__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
FixedImageWithCroppedImageOverlay.png| Fixed image with the moving image overlaid
Image:CorrelationMap.png|Correlation Map
Image:CorrelationMapWithCroppedRegionOverlay.png|GridImage
CorrelationMapWithFixedImageOverlay.png|GridImage
</gallery>

==Key Investigators==
* GE: Dirk Padfield
* UIowa: Hans Johnson
* MSC/NLM: Bradley Lowekamp

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

<h3>Objective</h3>

Integrate the Masked FFT Normalized Correlation algorithm from ITK into Slicer.

</div>

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

<h3>Approach, Plan</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

</div>
</div>

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

==References==
* http://www.itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html
* http://www.itk.org/Doxygen/html/classitk_1_1FFTNormalizedCorrelationImageFilter.html

File:FixedImageWithCroppedImageOverlay.png

2013-06-21T16:27:28Z

Dirkpadfield:

File:CorrelationMapWithFixedImageOverlay.png

2013-06-21T16:27:19Z

Dirkpadfield:

File:CorrelationMapWithCroppedRegionOverlay.png

2013-06-21T16:27:10Z

Dirkpadfield:

File:CorrelationMap.png

2013-06-21T16:26:37Z

Dirkpadfield:

2013 Summer Project Week:MaskedFFTNormalizedCorrelationOverlay

2013-06-21T16:26:15Z

Dirkpadfield:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:CorrelationMap.png|Correlation Map
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* GE: Dirk Padfield
* UIowa: Hans Johnson
* MSC/NLM: Bradley Lowekamp

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

<h3>Objective</h3>

Integrate the Masked FFT Normalized Correlation algorithm from ITK into Slicer.

</div>

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

<h3>Approach, Plan</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

</div>
</div>

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

==References==
* http://www.itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html
* http://www.itk.org/Doxygen/html/classitk_1_1FFTNormalizedCorrelationImageFilter.html

2013 Summer Project Week:MaskedFFTNormalizedCorrelationOverlay

2013-06-21T16:23:03Z

Dirkpadfield: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* GE: Dirk Padfield
* UIowa: Hans Johnson
* MSC/NLM: Bradley Lowekamp

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

<h3>Objective</h3>

Integrate the Masked FFT Normalized Correlation algorithm from ITK into Slicer.

</div>

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

<h3>Approach, Plan</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

</div>
</div>

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

==References==
* http://www.itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html
* http://www.itk.org/Doxygen/html/classitk_1_1FFTNormalizedCorrelationImageFilter.html

2013 Summer Project Week:MaskedFFTNormalizedCorrelationOverlay

2013-06-21T16:22:47Z

Dirkpadfield: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* GE: Dirk Padfield
* UIowa: Hans Johnson
* MSC/NLM: Bradley Lowekamp

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

<h3>Objective</h3>

Integrate the Masked FFT Normalized Correlation algorithm from ITK into Slicer.

</div>

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

<h3>Approach, Plan</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

</div>
</div>

==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 YES
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)

==References==
* http://www.itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html
* http://www.itk.org/Doxygen/html/classitk_1_1FFTNormalizedCorrelationImageFilter.html

2013 Summer Project Week:MaskedFFTNormalizedCorrelationOverlay

2013-06-21T16:22:00Z

Dirkpadfield: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected Image:SimpleFilters-G…'

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SimpleFilters-ConfidenceConnected.png|ConfidenceConnected
Image:SimpleFilters-GridImageSource.png|GridImage
</gallery>

==Key Investigators==
* GE: Dirk Padfield
* UIowa: Hans Johnson
* MSC/NLM: Bradley Lowekamp

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

<h3>Objective</h3>

Integrate the Masked FFT Normalized Correlation algorithm from ITK into Slicer.

</div>

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

<h3>Approach, Plan</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

<ul>
<li> SimpleITK filter: Filters chosen from drop-down menu, with dynamically created parameter widgets
<li> Input: Dynamically created for the number of images required by the SimpleITK filter selected that is MRML-aware
<li> Output: Output image widget
<li> Script: Textual display of Python script the module will evaluate. An "Apply" button will execute the Python code
</ul>

</div>

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

<h3>Progress</h3>

so that the correlation map overlays correctly with the fixed image and the maxima of the correlation map

</div>
</div>

==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 YES
##Built-in - MAYBE?
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==
* http://www.itk.org/Doxygen/html/classitk_1_1MaskedFFTNormalizedCorrelationImageFilter.html
* http://www.itk.org/Doxygen/html/classitk_1_1FFTNormalizedCorrelationImageFilter.html

2013 Summer Project Week

2013-06-21T16:17:54Z

Dirkpadfield: /* Infrastructure */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

<gallery widths="800px" heights="300px" perrow="1" caption="Lunch in the Amphitheater at Stata, June 20 2013">
Image:Lunch at Project week IMG 0367.JPG|Shade was a popular commodity
</gallery>

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|
'''9:30-10:30am''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]] <br>
'''12pm''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|[http://www.na-mic.org/Wiki/index.php/File:NamicToAmphi.png Lunch in Outdoor Amphitheather!]
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-262]]
|
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

==Some Stats==
73 Projects, 104 Attendees. First time attendees 25.

===Huntington's Disease===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Manasi, Dave, Josh, Hans, Ross)


7 projects

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)


5 projects

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao, LiangJia Zhu, Josh Cates, Rob MacLeod, Sylvain Bouix, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)


8 projects

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Creating DICOM series from ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Karl Fritscher, Christian Wachinger, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, Alireza Mehrtash)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab - without building Slicer or Matlab MEX files]] (Andras Lasso, Jc)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim)


8 projects

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Ultrasound_Needle_Detection| Ultrasound Needle Detection]] (Alireza Mehrtash, Daniel Kostro, Matthew Toews, Tamas Ungi, William Wells, Tina Kapur)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:ProstateBRP| MRI-guided robotic prostate interventinos]] (Junichi Tokuda, Greg Fischer, Nirav Patel, Nobuhiko Hata, Clare Tempnay)


12 projects

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche, James Ross)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, James, Ross, Rola Harmouche, Raul San Jose)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)


3 projects

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:VicomTech| VicomTech visit: Imaging solutions and Slicer use]] (Ivan Macia)
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Francois Budin, Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Nathaniel Reynolds, Lilla Zollei, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Kayhan Batmanghelich, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)
* [[2013_Summer_Project_Week:Documentation for Slicer 4.2 Data Loading and 3D Visualization|Documentation for Slicer 4.2 Data Loading and 3D Visualization]] (Parth Amin WIT, Matt Flynn WIT, Dr. Pujol HMS, Pr. Jaume WIT)
* [http://wiki.na-mic.org/Wiki/index.php/Projects:WIT_mold_holder 3D Printing of a Prostate Slicer] (Maria Gonzalez-Puente WIT, Dr. Fedorov BWH, Pr. Jaume, WIT)
* [[2013_Summer_Project_Week:WM Geometry Tools|Integration in Slicer of white matter geometry tools]] (Peter Savadjiev, Carl-Fredrik Westin)


16 projects

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo Zaffino, Greg Sharp, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Dave Welch, Brad Lowekamp, Hans Johnson, Steve)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter (time) Hierarchy]] (Adam Rankin, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:ITK_Shared_IO_Libraries| ITK Shared I/O Libraries]] (Jim,Brad Lowekamp, Jc)
* [[2013_Summer_Project_Week:Python_Embedding| Python Embedding Library]] (Rui, Jim, Jc, Steve)
* [[2013_Summer_Project_Week:MaskedFFTNormalizedCorrelationOverlay | Masked FFT Normalized Correlation Overlay]] (Dirk, Hans, Brad)

14 projects

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

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

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

== '''Logistics''' ==

*'''Dates:''' June 17-21, 2013.
*'''Location:''' [[MIT_Project_Week_Rooms| Stata Center / RLE MIT]].
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, 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. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Kayhan Batmanghelich, MIT, kayhan@csail.mit.edu
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Taylor Braun-Jones, GE Healthcare, taylor.braun-jones@ge.com
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Alexandra Golby, BWH, agolby@partners.org
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Dan Groszmann, GE Healthcare, daniel.groszmann@ge.com
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Sylvain Jaume, WIT, jaumes@wit.edu
#Daniel Jimenez, daniel.jimenez@gmail.com
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Nirav Patel, WPI, napatel@wpi.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#William Plishker, IGI Technologies, will@igitechnologies.com
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Tobias Schroeder, GE Healthcare, tobias.schroeder@ge.com
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Project Week:SteeredRegistration

2013-01-11T17:12:25Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=500px heights=500px caption="Previous Interactive Registration">
Image:InteractiveRegistration.png | Previous interaction
</gallery>

<gallery widths=500px heights=500px caption="Slicer2 Interactive Registration">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T17:11:20Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:InteractiveRegistration.png | Previous interaction
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T17:10:57Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=300px heights=300px caption="vtkAffineWidget">
Image:InteractiveRegistration.png | Previous interaction
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T17:10:28Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<br><br>

<gallery widths=300px heights=300px caption="vtkAffineWidget">
Image:InteractiveRegistration.png | Previous interaction
</gallery>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T17:10:12Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<br>
<gallery widths=300px heights=300px caption="vtkAffineWidget">
Image:InteractiveRegistration.png | Previous interaction
</gallery>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T17:09:31Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=300px heights=300px caption="vtkAffineWidget">
Image:InteractiveRegistration.png | Previous interaction
</gallery>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

File:InteractiveRegistration.png

2013-01-11T17:08:37Z

Dirkpadfield:

2013 Project Week:SteeredRegistration

2013-01-11T16:56:44Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=500px heights=500px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:56:14Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=400px heights=400px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Interaction GUI
Image:Slicer2InteractiveRegistration2.jpg | Viewer
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:55:27Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:Slicer2InteractiveRegistration1.jpg | Affine widget
Image:Slicer2InteractiveRegistration2.jpg | Rotation
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:54:54Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

<gallery>
Image:Slicer2InteractiveRegistration1.jpg | Affine widget
Image:Slicer2InteractiveRegistration2.jpg | Rotation
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

File:Slicer2InteractiveRegistration2.jpg

2013-01-11T16:53:57Z

Dirkpadfield:

File:Slicer2InteractiveRegistration1.jpg

2013-01-11T16:53:44Z

Dirkpadfield:

2013 Project Week:SteeredRegistration

2013-01-11T16:51:14Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=240px heights=240px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:49:09Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=300px heights=300px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:48:35Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=276px heights=376px caption="vtkAffineWidget">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:48:05Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery widths=276px heights=376px caption="HD Subjects">
File:Sub_10001_3shapes.gif|Subject 10001
File:Sub_10018_3shapes.gif|Subject 10018
File:Sub_10027_3shapes.gif|Subject 10027
</gallery>

<gallery widths=276px heights=376px caption="HD Subjects">
Image:AffineWidgetStart.bmp | Affine widget
Image:AffineWidgetRotate.bmp | Rotation
Image:AffineWidgetScale.bmp | Scaling
Image:AffineWidgetTranslate.bmp | Translation
Image:AffineWidgetEnd.bmp | End
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:45:41Z

2013-01-11T16:25:49Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images (see figures). We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

</div>
</div>

<gallery>
Image:AffineWidgetStart.jpg | Affine widget
Image:AffineWidgetRotate.jpg | Rotation
Image:AffineWidgetScale.jpg | Scaling
Image:AffineWidgetTranslate.jpg | Translation
Image:AffineWidgetEnd.jpg | End
</gallery>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:25:15Z

Dirkpadfield: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images. We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

<gallery>
Image:AffineWidgetStart.jpg | Affine widget <br>
Image:AffineWidgetRotate.jpg | Rotation
Image:AffineWidgetScale.jpg | Scaling
Image:AffineWidgetTranslate.jpg | Translation
Image:AffineWidgetEnd.jpg | End
</gallery>

</div>
</div>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==

2013 Project Week:SteeredRegistration

2013-01-11T16:24:51Z

Dirkpadfield:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:InteractiveReg-translation.png‎|Interaction: Translate
Image:InteractiveReg-rotation.png‎|Interaction: Rotate
Image:InteractiveReg-lmk.png‎|Interaction: Landmark marking
Image:translate-before.png‎|Before translation from user input
Image:translate-after.png‎|After translation from user input
</gallery>

==Key Investigators==
* GRC: Dirk Padfield, Jim Miller
* Isomics: Steve Pieper
* BWH: Tina Kapur, Ron Kikinis

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

<h3>Objective</h3>
We are developing methods to perform interactive registration in 3D Slicer. The final goal is to provide the user an interface to interact with the registration program during the matching progress. This will enable the user to run the automated registration and to correct it real-time through gestures.

</div>

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

<h3>Approach, Plan</h3>

Our approach for developing the interactive registration module is to first construct the loadable extension to perform intensity-based registration, display the intermediate results, and allow the user to correct the progress at any point if the intermediate results are visually unsatisfactory. Providing translation, rotation, and scale for rigid registration and perhaps landmarks or directional markers for deformable registration will be enabled by mouse click and drag gestures. These will be used to correct/update the current transformation, which will then be fed back as the update to the automated registration algorithm. The goal is to have short delays in the user interaction by continually running short automated registration iterations followed by any user interactions waiting in the event cue. As a test the user could drag the images apart, watch them become aligned again, and then drag them apart again. The module is particuarly useful when the registration algorithm goes astray since the user can then quickly bring the images back into approximate alignment and let the automated algorithm compute the fine registration.

</div>

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

<h3>Progress</h3>
So far, we have implemented user interaction for translation, rotation, and scale. To avoid having to move back and forth from the image to the GUI in order to switch between translation, rotation, and scale, we tested a vtkAffineWidget that represents these interactions in a widget that feeds back to the images. We also looked at the interactive registration available in Slicer2 to see which parts of that framework could be replicated in Slicer4. In the next step, we plan to have a first version of the interaction loop that integrates the automated registration with the manual feedback.

<gallery>
Image:AffineWidgetStart.jpg | Affine widget
Image:AffineWidgetRotate.jpg | Rotation
Image:AffineWidgetScale.jpg | Scaling
Image:AffineWidgetTranslate.jpg | Translation
Image:AffineWidgetEnd.jpg | End
</gallery>

</div>
</div>

==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
##Extension -- loadable YES
#Other (Please specify)

==References==