests to MABMIS results
** extension of tests to MALF (ANTs) results
* Visual comparison of shape analysis.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
</div>
</div>

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-24T14:36:19Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut: Result Example After Rendering with Slicer Model Maker
File:ProbabilityMaps.png|BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI
File:GradientFeatureComparison.png |BRAINSCut: One of Feature Images.
File:Caudates.png|BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces
File:Putamens.png|BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace
File:BRAINSCutThalamus.png|BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace
File:HippoWithSOnly.png|BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim, Hans Johnson, Mark Scully

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#Integration of BRAINSCut into Slicer3/Slicer4
#Integration of GMI feature images into BRAINSCut
#Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Check dependencies of BRAINSCut and integrate into Slicer CLM.
#Process test data set to verify
# Submit caudate results to the CAUSE07 Challenge 'http://www.cause07.org/'
</div>
</div>

<h3>Progress</h3>

# BRAINSCut Incorporating with Slicer3 DONE
# Generating BRAINSCut model for subcortical structures: caudate, putamen, thalamus, and hippocampus. DONE
# Verifying generated model by comparing manual traces. DONE
# Process 230 data to generate hippocampus. DONE

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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper (Mar 2010)

==Download Page==

http://www.nitrc.org/projects/brainscut

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-23T21:24:18Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut: Result Example After Rendering with Slicer Model Maker
File:ProbabilityMaps.png|BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI
File:GradientFeatureComparison.png |BRAINSCut: One of Feature Images.
File:Caudates.png|BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces
File:Putamens.png|BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace
File:BRAINSCutThalamus.png|BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace
File:HippoWithSOnly.png|BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#Integration of BRAINSCut into Slicer3/Slicer4
#Integration of GMI feature images into BRAINSCut
#Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
# Check dependencies of BRAINSCut and integrate into Slicer CLM.
#Process test data set to verify
</div>
</div>

<h3>Progress</h3>

# BRAINSCut Incorporating with Slicer3 DONE
# Generating BRAINSCut model for subcortical structures: caudate, putamen, thalamus, and hippocampus. DONE
# Verifying generated model by comparing manual traces. DONE
# Process 230 data to generate hippocampus. DONE

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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper (Mar 2010)

==Download Page==

http://www.nitrc.org/projects/brainscut

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-23T18:00:25Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut: Result Example After Rendering with Slicer Model Maker
File:ProbabilityMaps.png|BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI
File:GradientFeatureComparison.png |BRAINSCut: One of Feature Images.
File:Caudates.png|BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces
File:Putamens.png|BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace
File:BRAINSCutThalamus.png|BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace
File:HippoWithSOnly.png|BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3/Slicer4
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.

</div>
</div>

<h3>Progress</h3>

# BRAINSCut Incorporating with Slicer3
# Generating BRAINSCut model for subcortical structures: caudate, putamen, thalamus, and hippocampus.
# Verifying generated model by comparing manual traces.

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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper (Mar 2010)

==Download Page==

http://www.nitrc.org/projects/brainscut

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

File:Putamens.png

2011-06-23T17:38:16Z

Reginakim:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-23T17:37:53Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut: Result Example After Rendering with Slicer Model Maker
File:ProbabilityMaps.png|BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI
File:GradientFeatureComparison.png |BRAINSCut: One of Feature Images.
File:Caudates.png|BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces
File:Putamens.png|BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace
File:BRAINSCutThalamus.png|BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace
File:HippoWithSOnly.png|BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3/Slicer4
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.

</div>
</div>

<h3>Progress</h3>



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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper(Mar 2010)

==Download Page==

http://www.nitrc.org/projects/brainscut

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

File:BRAINSCutThalamus.png

2011-06-23T17:36:24Z

Reginakim:

File:HippoWithSOnly.png

2011-06-23T17:35:27Z

Reginakim:

File:Globus.png

2011-06-23T17:34:56Z

Reginakim:

File:Caudates.png

2011-06-23T17:34:39Z

Reginakim:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-23T17:31:37Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut: Result Example After Rendering with Slicer Model Maker
File:ProbabilityMaps.png|BRAINSCut: Probability Map Example for Sub-cortical regions of brain to identify ROI
File:GradientFeatureComparison.png |BRAINSCut: One of Feature Images.
File:Caudates.pdf|BRAINSCut: Caudate test statistics between BRAINSCut output and Manual Traces
File:Putamens.pdf|BRAINSCut: Putamen test statistics between BRAINSCut output and Manual Trace
File:Thalamus.pdf|BRAINSCut: Thalamus test statistics between BRAINSCut output and Manual Trace
File:HippoWithSOnly.pdf|BRAINSCut: Hippocampus test statistics between BRAINSCut output and Manual Trace
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3/Slicer4
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.

</div>
</div>

<h3>Progress</h3>



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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper(Mar 2010)

==Download Page==

http://www.nitrc.org/projects/brainscut

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

File:HippoWithSOnly.pdf

2011-06-23T17:30:40Z

Reginakim:

File:Thalamus.pdf

2011-06-23T17:28:38Z

Reginakim:

File:Putamens.pdf

2011-06-23T17:27:53Z

Reginakim:

File:Caudates.pdf

2011-06-23T17:26:57Z

Reginakim:

File:GradientFeatureComparison.png

2011-06-23T17:23:44Z

Reginakim:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-23T15:16:20Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut Result Example After Rendering with Slicer Model Maker
File:ProbabilityMaps.png|BRAINSCut Probability Map Example for Sub-cortical regions of brain to identify ROI
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3/Slicer4
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.

</div>
</div>

<h3>Progress</h3>



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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper(Mar 2010)

==Download Page==

http://www.nitrc.org/projects/brainscut

==Delivery Mechanism==

This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

File:ProbabilityMaps.png

2011-06-23T15:09:46Z

Reginakim:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-23T15:09:05Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut Result Example
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

<div style="margin: 20px;">
<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3/Slicer4
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

<div style="width: 40%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.

</div>
</div>

<h3>Progress</h3>



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

==References==

#Powell, S., Magnotta, V., Johnson, H., and . . . , V. J., “Registration and machine learning-based automated segmentation of subcortical and cerebellar brain . . . ,” NeuroImage (Jan 2008)
#Eun Young Kim, Hans Johnson, "Multi-structure segmentation of multi-modal brain images using artificial neural networks", SPIE Proceedings Paper(Mar 2010)
==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

File:BRAINSCutTutorial TutorialContestSummer2011.ppt

2011-06-21T13:33:29Z

Reginakim: uploaded a new version of "File:BRAINSCutTutorial TutorialContestSummer2011.ppt"

BRAINSCut Tutorial NAMIC2011SummerConstest

2011-06-21T13:30:15Z

Reginakim:

Tutorial

ppt [[File:BRAINSCutTutorial TutorialContestSummer2011.ppt]]

pdf [[File:BRAINSCutTutorial TutorialContestSummer2011.pdf]]

Data File [[File:BRAINSCutTutorial_TutorialContestSummer2011.zip]]

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-20T21:37:32Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut Result Example
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

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

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3/Slicer4
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

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

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.
#:

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-20T20:09:24Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
File:BRAINSCutFigure.png|BRAINSCut Result Example
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

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

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3 Module
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

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

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.
#:

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-13T20:18:43Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image::BRAINSCutFigure.png|BRAINSCut Result Example
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

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

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3 Module
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

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

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.
#:

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-13T20:18:19Z

Reginakim:

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image::BRAINSCutFigure.png
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

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

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3 Module
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

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

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.
#:

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

File:BRAINSCutFigure.png

2011-06-13T20:17:18Z

Reginakim:

2011 Summer Project Week Integrate BRAINSCut into Slicer3

2011-06-13T20:09:58Z

Reginakim: Created page with '__NOTOC__ <gallery> Image:PW-MIT2011.png|Projects List Image:notfound.png|Interesting picture to be added... </gallery> '''Integrate BRAIN…'

__NOTOC__
<gallery>
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
</gallery>

'''Integrate BRAINSCut into Slicer3'''

==Key Investigators==
* University of Iowa: Eunyoung(Regina) Kim

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

<h3>Objective</h3>

#:Integration of BRAINSCut into Slicer3 Module
#:Integration of GMI feature images into BRAINSCut
#:Test BRAINSCut

</div>

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

<h3>Approach, Plan</h3>
#:Check dependencies of BRAINSCut
#:and integrate into Slicer CLM.
#:

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week

2011-06-13T20:01:55Z

Reginakim:

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#Segmentation of Longitudinal TBI data (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
#Refactoring of the tractography display widget (Isaiah)
#Laterality (Lauren)
#Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
#Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Jean-Christophe, Julien Finet, Yiming Ge, Ping Cao)
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th 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 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[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 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
#Bompard, Lucile- UNC NIRAL
#Belhachemi, Dominique- University of Pennsylvania
#Blumfiled, Anthony- Radnostics
#Budin, Francois- UNC NIRAL
#Callahan, Steve- University of Utah
#Cates, Joshua- University of Utah
#Datar, Manasi- University of Utah
#Davey, Colin-
#Farzinfar, Mahshid- UNC
#Finet, Julien- Kitware
#Fishbaugh, James- University of Utah
#Gardner, Greg- University of Utah
#Globinsky, Ronen- Yale University
#Goubran, Maged- Robarts Research Institute
#Haehn, Daniel- University of Pennsylvania
#Halle, Mike - BWH/HMS
#Heffter, Tamas- Queen's University
#Irimia, Andrei- University of California, Los Angeles
#Johnson, Hans- University of Iowa
#Kapur, Tina- Brigham and Women's Hospital; Harvard Medical School
#Kikinis, Ron- Brigham and Women's Hospital; Harvard Medical School
#Kim, Regina- University of Iowa
#Kostrzewski, Szymon- Ecole Polytechnique Federale de Lausanne EPFL
#Lee, Dillon- University of Utah
#Li, Yinpeng- UNC-NIRAL
#Lou, Yifei- Georgia Institute of Technology
#Mastrogiacomo, Katie- Brigham and Women's Hospital
#Matsui, Joy- University of Iowa
#Meier, Dominik- BWH
#Milchenko, Mikhail- Washington University in St. Louis
#Miller, James- GE Research
#Pace, Danielle- Kitware
#Paniagua, Beatriz- University of North Carolina at Chapel Hill
#Papademetris, Xenophon- Yale University
#Patwardhan, Kedar- GE Global Research
#Pieper, Steve- Isomics, Inc.
#Pinter, Csaba- Queen's University
#Pohl, Kilian- UPenn
#Prastawa, Marcel- University of Utah
#Rajchl, Martin- Robarts Research Institute
#Schuh, Andreas- University of Pennsylvania
#Scully, Mark- University of Iowa
#Sharp, Gregory- MGH
#Shi, Yundi- UNC Chapel Hill
#Vachet, Clement- UNC Chapel Hill
#Wang, Bo- University of Utah
#Wells, Sandy- BWH/HMS
#Yamada, Atsushi- Brigham and Women's Hospital
#Yarmarkovich, Alexander- Isomics

File:BRAINSCutTutorial TutorialContestSummer2011.zip

2011-06-13T19:56:10Z

Reginakim:

BRAINSCut Tutorial NAMIC2011SummerConstest

2011-06-13T19:44:22Z

Reginakim:

Tutorial

ppt [[File:BRAINSCutTutorial TutorialContestSummer2011.ppt]]

pdf [[File:BRAINSCutTutorial TutorialContestSummer2011.pdf]]

Data File

File:BRAINSCutTutorial TutorialContestSummer2011.ppt

2011-06-13T19:42:36Z

Reginakim: