NAMIC Wiki - User contributions [en]

2012 Summer Project Week:NiftyReg

2012-06-22T14:22:20Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

* The NRRD file format have been integrated into the NiftyReg package to ease its integration.
* The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
* reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.
* The project CMake organisation has been altered to enable easy integration of the other executables.

</div>
</div>

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

== Reg_aladin Module screenshot==
[[File:NiftyRegExtension_reg_aladin_module.png|800 px]]
[[file:ExtensionManager_NiftyReg.png|400]]

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:NiftyReg

2012-06-22T14:19:35Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

The NRRD file format have been integrated into the NiftyReg package to ease its integration.

The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.

The project CMake organisation has been altered to enable easy integration of the other executables.

</div>
</div>

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

== Reg_aladin Module screenshot==
[[File:NiftyRegExtension_reg_aladin_module.png|800 px]]
[[file:ExtensionManager_NiftyReg.png|400]]

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:NiftyReg

2012-06-22T14:17:21Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

The NRRD file format have been integrated into the NiftyReg package to ease its integration.

TCLAP has been incorporated into the NiftyReg project in order to enable the creation of a Slicer extension.

The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.

</div>
</div>

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

== Reg_aladin Module screenshot==
[[File:NiftyRegExtension_reg_aladin_module.png|800 px]]
[[file:ExtensionManager_NiftyReg.png|400]]

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

File:ExtensionManager NiftyReg.png

2012-06-22T14:14:53Z

Mmodat:

2012 Summer Project Week:NiftyReg

2012-06-21T17:13:12Z

Mmodat: /* Delivery Mechanism */

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

The NRRD file format have been integrated into the NiftyReg package to ease its integration.

TCLAP has been incorporated into the NiftyReg project in order to enable the creation of a Slicer extension.

The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.

</div>
</div>

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

== Reg_aladin Module screenshot==
[[File:NiftyRegExtension_reg_aladin_module.png|800 px]]

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

File:NiftyRegExtension reg aladin module.png

2012-06-21T17:06:57Z

Mmodat:

2012 Summer Project Week:NiftyReg

2012-06-21T17:05:35Z

Mmodat: /* Key Investigators */

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

The NRRD file format have been integrated into the NiftyReg package to ease its integration.

TCLAP has been incorporated into the NiftyReg project in order to enable the creation of a Slicer extension.

The XML file for one of the executable of NiftyReg: reg_aladin has been created and the slicer module created.
reg_aladin is the global registration tool from NiftyReg. It is based on a block-matching approach to establish correspondences and a trimmed least square optimisation to determine the robust global transformation.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module -
##Built-in -
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:DifficultRegistration

2012-06-21T16:11:07Z

Mmodat: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Ct-body-atlas.jpg
Image:Ct-body-cropped.jpg
Image:Ct-body-legs.jpg
Image:Mr-brain-atlas.jpg
Image:Mr-brain-tbi.jpg
Image:Mr-brain-rotated.jpg
Image:Mr-brain-rhesus.jpg
</gallery>

==Key Investigators==
* Erasmus Medical Center: Stefan Klein
* University College London: Marc Modat
* UNC: Aditya Gupta, Martin Styner
* BWH: Matthew Toews, Petter Risholm, Dominik Meier, William Wells

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

<h3>Objective</h3>
To identify solutions to difficult image registration problems that challenge the limits of current technology. Aspects of difficulty will include:
<ul>
<li>inter-subject registration
<li>truncation, missing tissue
<li>unknown initialization
<li>inter-species registration
<li>articulated deformation
</ul>
</div>

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

<h3>Approach, Plan</h3>
A set of difficult pair-wise registration problems will be considered. Participants will discuss workable solutions based on their expertise and background, and these solutions will be documented.
<br>
Registration cases can be found [http://www.matthewtoews.com/namic2012 here].
</div>

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

<h3>Progress</h3>TBA
*CT: atlas and torso have flipped orientation: Correction Xforms here: [[Media:FlipCT_Atlas+Torso.zip|Flip CT atlas&torso, zip file with 2 .tfm files]]
</div>
</div>

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

==Delivery Mechanism==
<b>Attention Participants:</b> Please log in and update/correct entries in the table below. For bonus points, please provide links or solutions to image registration problems on this page.<br>
<table border="1">
<th>Participant</th><th>Affiliation</th><th>Context</th><th>Techniques</th><th>Solutions/Links
</th><tr><td>
Steven Aylward</td><td>Kitware</td><td>CT, US, ressection, brain tumors, changing pathology, sliding organ</td><td>Sliding Geometry, Geometric Metamorphosis</td><td>
</td><tr><td>
Karl Diedrich</td><td>AZE</td><td>Rigid registration, abdomen</td><td>Multi-resolution registration</td><td>
</td><tr><td>
James Fishbaugh</td><td>SCI</td><td>Shape analysis and registration</td><td></td><td>
</td><tr><td>
Aditya Gupta</td><td>UNC</td><td>DTI, enlarged lateral ventricles</td><td></td><td>
</td><tr><td>
Stefan Klein</td><td>Erasmus Medical Center</td><td>General Registration</td><td></td><td>
</td><tr><td>
Ivan Kolesov</td><td>Georia Tech</td><td>Articulated, point-based registration</td><td></td><td>
</td><tr><td>
Dominik Meier</td><td>BWH</td><td>General registration</td><td>Slicer: BRAINS</td><td>
IntraOp:[[Image:IntraOp_Slicer-BRAINS_BSpline.gif|60px|lleft|IntraOp via BRAINS]]<br>
TBI:[[Image:TBI_Slicer-BRAINS_BSpline.gif|60px|lleft|TBI via BRAINS]]<br>
CT torso: FAILED</td><tr><td>
Marc Modat</td><td>UCL</td><td>neuro-deg. diseases, longitudinal</td><td>NiftiReg</td><td>[http://www.na-mic.org/Wiki/images/d/d5/NiftyReg_projectWeek_test.pdf Some test res]</td><tr><td>
Albert Motillo</td><td>GE</td><td>Parsing CT, Detection</td><td></td><td>
</td><tr><td>
Simrin Nagpal</td><td>Queens University</td><td>CT/US registration</td><td></td><td>
</td><tr><td>
Samon Nuranian</td><td>UBC</td><td>US-guided intervension, spine</td><td></td><td>
</td><tr><td>
Andre Remi</td><td>UCLA</td><td>Longitudinal changes in TBI, tissue types</td><td></td><td>
</td><tr><td>
Peter Risholm</td><td>BWH</td><td>Brain, head and neck, radiation therapy</td><td>Probabilistic Uncertainty</td><td>
</td><tr><td>
Samira Sojoudi</td><td>UBC</td><td>Spine, CT/US registration</td><td></td><td>
</td><tr><td>
Matthew Toews</td><td>BWH</td><td>General registration</td><td>SIFT landmark correspondence</td><td>
</td><tr><td>
Bo Wang</td><td>Utah</td><td>TBI image segmentation</td><td></td><td>
</td><tr><td>
Kevin Wang</td><td>Princess Margaret Hospital</td><td>Adaptive radiation therapy, longitudinal</td><td></td><td>
</td><tr><td>
William Wells</td><td>BWH</td><td>Interventional applications</td><td>Theory: Segmentation, Registration</td><td></td>
<table>

== Links for Data ==
* [http://www.matthewtoews.com/namic2012 Matt's initial examples]
* [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable Slicer Registration Case Library]
* [http://dmip1.rad.jhmi.edu/xcat/ XCAT]
* [http://wiki.na-mic.org/Wiki/index.php/File:EnlargedLVCase_Normal.zip DTI Files Enlarged LV registration with normal control]
* [http://wiki.na-mic.org/Wiki/index.php/File:Krabbe_Controls_DWI.zip DWI Files Enlarged LV registration with normal control]
* [http://www.na-mic.org/Wiki/index.php/DBP3:UCLA#Data TBI Cases]
* [http://www.nitrc.org/projects/tumorsim/ TumorSim] longitudinal data: To appear at http://midas3.kitware.com

== Links for Tools & Methods ==
* Sliding Geometries Registration: http://public.kitware.com/Wiki/TubeTK
* Geometric Metamorphosis: https://github.com/calaTK/calaTK

== Links for Papers ==
* Sliding Geometries
** ISBI 2011: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141338/
** Abdominal Imaging, MICCAI, 2011: http://www.springerlink.com/content/552824638l375645/
* Geometric MetaMorphosis
** MICCAI 2011: http://www.springerlink.com/content/7r077665012078r5/

</div>

File:NiftyReg projectWeek test.pdf

2012-06-21T16:09:00Z

Mmodat: Some initial registration test which some of them failed dramatically !!!

Some initial registration test which some of them failed dramatically !!!

2012 Summer Project Week:DifficultRegistration

2012-06-21T14:07:13Z

Mmodat:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Ct-body-atlas.jpg
Image:Ct-body-cropped.jpg
Image:Ct-body-legs.jpg
Image:Mr-brain-atlas.jpg
Image:Mr-brain-tbi.jpg
Image:Mr-brain-rotated.jpg
Image:Mr-brain-rhesus.jpg
</gallery>

==Key Investigators==
* Erasmus Medical Center: Stefan Klein
* University College London: Marc Modat
* UNC: Aditya Gupta, Martin Styner
* BWH: Matthew Toews, Petter Risholm, Dominik Meier, William Wells

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

<h3>Objective</h3>
To identify solutions to difficult image registration problems that challenge the limits of current technology. Aspects of difficulty will include:
<ul>
<li>inter-subject registration
<li>truncation, missing tissue
<li>unknown initialization
<li>inter-species registration
<li>articulated deformation
</ul>
</div>

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

<h3>Approach, Plan</h3>
A set of difficult pair-wise registration problems will be considered. Participants will discuss workable solutions based on their expertise and background, and these solutions will be documented.
<br>
Registration cases can be found [http://www.matthewtoews.com/namic2012 here].
</div>

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

<h3>Progress</h3>TBA
*CT: atlas and torso have flipped orientation: Correction Xforms here: [[Media:FlipCT_Atlas+Torso.zip|Flip CT atlas&torso, zip file with 2 .tfm files]]
</div>
</div>

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

==Delivery Mechanism==
<b>Attention Participants:</b> Please log in and update/correct entries in the table below. For bonus points, please provide links or solutions to image registration problems on this page.<br>
<table border="1">
<th>Participant</th><th>Affiliation</th><th>Context</th><th>Techniques</th><th>Solutions/Links
</th><tr><td>
Steven Aylward</td><td>Kitware</td><td>CT, US, ressection, brain tumors, changing pathology, sliding organ</td><td>Sliding Geometry, Geometric Metamorphosis</td><td>
</td><tr><td>
Karl Diedrich</td><td>AZE</td><td>Rigid registration, abdomen</td><td>Multi-resolution registration</td><td>
</td><tr><td>
James Fishbaugh</td><td>SCI</td><td>Shape analysis and registration</td><td></td><td>
</td><tr><td>
Aditya Gupta</td><td>UNC</td><td>DTI, enlarged lateral ventricles</td><td></td><td>
</td><tr><td>
Stefan Klein</td><td>Erasmus Medical Center</td><td>General Registration</td><td></td><td>
</td><tr><td>
Ivan Kolesov</td><td>Georia Tech</td><td>Articulated, point-based registration</td><td></td><td>
</td><tr><td>
Dominik Meier</td><td>BWH</td><td>General registration</td><td>Slicer: BRAINS</td><td>
IntraOp:[[Image:IntraOp_Slicer-BRAINS_BSpline.gif|60px|lleft|IntraOp via BRAINS]]<br>
TBI:[[Image:TBI_Slicer-BRAINS_BSpline.gif|60px|lleft|TBI via BRAINS]]<br>
CT torso: FAILED</td><tr><td>
Marc Modat</td><td>UCL</td><td>neuro-deg. diseases, longitudinal</td><td>NiftiReg</td><td>
</td><tr><td>
Albert Motillo</td><td>GE</td><td>Parsing CT, Detection</td><td></td><td>
</td><tr><td>
Simrin Nagpal</td><td>Queens University</td><td>CT/US registration</td><td></td><td>
</td><tr><td>
Samon Nuranian</td><td>UBC</td><td>US-guided intervension, spine</td><td></td><td>
</td><tr><td>
Andre Remi</td><td>UCLA</td><td>Longitudinal changes in TBI, tissue types</td><td></td><td>
</td><tr><td>
Peter Risholm</td><td>BWH</td><td>Brain, head and neck, radiation therapy</td><td>Probabilistic Uncertainty</td><td>
</td><tr><td>
Samira Sojoudi</td><td>UBC</td><td>Spine, CT/US registration</td><td></td><td>
</td><tr><td>
Matthew Toews</td><td>BWH</td><td>General registration</td><td>SIFT landmark correspondence</td><td>
</td><tr><td>
Bo Wang</td><td>Utah</td><td>TBI image segmentation</td><td></td><td>
</td><tr><td>
Kevin Wang</td><td>Princess Margaret Hospital</td><td>Adaptive radiation therapy, longitudinal</td><td></td><td>
</td><tr><td>
William Wells</td><td>BWH</td><td>Interventional applications</td><td>Theory: Segmentation, Registration</td><td></td>
<table>

== Links for Data ==
* [http://www.matthewtoews.com/namic2012 Matt's initial examples]
* [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable Slicer Registration Case Library]
* [http://dmip1.rad.jhmi.edu/xcat/ XCAT]
* [http://wiki.na-mic.org/Wiki/index.php/File:EnlargedLVCase_Normal.zip DTI Files Enlarged LV registration with normal control]
* [http://wiki.na-mic.org/Wiki/index.php/File:Krabbe_Controls_DWI.zip DWI Files Enlarged LV registration with normal control]
* [http://www.na-mic.org/Wiki/index.php/DBP3:UCLA#Data TBI Cases]
* [http://www.nitrc.org/projects/tumorsim/ TumorSim] longitudinal data: To appear at http://midas3.kitware.com

== Links for Tools & Methods ==
* Sliding Geometries Registration: http://public.kitware.com/Wiki/TubeTK
* Geometric Metamorphosis: https://github.com/calaTK/calaTK

== Links for Papers ==
* Sliding Geometries
** ISBI 2011: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141338/
** Abdominal Imaging, MICCAI, 2011: http://www.springerlink.com/content/552824638l375645/
* Geometric MetaMorphosis
** MICCAI 2011: http://www.springerlink.com/content/7r077665012078r5/

</div>

2012 Summer Project Week:NiftyReg

2012-06-18T16:46:17Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

The NRRD file format have been integrated into the NiftyReg package to ease its integration.

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module -
##Built-in -
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:NiftyReg

2012-06-18T15:58:20Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives is to make NiftyReg available in Slicer.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module -
##Built-in -
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:NiftyReg

2012-06-18T15:44:00Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: <nowiki>svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg/trunk/nifty_reg niftyreg</nowiki>

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives are (1) to make NiftyReg available in Slicer and (2) to create a ITK wrapper filter.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module -
##Built-in -
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>

2012 Summer Project Week:NiftyReg

2012-06-18T15:42:35Z

Mmodat:

__NOTOC__
<gallery>

Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Nifty_reg_logo.png|NiftyReg
</gallery>

== What is Niftyreg? ==
* Light-weight package for medical image registration.
* Global (rigid/affine) registration based on a block-matching technique.
* Local deformation (non-rigid) based on a cubic B-Spline parametrisation.
* Implementation: C/C++ [SIMD, OpenMP, CUDA]
* All dependencies are included into the project (nifticlib, zlib, [NRRD, png]).
* Installation through CMake and step-by-step install can be found [http://sourceforge.net/projects/niftyreg/files/install_NiftyReg_macLinux.pdf/download here]
* Trunk can be downloaded through svn: svn co https://niftyreg.svn.sourceforge.net/svnroot/niftyreg niftyreg

==Key Investigators==
* University College London: Marc Modat
* BWH: Sonia Pujol

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

<h3>Objective</h3>
[http://www.cs.ucl.ac.uk/staff/m.modat/Marcs_Page/Software.html NiftyReg] is an open-source package for rigid, affine and non-linear registration developed the team of Dr. Sebastien Ourselin at the Centre for Medical Imaging Computing, University College London, UK. The objectives are (1) to make NiftyReg available in Slicer and (2) to create a ITK wrapper filter.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to develop a CLI module for NiftyReg in Slicer4.

</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module -
##Built-in -
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==
*Modat et al. Fast free-form deformation using graphics processing units. Comput Meth Prog Bio (2010) vol. 98 (3) pp. 278-84
*Daga et al. Accurate Localisation of Optic Radiation during Neurosurgery in an Interventional MRI Suite. IEEE Transactions on Medical Imaging (2012)
*Modat. Parametric non-rigid registration using a stationary velocity field. Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012 IEEE Workshop on (2012) pp. 145 - 150

</div>