NAMIC Wiki - User contributions [en]

2011 Summer Project Week Slicer DICOM RT Brachytherapy

2011-06-24T02:58:14Z

Fjanoos: /* Key Investigators */

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

Project Title: '''Visualizing Prostate and Gynecological Brachytherapy Images, Plans, and Dose in Slicer'''
==Key Investigators==
*BWH: Tina Kapur, Jan Egger, Firdaus Janoos, Andrey Fedorov
*MGH: Greg Sharp

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

<h3>Objective</h3>

To load and visualize planning contours and planned dose distributions generated by Nucletron Oncentra Planning System in Slicer.
</div>

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

<h3>Approach, Plan</h3>
We plan to port existing Matlab and C++ codes into Slicer for reading the files generated by the Nucleotron Oncentra Planning System. In addition, we will have to implement new functionality from the Nucleotron specifications.
We expect that we will be able to visualize the contours using the Plastimatch Extension Module.
</div>

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

<h3>Progress</h3>

We have integrated functionality into Slicer3d v 4 to read the US image data (i.e. greyscale) exported by the Nucleotron system in .l3d format. We have also implemented a command line module to convert the .l3d file into NIFTI files and raw binary files. If needed, a DICOM convert feature could be easily added.

Regarding the structure and dose planning information contained in .ldd format files – we have implemented functionality to read the contour data into Slicer3D. However, we have yet to implement visualization capability. Firstly, we would need convert the contours (which are in a polyline format) into label maps – and visualize them as volumes. Alternatively, we could directly visualize the polyline data by converting it into a surface mesh.

Also, integration of this functionality into Plastimatch is planned.



</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#N/A

2011 Summer Project Week Slicer DICOM RT Brachytherapy

2011-06-23T20:20:49Z

Fjanoos: /* Key Investigators */

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

Project Title: '''Visualizing Prostate and Gynecological Brachytherapy Images, Plans, and Dose in Slicer'''
==Key Investigators==
*BWH: Tina Kapur, Jan Egger, Firdaus Janoos, Andrey Fedorov
*MGH: Greg Sharp

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

<h3>Objective</h3>

To load and visualize planning contours and planned dose distributions generated by Nucletron Oncentra Planning System in Slicer.
</div>

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

<h3>Approach, Plan</h3>
We plan to port existing Matlab and C++ codes into Slicer for reading the files generated by the Nucleotron Oncentra Planning System. In addition, we will have to implement new functionality from the Nucleotron specifications.
We expect that we will be able to visualize the contours using the Plastimatch Extension Module.
</div>

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

<h3>Progress</h3>
Implemented functionality to read US data exported by Nucleotron system (.l3d). Can read contour information from .ldd files - working on contour interpolation/smoothing, converting contours to label maps and visualization of contours.
Planned: Integration into Plastimatch.



</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#N/A

2011 Summer Project Week Slicer DICOM RT Brachytherapy

2011-06-23T20:19:20Z

Fjanoos: /* Key Investigators */

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

Project Title: '''Visualizing Prostate and Gynecological Brachytherapy Images, Plans, and Dose in Slicer'''
==Key Investigators==
*BWH: Tina Kapur, Jan Egger, Firdaus Janoos, Andrey Fedorov
*MGH: Greg Sharp

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

<h3>Objective</h3>

To load and visualize planning contours and planned dose distributions generated by Nucletron Oncentra Planning System in Slicer.
</div>

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

<h3>Approach, Plan</h3>
We plan to port existing Matlab and C++ codes into Slicer for reading the files generated by the Nucleotron Oncentra Planning System. In addition, we will have to implement new functionality from the Nucleotron specifications.
We expect that we will be able to visualize the contours using the Plastimatch Extension Module.
</div>

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

<h3>Progress</h3>
Implemented functionality to read US data exported by Nucleotron system (.l3d). Can read contour information from .ldd files - working on contour interpolation/smoothing, converting contours to label maps and visualization of contours.



</div>

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

==References==

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#N/A

2011 Summer Project Week Slicer DICOM RT Brachytherapy

2011-06-19T19:49:54Z

Fjanoos: /* Key Investigators */

Events:Computational Methods for Radiation Oncology

2011-05-05T11:30:44Z

Fjanoos: /* Confirmed Participants */

Back to [[Events]]

==Date and Location==
Date: Thursday, May 5, 2011

Location: Surgery Education Office, Room CA-034, Carrie Hall, 15 Francis Street. ([[Media:Directions to CA-034 Carrie Hall 15 Francis Street Boston.doc|Directions]])

In addition, the following information is useful for first time visitors to the hospital:
*http://www.brighamandwomens.org/about_bwh/locations/directions/default.aspx
*On the "Pike map" PDF link (bottom of page), the Carrie Hall building is closest to the 15 Francis St entrance -- enter through the columns.
*On Google Street View/Map, the Carrie Hall building is near the label "Howard Hughes Medical Institute".

==Agenda==

To brainstorm computational methods for radiation oncology between UNC, NA-MIC, BWH.

*8am: Breakfast
*8:30-10:30am: UNC -presentations about capabilities of current projects, short term and longer term plans
**Julian Rosenman PLUNC 18 minutes
**Gregg Tracton Software for PLUNC, segmentation, registration 10 minutes
**Stephen Pizer Registration by regression (2 methods), Segmentation via posterior optimization, training probability distributions on s reps and quantile functions, segmentation via correspondence-preserving warps, ant aliasing 23 minutes
**Sha Chang Nanotube imaging, incl. for IGRT 10 minutes
**Brandon Frederick Iterative tomographic reconstruction, CTs at treatment time, gpu’s 15 minutes
**Derek Merck 3D visualization via model-guided rendering, 3D visualization in PLUNC for RTP 15 minutes
**Ilknur Kabul Texturing of surfaces, onion skins, and cut planes; interpolation of textures 10 minutes
**Hina Shah Registration of endoscopic cine and CT of throat,fused displays of these two registered sources 8 minutes
**Ron Alterovitz Planning for brachytherapy with curved needles, FEM software 12 minutes
*10:30 am: Break
*10:50am-12:30pm: NA-MIC/Harvard presentations about capabilities of current projects, short term and longer term plans
**Slicer3 to Slicer 4, Radiation Therapy support today, and plans for the next year [[media:Pieper-CMRO-2011-05-05.ppt|(slides)]] (Steve Pieper) (30 minutes)
**[[Media:SparKitIntroBostonRadOnc2011.pdf|SPARKit, Canadian grant for providing open source software platform for radiotherapy, potentially based on NA-MIC Kit]] (Andras Lasso) (10minutes)
**Head and Neck Cancer NA-MIC DBP ([[Media:2011-CMRO-Sharp.pdf|slides]]) (Greg Sharp) (15 minutes)
**Gynecologic Cancer Brachytherapy Plans (Tina Kapur) (15 minutes)
**Shadie, shading language for volume visualization(Hanspeter Pfister, Milos Hasan, George Chen, John Wolfgang) (20 minutes)
*12:30pm: Lunch
*1pm: Intro of afternoon objectives (Julian Rosenman)
*1:10pm: What UNC/Boston system combinations ought to be developed -- the Boston perspective (Tina Kapur)
*1:30pm: What Boston/UNC system combinations ought to be developed -- the UNC perspective (Steve Pizer)
*2:00-2:30pm: Comments from Kitware about their capabilities relevant to proposed combinations (Brad Davis)
*2:30pm: Break and subgroup formation (e.g., merging surgical and radiation treatment planning system; 3D visualization software for treatment planning; image analysis software for treatment planning)
*3:00-4pm: Subgroups sketch out mechanics for collaborations (http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html?)
*4:00-5:0pm: Summary: what we do next?

==Confirmed Participants==

#Julian Rosenman
#Gregg Tracton
#Stephen Pizer
#Sha Chang
#Brandon Frederick
#Derek Merck
#Ilknur Kabul
#Hina Shah
#Ron Alterovitz
#Ron Kikinis
#Sandy Wells
#Steve Pieper
#Andras Lasso
#Greg Sharp
#Tina Kapur
#Hanspeter Pfister
#Milos Hasan
#George Chen
#John Wolfgang
#Petter Risholm
#Andrey Fedorov
#James Balter
#Brad Davis
#Andinet Enquobahrie
#Firdaus Janoos

2008 Winter Project Week:microslicer 3

2007-12-19T20:30:09Z

Fjanoos: New page: {| |Return to [[2008_Winter_Project_Week ]] |valign="top"|The Cingulum Bundle Anchor Tract |} __...

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]
|}

__NOTOC__
===Key Investigators===
* Georgia Tech: John Melonakos, Vandana Mohan
* Kitware: Luis Ibanez
* BWH: Mark Niethammer, Marek Kubicki

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.

The objectives of this project are to port the Fast Sweeping and optimal geodesic path tractography code to ITK as well as the code to provide for volumetric segmentation of DW-MRI data.

See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details.

</div>

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

<h1>Approach, Plan </h1>
Our approach is described by the references below. Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week

2007-12-19T20:29:50Z

Fjanoos: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#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]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy Plesniak,Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#[[2008_Winter_Project_Week:microslicer_3 | Doing microscopy image analysis with Slicer3]] [Ohio State U](Kishore M., Raghu M., Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [Ohio State University](Firdaus J.,Raghu M., Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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)
# By December 17, 2008: [[2008_Winter_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.
# 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...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

2008 Winter Project Week:fmri image analysis

2007-12-19T20:16:44Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.
</div>

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

<h1>Progress</h1>
<div>
We have implemented the inter-slice motion correction module for Slicer3 and are now testing it on various data-sets. We are currently working on inter-volume registration and spatial normalization to a reference space (viz. Talairach and MNI.)
</div>
</div>

<div style="width: 100%; float: left;">
<h2>References</h2>
<ul>
<li> K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. <b>Statistical Parametric Mapping: The Analysis of Functional Brain Images</b>. Academic Press, 2007
<li>P. Jezzard, P. M. Matthews, Stephen M. Smith, <b>Functional MRI: An Introduction to Methods</b>, Oxford Univ. Press, 2001
<li> K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. <b> Spatial registration and normalization of images.</b> Human Brain Mapping, 2:165-189, 1995.
<li> J. Ashburner and K. J. Friston. <b>Multimodal image coregistration and partitioning - a unified framework.</b> NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000
</ul>
</div>

2008 Winter Project Week:fmri image analysis

2007-12-19T20:16:16Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.
</div>

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

<h1>Progress</h1>
<div>
We have implemented the inter-slice motion correction module for Slicer3 and are now testing it on various data-sets. We are currently working on inter-volume registration and spatial normalization to a reference space (viz. Talairach and MNI.)
</div>

</div>
<div style="width: 50%; float: left;">

<h2>References</h2>
<ul>
<li> K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. <b>Statistical Parametric Mapping: The Analysis of Functional Brain Images</b>. Academic Press, 2007
<li>P. Jezzard, P. M. Matthews, Stephen M. Smith, <b>Functional MRI: An Introduction to Methods</b>, Oxford Univ. Press, 2001
<li> K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. <b> Spatial registration and normalization of images.</b> Human Brain Mapping, 2:165-189, 1995.
<li> J. Ashburner and K. J. Friston. <b>Multimodal image coregistration and partitioning - a unified framework.</b> NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000
</ul>

</div>

2008 Winter Project Week:fmri image analysis

2007-12-19T20:13:58Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.
</div>

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

<h1>Progress</h1>
<div>
We have implemented the inter-slice motion correction module for Slicer3 and are now testing it on various data-sets. We are currently working on inter-volume registration and spatial normalization to a reference space (viz. Talairach and MNI.)
</div>

<div>

<h2>References</h2>
<ul>
<li> K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. <b>Statistical Parametric Mapping: The Analysis of Functional Brain Images</b>. Academic Press, 2007
<li>P. Jezzard, P. M. Matthews, Stephen M. Smith, <b>Functional MRI: An Introduction to Methods</b>, Oxford Univ. Press, 2001
<li> K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. <b> Spatial registration and normalization of images.</b> Human Brain Mapping, 2:165-189, 1995.
<li> J. Ashburner and K. J. Friston. <b>Multimodal image coregistration and partitioning - a unified framework.</b> NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000
</ul>

</div>

2008 Winter Project Week:fmri image analysis

2007-12-19T20:13:00Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.
</div>

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

<h1>Progress</h1>
<div>
We have implemented the inter-slice motion correction module for Slicer3 and are now testing it on various data-sets. We are currently working on inter-volume registration and spatial normalization to a reference space (viz. Talairach and MNI.)
</div>

<h2>References</h2>
<ul>
<li> K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. <b>Statistical Parametric Mapping: The Analysis of Functional Brain Images</b>. Academic Press, 2007
<li>P. Jezzard, P. M. Matthews, Stephen M. Smith, <b>Functional MRI: An Introduction to Methods</b>, Oxford Univ. Press, 2001
<li> K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. <b> Spatial registration and normalization of images.</b> Human Brain Mapping, 2:165-189, 1995.
<li> J. Ashburner and K. J. Friston. <b>Multimodal image coregistration and partitioning - a unified framework.</b> NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000
</ul>

2008 Winter Project Week:fmri image analysis

2007-12-19T20:10:42Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.
</div>

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

<h1>Progress</h1>
<div>
We have implemented the inter-slice motion correction module for Slicer3 and are now testing it on various data-sets. We are currently working on inter-volume registration and spatial normalization to a reference space (viz. Talairach and MNI.)
</div>

<h2>References</h2>
<ul>
<li> K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. <b>Statistical Parametric Mapping: The Analysis of Functional Brain Images</b>. Academic Press, 2007
<li> J. Ashburner. <b>Computational Neuroanatomy</b>. PhD thesis, University College London, 2000.
<li> K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. <b> Spatial registration and normalization of images.</b> Human Brain Mapping, 2:165-189, 1995.
<li> J. Ashburner and K. J. Friston. <b>Multimodal image coregistration and partitioning - a unified framework.</b> NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000
</ul>

2008 Winter Project Week:fmri image analysis

2007-12-19T20:09:43Z

Fjanoos: /* References */

2008 Winter Project Week:fmri image analysis

2007-12-19T20:09:19Z

Fjanoos: /* June 2007 Project Week */

2008 Winter Project Week:fmri image analysis

2007-12-19T20:03:19Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week:fmri image analysis

2007-12-19T19:59:24Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
<br>a) Slice timing correction (open)
<br>b) Inter-slice motion correction (done)
<br>c) Spatial normalization (open)
<br>d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is described by the references below. Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week:fmri image analysis

2007-12-19T19:59:05Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
To implement an fMRI analysis pipeline in the Slicer 3 framework including:
a) Slice timing correction (open)
b) Inter-slice motion correction (done)
c) Spatial normalization (open)
d) Co-registration of functional and structural data (open)

</div>

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

<h1>Approach, Plan </h1>
Our approach is described by the references below. Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

File:Project week.jpg

2007-12-19T19:54:31Z

Fjanoos: fMRI Image of the Brain after Interslice Motion Correction

fMRI Image of the Brain after Interslice Motion Correction

2008 Winter Project Week:fmri image analysis

2007-12-19T19:53:53Z

Fjanoos:

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]
|valign="top"|[[Image:project_week.jpg |thumb|320px|fMRI Image of the Brain after Inter-slice Motion Correction]]
|}

__NOTOC__
===Key Investigators===
* Ohio State University: Firdaus Janoos, Raghu Machiraju
* BWH: Steve Pieper, Wendy Plesniak
* Kitware: Luis Ibanez

<div style="margin: 20px;">

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

<h1>Objective</h1>
We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.

The objectives of this project are to port the Fast Sweeping and optimal geodesic path tractography code to ITK as well as the code to provide for volumetric segmentation of DW-MRI data.

See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details.

</div>

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

<h1>Approach, Plan </h1>
Our approach is described by the references below. Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
</div>

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

<h1>Progress</h1>

====June 2007 Project Week====
During this Project Week, we did a lot of algorithmic design work, focusing on leveraging optimal or geodesic path information to provide for volumetric segmentations of fiber bundles. Working with Marek Kubicki and the Harvard DBP, we were able to begin the process of applying our algorithm to the full cingulum bundle with new labelmaps and to a new fiber bundle - Arcuate. We have recently achieved significant results in volumetric segmentations using a locally-constrained region-based technique (see the images above).

====Jan 2007 Project Half Week====
We finished the itkDirectionalIterator which will be needed in the Fast Sweeping implementation. Furthermore, we made progress in porting our Matlab code to ITK.

</div>

<br style="clear: both;" />

</div>

===References===
* J. Melonakos, M. Niethammer, V. Mohan, M. Kubicki, J. Miller, A. Tannenbaum. Locally-Constrained Region-Based Methods for DW-MRI Segmentation. Submitted to MMBIA 2007.
* V. Mohan, J. Melonakos, M. Niethammer, M. Kubicki, and A. Tannenbaum. Finsler Level Set Segmentation for Imagery in Oriented Domains. BMVC 2007.
* J. Melonakos, V. Mohan, M. Niethammer, K. Smith, M. Kubicki, and A. Tannenbaum. Finsler Tractography for White Matter Connectivity Analysis of the Cingulum Bundle. MICCAI 2007.
* J. Melonakos, E. Pichon, S. Angenet, and A. Tannenbaum. Finsler Active Contours. IEEE Transactions on Pattern Analysis and Machine Intelligence, to appear in 2007.
* E. Pichon and A. Tannenbaum. Curve segmentation using directional information, relation to pattern detection. In IEEE International Conference on Image Processing (ICIP), volume 2, pages 794-797, 2005.
* E. Pichon, C-F Westin, and A. Tannenbaum. A Hamilton-Jacobi-Bellman approach to high angular resolution diffusion tractography. In International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), pages 180-187, 2005.

2008 Winter Project Week:fmri image analysis

2007-12-19T19:48:25Z

Fjanoos: New page: {| |Return to [[2008_Winter_Project_Week ]] |valign="top"|The Cingulum Bundle Anchor Tract |} __...

2008 Winter Project Week

2007-12-19T19:44:21Z

Fjanoos: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#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]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy Plesniak,Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M., Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Analysis with Slicer 3]] [Ohio State University](Firdaus J.,Raghu M., Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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)
# By December 17, 2008: [[2008_Winter_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.
# 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...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

2008 Winter Project Week

2007-12-19T19:43:48Z

Fjanoos: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#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]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy Plesniak,Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M., Brad Davis,Stephen Aylward, Steve Pieper)
#[[2008_Winter_Project_Week:fmri_image_analysis | fMRI Image analysis with Slicer 3]] [Ohio State University](Firdaus J.,Raghu M., Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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)
# By December 17, 2008: [[2008_Winter_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.
# 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...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

2008 Winter Project Week

2007-12-19T19:42:31Z

Fjanoos: /* All Other Projects */

Back to [[Project Events]], [[AHM_2008]], [[Events]]

== Projects ==
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]
*[[2007_Programming/Project_Week_MIT#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]]
*Next Project Week is at MIT -- June 23-27, 2008

===DBP Roadmap Projects===
Please note that the first four categories below correspond to four clinical Roadmap application projects that will be pursued in focused parallel tracks at the meeting, each corresponding to a DBP problem.
====[[DBP2:Harvard:Brain_Segmentation_Roadmap|DBP Harvard Roadmap Project: Stochastic Tractography for Velocardio Facial Syndrome (VCFS)]]====
*[[2008_Winter_Project_Week:StochasticTract_Arcuate|Stochastic tractography of the arcuate fasciculus in schizophrenia]] (Marek Kubicki, Tri Ngo, Doug Markant)

====[[DBP2:UNC:Cortical_Thickness_Roadmap|DBP UNC Roadmap Project: Cortical Thickness Measurement for Autism]]====
*[[2008_Winter_Project_Week:Cortical_Thickness|Cortical thickness analysis of pediatric brains]] (Heather Cody Hazlett, Martin Styner, Clement Vachet, Jim Miller)

====[[DBP2:MIND:Roadmap|DBP MIND Roadmap Project: Brain Lesion Analysis in Neuropsychiatric Systemic Lupus Erythematosus]]====
*[[2008_Winter_Project_Week:Lesions|Towards an end to end lesion analysis feature in Slicer3]] (Mark Scully, Jeremy Bockholt, Brad Davis, Marcel Prastawa, Sonia Pujol, Vincent Magnotta)

====[[DBP2:JHU:Roadmap|DBP JHU Roadmap Project: Segmentation and Registration for Robotic Prostate Intervention]]====
#[[2008_Winter_Project_Week:Robotic_Prostate_Interventions | Robotic Prostate Interventions]] (David Gobbi, Csaba Csoma, Junichi Tokuda, Katie Hayes)
#[[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)

===All Other Projects===
# [[2008_Winter_Project_Week_GroupwiseReg | Groupwise Registration and Atlas Building]] (Brad Davis, Serdar Balci, Casey Goodlett)
# [[2008_Winter_Project_Week:MRISC|Joint Segmentation and Classification of MR Images Based on Structure-specific Affine Registration]] (Mert Sabuncu, Kilian Pohl)
# [[2008_Winter_Project_Week:CorPar|Cortical Surface Parcellation]] (Thomas Yeo, Mert Sabuncu)
# [[2008_Winter_Project_Week:Dorsolateral_Prefrontal_Cortex_Segmentation|Dorsolateral Prefrontal Cortex Segmentation]] (Marek Kubicki, Sylvain Bouix, John Melonakos, Brad Davis, Polina Golland)
#[[2008_Winter_Project_Week:Particle_Correspondence_DTI|Incorporating DTI data into entropy-based particle system for cortical correspondence]] (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)
#[[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Marek Kubicki)
#[[2008_Winter_Project_Week:Fluid_Mechanics_Tractography|Fluid Mechanics Based DTI Tractography]] (Nathan Hageman)
#[[2008_Winter_Project_Week:MRMLScenesForExecutionModel |MRML Scenes for the Execution Model including Transforms]] (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)
#Unstructured Grids and Mesh Support(Curt, Alex, Steve, Will, Vince, Bob O'Bara)
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith, Dan Blezek)
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca Antiga, Steve Pieper)
#[[2008_Winter_Project_Week:EventBrokerInSlicer3 |Event broker in Slicer3]] (Jim, Steve, Alex Y, Luca, Dan Blezek)
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)
#Drafting Human Interface and Slicer Style Guidelines (Wendy Plesniak,Sebastien Barre)
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week_VolumeRenderingUsingCuda|Volume rendering using Cuda]] (Andy Freudling, Steve Pieper, Grauer)
#[[2008_Winter_Project_Week:3DWWidgets |3D W Widgets and Picking]] (Will Schroeder, Nicole Aucoin, Curt Lisle, Kiran Shivana)
#[[2008_Winter_Project_Week:OutOfCoreMRML | MRML support for out of core processing with fMRI and DTI as use cases]] (Steve Pieper, Jim Miller, Wendy Plesniak, Alex Yarmakovich, Will Schroeder)
#[[2008_Winter_Project_Week:XNAT_Integration | XNAT Integration]] ([http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake]) (Dan Marcus, Steve Pieper, Stephen Aylward, Jeff Grethe, Julien Jomier)
#KWWidgets Roadmap (Sebastien Barre, Wendy Plesniak, Katie Hayes)
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)
#Astronomical coordinate system support (Mike Halle, Doug Alan)
#[[2008_Winter_Project_Week:Meshing Techniques into NA-MIC Toolkit|New Meshing Techniques into NA-MIC]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta)
#[[2008_Winter_Project_Week:Finite Element Meshing into NA-MIC|Meshing Workflow into Slicer]] [Univ. of Iowa] (Nicole Grosland, Vince Magnotta, Kiran Shivana, Steve Pieper, Curt Lisle, Brad Davis)
#[[2008_Winter_Project_Week:SmallAnimalEvalNCI |Evaluating NA-MIC Tools for Small Animal Imaging Workflows]] [NCI] (Curt Lisle, Jack Collins, Killian Pohl)
#[[2008_Winter_Project_Week:GoFigure |GoFigure:High-Level Microscopy Image analysis Application and Algorithms]] [CalTech-Harvard Medical School] (Alex G, Sean Megason, Arnaud Gelas?)
#[[2008_Winter_Project_Week:IGT_IGSTK_Slicer| IGSTK-Slicer]] [Georgetown] (Haiying Liu, Patrick Cheng, Noby Hata, Junichi Tokuda)
#[[2008_Winter_Project_Week:IGT_Intelligent_Surgical_Instrument_Projects| Japanese Intelligent Surgical Instrument Project]] [AIST] (Noby Hata, Chinzei, Hong)
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M., Brad Davis,Stephen Aylward, Steve Pieper)
#[[fmri image analysis with Slicer 3[Ohio State U]]](Firdaus J.,Raghu M., Luis Ibanez,Steve Pieper, Wendy Plesniak)
#[[2008_Winter_Project_Week:Resampling_DTIs_with_Slicer3|Resampling DTIs with Slicer 3]] (Francois Budin, Sylvain Bouix)

== Dates.Venue.Registration ==

'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''.
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.

'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.

<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big>

Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]

([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])

===Introduction to NA-MIC Project Week===

Please read the introduction to these events [[Project_Events#Introduction|here]].

=== Agenda===

[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]

=== Preparation ===

# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
## 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)
# By December 17, 2008: [[2008_Winter_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.
# 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...

== Previous Project Events ==

A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].

File:Spm reg.png

2007-10-25T17:55:54Z

Fjanoos:

File:Kl rigid.png

2007-10-25T17:55:38Z

Fjanoos:

File:Mattes ridid.png

2007-10-25T17:53:06Z

Fjanoos:

File:Ms aff.png

2007-10-25T17:52:41Z

Fjanoos:

File:Ms rigid.png

2007-10-25T17:52:16Z

Fjanoos:

File:Unreg.png

2007-10-25T17:51:56Z

Fjanoos:

Inter-slice Motion Correction for fMRI

2007-10-25T17:51:28Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Algorithms Used From ITK ==

=== Metrics ===

# Mean Squared - smooth, and for rigid registration, the minimum is fairly correct (physically)
# MI (Wells, Mattes) - very non-smooth - lot of discontinuities. For all motions, results are wrong (possibly because cannot identify a good minimum pt)
# KL-Divergence (Chung, Wells,'' et. al.'') - again very non-smooth. Cannot identify a good minimum point.

=== Transformations ===
# Rigid - works well for ms metric, not so correct for statistical metrics.
# Affine - works for ms metric, does not work for the statistical metrics.
# B-spline non-rigid - tested with ms and kl. Extremely poor results.

== Results ==

'''Original fMRI '''

[[Image:unreg.png]]

'''MS Metric with rigid transform'''

[[Image:ms_rigid.png]]

'''MS Metric with affine transform'''

[[Image:ms_aff.png]]

'''Mattes MI metric with rigid transform '''

[[Image:mattes_ridid.png]]

'''KL metric with rigid transform '''

[[Image:kl_rigid.png]]

'''SPM Registered '''

[[Image:spm_reg.png]]

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-10-25T17:50:46Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Algorithms Used From ITK ==

=== Metrics ===

# Mean Squared - smooth, and for rigid registration, the minimum is fairly correct (physically)
# MI (Wells, Mattes) - very non-smooth - lot of discontinuities. For all motions, results are wrong (possibly because cannot identify a good minimum pt)
# KL-Divergence (Chung, Wells,'' et. al.'') - again very non-smooth. Cannot identify a good minimum point.

=== Transformations ===
# Rigid - works well for ms metric, not so correct for statistical metrics.
# Affine - works for ms metric, does not work for the statistical metrics.
# B-spline non-rigid - tested with ms and kl. Extremely poor results.

== Results ==

'''Original fMRI '''

[[Image:original.png]]

'''MS Metric with rigid transform'''

[[Image:ms_rigid.png]]

'''MS Metric with affine transform'''

[[Image:ms_aff.png]]

'''Mattes MI metric with rigid transform '''

[[Image:mattes_ridid.png]]

'''KL metric with rigid transform '''

[[Image:kl_rigid.png]]

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-10-24T23:52:14Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Algorithms Used From ITK ==

=== Metrics ===

# Mean Squared - smooth, and for rigid registration, the minimum is fairly correct (physically)
# MI (Wells, Mattes) - very non-smooth - lot of discontinuities. For all motions, results are wrong (possibly because cannot identify a good minimum pt)
# KL-Divergence (Chung, Wells,'' et. al.'') - again very non-smooth. Cannot identify a good minimum point.

=== Transformations ===
# Rigid - works well for ms metric
# Affine - does not work for any metric
# B-spline non-rigid - tested with ms and kl. Extremely poor results.

== Results ==

'''Original fMRI '''

[[Image:firdaus_image_004.png]]

'''MS Metric with Rigid Motion'''

[[Image:original.jpg]]

'''MS Metric with Affine Transform'''

[[Image:affine-rms-registered.jpg]]

[[Image:firdaus_affine_rms.png]]

'''Mattes MI metric with rigid transform '''

'''Mattes MI metric with affine transform '''

[[Image:firdaus_affine_mi.png]]

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-10-24T23:48:34Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Algorithms Used From ITK ==

=== Metrics ===

# Mean Squared - smooth, and for rigid registration, the minimum is fairly correct (physically)
# MI (Wells, Mattes) - very non-smooth - lot of discontinuities. For all motions, results are wrong (possibly because cannot identify a good minimum pt)
# KL-Divergence (Chung, Wells,'' et. al.'') - again very non-smooth. Cannot identify a good minimum point.

=== Transformations ===
# Rigid - works well for ms metric
# Affine - does not work for any metric
# B-spline non-rigid - tested with ms and kl. Extremely poor results.

== Results ==

'''Original fMRI '''

[[Image:firdaus_image_004.png]]

'''MS Metric with Rigid Motion'''

[[Image:original.jpg]]

'''MS Metric with Affine Transform'''

[[Image:affine-rms-registered.jpg]]

[[Image:firdaus_affine_rms.png]]

'''Mattes MI metric with affine transform '''

[[Image:firdaus_affine_mi.png]]

''' something '''

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-10-24T23:47:23Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Algorithms Used From ITK ==

=== Metrics ===

# Mean Squared - smooth, and for rigid registration, the minimum is fairly correct (physically)
# MI (Wells, Mattes) - very non-smooth - lot of discontinuities. For all motions, results are wrong (possibly because cannot identify a good minimum pt)
# KL-Divergence (Chung, Wells,'' et. al.'') - again very non-smooth. Cannot identify a good minimum point.

=== Transformations ===
# Rigid - works well for ms metric
# Affine - does not work for any metric
# B-spline non-rigid - tested with ms and kl. Extremely poor results.

== Results ==

'''Original fMRI '''

[[Image:firdaus_image_004.png]]

'''MS Metric with Rigid Motion'''

[[Image:original.jpg]]

'''MS Metric with Affine Transform'''

[[Image:firdaus_affine_rms.png]]

'''Mattes MI metric with affine transform '''

[[Image:firdaus_affine_mi.png]]

''' something '''
[[Image:affine-rms-registered.jpg]]

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-10-24T23:46:54Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Algorithms Used From ITK ==

=== Metrics ===

# Mean Squared - smooth, and for rigid registration, the minimum is fairly correct (physically)
# MI (Wells, Mattes) - very non-smooth - lot of discontinuities. For all motions, results are wrong (possibly because cannot identify a good minimum pt)
# KL-Divergence (Chung, Wells,'' et. al.'') - again very non-smooth. Cannot identify a good minimum point.

=== Transformations ===
# Rigid - works well for ms metric
# Affine - does not work for any metric
# B-spline non-rigid - tested with ms and kl. Extremely poor results.

== Results ==

'''Original fMRI '''

[[Image:firdaus_image_004.png]]

'''MS Metric with Rigid Motion'''

[[Image:original.jpg]]

'''MS Metric with Affine Transform'''
[[Image:firdaus_affine_rms.png]]

'''Mattes MI metric with affine transform '''
[[Image:firdaus_affine_mi.png]]

''' something '''
[[Image:affine-rms-registered.jpg]]

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

File:Original image 004.png

2007-10-24T21:45:54Z

Fjanoos:

Inter-slice Motion Correction for fMRI

2007-10-24T21:45:38Z

Fjanoos: /* Results */

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.
* Coding completed. However, results are far from satisfactory.
* Progress (maybe) stymied by "poor" resolution of data.
* Progress (maybe) stymied by "not-so-viable" metrics (MI, etc.).

== Results ==

=== Original Images ===

[[Image:original_image_004.png]]
Original data with motion artefacts

=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

=== Non-Rigid ===
* B-spline deformation with KL metric produces very minimal change (in a least squares sense), while MI produces more changes but doesn't look correct.

=== Images ===
[[Image:firdaus_image_004.png]]
Original fMRI

[[Image:original.jpg]]
'''Volume rendering of original volume'''

[[Image:resampled.jpg]]
'''Volume rendering of up-sampled volume (0.5x0.5mm in axial plane)'''

[[Image:affine-rms-registered.jpg]]
'''Volume rendering of co-registered volume'''

[[Image:firdaus_affine_rms.png]]
Volume rendering of affine motion with mean square error metric

[[Image:firdaus_affine_mi.png]]
Affine motion with Mattes MI error metric

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* '''Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.'''
* '''Even the slightest change in initialization results in a large deviation in the registration result.
'''

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-09-11T14:33:24Z

Fjanoos: `

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.

== Results ==
=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

=== Non-Rigid ===
* B-spline deformation with KL metric produces very minimal change (in a least squares sense), while MI produces more changes but doesn't look correct.

=== Images ===
[[Image:firdaus_image_004.png]]
Original fMRI

[[Image:firdaus_affine_rms.png]]
Affine motion with mean square error metric

[[Image:firdaus_affine_mi.png]]
Affine motion with Mattes MI error metric

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.
* Even the slightest change in initialization results in a large deviation in the registration result.

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-09-10T11:08:30Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.

== Results ==
=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

=== Non-Rigid ===
* B-spline deformation with KL metric produces very minimal change (in a least squares sense), while MI produces more changes but doesn't look correct.

=== Images ===
[[Image:firdaus_image_004.png]]
Original fMRI

[[Image:firdaus_affine_rms.png]]
Affine motion with mean square error metric

[[Image:firdaus_affine_mi.png]]
Affine motion with Mattes MI error metric

=== Issues ===
* As can be seen any registration result looks more jagged (along the sagittal and coronal sections).
* Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.
* Even the slightest change in initialization results in a large deviation in the registration result.

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

File:Firdaus affine mi.png

2007-09-10T11:03:04Z

Fjanoos: Affine motion with Mattes MI metric

Affine motion with Mattes MI metric

File:Firdaus affine rms.png

2007-09-10T11:02:43Z

Fjanoos: Affine motion with mean square metric

Affine motion with mean square metric

File:Firdaus image 004.png

2007-09-10T11:02:14Z

Fjanoos: Original fMRI

Original fMRI

Inter-slice Motion Correction for fMRI

2007-09-10T11:01:50Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.

== Results ==
=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

=== Non-Rigid ===
* B-spline deformation with KL metric produces very minimal change (in a least squares sense), while MI produces more changes but doesn't look correct.

[[Image:firdaus_image_004.png]]
Original fMRI

[[Image:firdaus_affine_rms.png]]
Affine motion with mean square error metric

[[Image:firdaus_affine_mi.png]]
Affine motion with Mattes MI error metric

=== Issues ===
* Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.
* Even the slightest change in initialization results in a large deviation in the registration result.
* Any registration result looks more jagged (along the sagittal and coronal sections)

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-09-10T11:00:18Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.

== Results ==
=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

=== Non-Rigid ===
* B-spline deformation with KL metric produces very minimal change (in a least squares sense), while MI produces more changes but doesn't look correct.

[[Image:original.png]]

=== Issues ===
* Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.
* Even the slightest change in initialization results in a large deviation in the registration result.
* Any registration result looks more jagged (along the sagittal and coronal sections)

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-09-05T07:40:45Z

Fjanoos:

== Objective ==
* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==
* Implemented and tested b-Spline/affine registration with Mattes-MI and KL metrics.

== Results ==
=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

=== Non-Rigid ===
* B-spline deformation with KL metric produces very minimal change (in a least squares sense), while MI produces more changes but doesn't look correct.

=== Issues ===
* Low sampling rate and image noise - all the metrics are extremely non-smooth as a result.
* Even the slightest change in initialization results in a large deviation in the registration result.
* Any registration result looks more jagged (along the sagittal and coronal sections)

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-08-30T09:07:26Z

Fjanoos:

== Objective ==

* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

== Progress ==

* Implemented and tested b-Spline/affine registration with Wells-MI and KL metrics.

== Results ==
=== Affine ===
* affine motion with all metrics degrades the inter-slice registration.

== Open questions ==
* Intensity normalization / histogram equalization - would these have any impact on inter-slice registration? Would they affect the computation of the joint-entropies for MI/KL metrics.
* Should there be some regularization factor on the registration to limit the motion ?

== To Do ==

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

== Key Investigators ==

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

== Links ==

Inter-slice Motion Correction for fMRI

2007-08-23T11:54:52Z

Fjanoos:

Objective:

* To perform inter-slice motion correction in fMR images using affine and non-rigid registration methods.

Progress:

* Implemented and tested b-Spline registration with Well Mutual Information metric.
* Working on affine motion correction using MI.

To Do:

* Right now, registration is done on a slice by slice basis. However, due to the low resolution of fMRI and the absence of gradients result in low registration accuracy. We are investigating using alternative image-to-image metrics like the KL divergence. We are also looking at simultaneously registering multiple slices.

Key Investigators:

* Firdaus Janoos, Raghu Machiraju, Steve Pieper, Wendy Plesniak.

Links: