NAMIC Wiki - User contributions [en]

Project Week 25/Surgical Planning In Stereotaxy

2017-06-30T13:00:53Z

Fepegar:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|
* Segmentations have been integrated in the core of the toolbox
* GUI has been improved, but there's still some work to do:
** Get inspiration from commercial consoles
** Ask neurosurgeons for feedback
* A [https://github.com/Slicer/Slicer/pull/741 new diverging colormap] has been contributed
|}

==Illustrations==
[[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
[[File:YeB atlas segmentation.jpg|800px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
[[File:FreeSurfer segmentation epilepsy.png|800px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]

[[File:Jacobian visualization.png|800px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear registration]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

Project Week 25/Surgical Planning In Stereotaxy

2017-06-30T12:57:51Z

Fepegar: Edit colormap image

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|
* Segmentations have been integrated in the core of the toolbox
* GUI has been improved, but there's still some work to do:
** Get inspiration from commercial consoles
** Ask neurosurgeons for feedback
* A [https://github.com/Slicer/Slicer/pull/741 pull request] for a new colormap has been created
|}

==Illustrations==
[[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
[[File:YeB atlas segmentation.jpg|800px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
[[File:FreeSurfer segmentation epilepsy.png|800px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]

[[File:Jacobian visualization.png|800px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear registration]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

File:Jacobian visualization.png

2017-06-30T12:54:26Z

Fepegar:

Coparison of colormaps used for Jacobian visualization

Project Week 25/Surgical Planning In Stereotaxy

2017-06-30T12:38:38Z

Fepegar: Make images larger

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|
* Segmentations have been integrated in the core of the toolbox
* GUI has been improved, but there's still some work to do:
** Get inspiration from commercial consoles
** Ask neurosurgeons for feedback
* A [https://github.com/Slicer/Slicer/pull/741 pull request] for a new colormap has been created
|}

==Illustrations==
[[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
[[File:YeB atlas segmentation.jpg|800px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
[[File:FreeSurfer segmentation epilepsy.png|800px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]
[[File:Diverging colormap for Jacobian visualization.png|800px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear deformation]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

Project Week 25/Surgical Planning In Stereotaxy

2017-06-30T12:36:24Z

Fepegar:

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|
* Segmentations have been integrated in the core of the toolbox
* GUI has been improved, but there's still some work to do:
** Get inspiration from commercial consoles
** Ask neurosurgeons for feedback
* A [https://github.com/Slicer/Slicer/pull/741 pull request] for a new colormap has been created
|}

==Illustrations==
[[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
[[File:YeB atlas segmentation.jpg|600px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
[[File:FreeSurfer segmentation epilepsy.png|600px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]
[[File:Diverging colormap for Jacobian visualization.png|600px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear deformation]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

Project Week 25/Surgical Planning In Stereotaxy

2017-06-30T10:15:15Z

Fepegar: Fill progress and next steps section

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|
* Segmentations have been integrated in the core of the toolbox
* GUI has been improved, but there's still some work to do:
** Get inspiration from commercial consoles
** Ask neurosurgeons for feedback
* A [https://github.com/Slicer/Slicer/pull/741 pull request] for a new colormap has been created
|}

==Illustrations==
[[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
[[File:YeB atlas segmentation.jpg|600px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
[[File:FreeSurfer segmentation epilepsy.png|600px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]
[[File:Diverging colormap for Jacobian visualization.png|600px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear deformation]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

File:FreeSurfer segmentation epilepsy.png

2017-06-30T10:12:42Z

Fepegar:

Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy

File:YeB atlas segmentation.jpg

2017-06-30T09:57:00Z

Fepegar:

Segmentation representing a histological atlas of the basal ganglia

File:Diverging colormap for Jacobian visualization.png

2017-06-30T09:51:33Z

Fepegar:

Comparison of different colormaps to visualize compression and expansion after a non linear registration

Project Week 25/Neuro-navigation breakout session

2017-06-26T10:01:14Z

Fepegar: Add Sara and Fernando as participans

= Introduction =

This will be an informal session that all project week participants that are interested in neuro-navigation should join. Just add your name to the participant list and show up at the session, optionally prepare 2-3 slides for introducing yourself to the group (tell about yourself, what you do in neuro-navigation, what your challenges are, what you plan to do). If you create slides then upload them to the wiki and add a link at your name.

* Time: Tuesday 2pm-3pm.
* Location: to be determined - it will be posted here.

= Participants =

If you do not have write access to the wiki then send your name (and slides) to Andras Lasso (lasso@queensu.ca).

# Andras Lasso ([http://perk.cs.queensu.ca PerkLab, Queen's]) - [[Media:20170625-NamicWeek-AndrasLassoIntro.pdf|intro slides]]
# Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
# Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)

Project Week 25/Surgical Planning In Stereotaxy

2017-06-26T09:07:08Z

Fepegar: Edit affiliations

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Csaba Pinter (Queen's University, Canada)
* Andras Lasso (Queen's University, Canada)
* Steve Pieper (Isomics, Inc., USA)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|

|}

==Illustrations==

[[File:Pydbs module.png|thumb|Post-operative scene in Deep Brain Stimulation (DBS)]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

Project Week 25

2017-06-26T08:28:50Z

Fepegar: Add "Surgical Planning In Stereotaxy" project

__NOTOC__
Back to [[Events]]

A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].

[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]
 

=Welcome to the web page for the 25th Project Week!=
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!

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

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

===Local Organizing Committee===
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].

==Logistics==
*'''Dates:''' June 26-30, 2017. Details in the calendar below.
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. [mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017". Special rates: Single room, full bed, 79 € per night (1 person)/ Single room, queen bed 89 € per night (1 person)/ Double room, queen bed 99 € per night (2 people)/Triple room, 110 € (3 people)
*'''Registration:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].
*'''Transportation from Airport to Hotel:''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport]. Please fill out this [https://goo.gl/forms/7vmhxZSHy8Z1A62z2 form] to request transportation
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map] (constantly updated)

==Calendar==
{{#widget:Google Calendar
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com
|timezone=America/New_York&dates=20170108%2F20170114
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)
|view=WEEK
|dates=20170626/20170701
}}

iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics

Breakout sessions:
* [[Project_Week_25/Neuro-navigation_breakout_session|Neuro-navigation breakout session]]

=Projects=

<big>Please duplicate [https://na-mic.org/wiki/Project_Week_Template this template] to create a page for your project. </big>

Please put a brief preliminary title for your project here with some names in parenthesis for potential team members
==Deep Learning Applications==
#[[Project_Week_25/NeedleSegmentation |CNN for Needle Segmentation from MRI Images]]
#[[Project_Week_25/CNN_for_multi-plane_prostate_segmentation | CNN for multi-plane prostate segmentation]]
#[[Project_Week_25/CNN for PseudoCT Generation from T1T2 MR|CNN for PseudoCT Generation from T1/T2 MRI]]
#[[Project_Week_25/Breast Cancer Analysis in DCE-MRI | Breast Cancer Segmentation in DCE-MRI via Deep Learning Approaches]]

==Augmented Reality and Virtual Reality==
#[[Project_Week_25/Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification | Improving Depth Perception in Interventional Augmented Reality Visualization/Sonification]]
# [[Project_Week_25/Next_Generation_GPU_Volume_Rendering | Next Generation of Volume Rendering in VTK ]]
#[[Project_Week_25/Development_and_Evaluation_of_New_AR_Visualization_Techniques_to_Support_Radiological_Interventions | Development and Evaluation of New AR Visualization Techniques to Support Radiological Interventions]]
#[[Project_Week_25/Intra-operative deformable_registration_based_on_dense_point_cloud_reconstruction |Intra-operative Deformable Registration Based on Dense Point Cloud Reconstruction for Augmented Reality in Laproscopic Surgery]]
#Slicer Export to VR (Juan Ruiz Alzola, Mike Halle)

==Navigating Ultrasound==
# [[Project_Week_25/Tracked-Ultrasound-Standardization-IV | Tracked Ultrasound Standardization IV: Controlling US Acquisition]]
#[[Project_Week_25/Segmentation for improving image registration of preoperative MRI with intraoperative ultrasound images for neuro-navigation |Segmentation for Improving Image Registration of Preoperative MRI with Intraoperative Ultrasound Images for Neuro-navigation]]
==DICOM==
#[[Project_Week_25/DICOM_for_Quantitative_Imaging_and_Integration_with_Processing_Applications|DICOM for Quantitative Imaging and Integration with Processing Applications]]
#[[Project_Week_25/Conversion of DICOM Single Frame MR to Enhanced Multiframe | Conversion of DICOM Single Frame MR to Enhanced Multiframe]]
#[[Project_Week_25/DICOM Segmentation Support for Cornerstone and OHIF Viewer | DICOM Segmentation Support for Cornerstone/ OHIF Viewer]]

==Chest Image Processing==
#[[Project_Week_25/SlicerCIP_Bronchiectasis | SlicerCIP: Tool for Quantitative Analysis of Bronchiectasis]]
#[[Project_Week_25/SlicerCIP_ReportsTool | SlicerCIP: Tool for Creation of Reports for Quantitive Analysis]]
==Platform==
#[[Project_Week_25/Interactive_Manipulation_of_Plots_and_Graphs | Interactive Manipulation of Plots and Graphs]]
#[[Project_Week_25/Internationalizing Slicer Modules|Internationalizing Slicer Modules]]
#[[Project_Week_25/Interfacing Slicer to Mobile Phone-controlled Sensors|Interfacing Slicer to Mobile Phone-controlled Sensors]]
#[[Project_Week_25/Slicer and 3D Printing|Slicer and 3D Printing]]
#[[Project_Week_25/Multimodal: | Multimodal, Multiresolution, Multivolume Data]]
#[[Project_Week_25/Human-Computer_Interaction_under_sterile_conditions |Human-Computer Interaction under Sterile Conditions]]

==Applications Smorgasbord==
#[[Project_Week_25/Steerable Catheters Path Planner Extension for Brain Surgery Applications | Steerable Catheters Path Planner Extension for Brain Surgery Applications]]
#[[Project_Week_25/Slice-to-Volume Registration to Support MRI guided Interventions | Slice-to-Volume Registration to Support MRI guided Interventions ]]
#[[Project_Week_25/Surgical_Planning_In_Stereotaxy | Surgical Planning In Stereotaxy ]]
#[[Project_Week_25/SALT_Spatiotemporal_Modeling: | Slicer SALT Validation: Spatiotemporal Modeling of Subcortical Structures ]]
#[[Project_Week_25/Wrist_Kinematics: | Kinematic Analysis of the Wrist from Dynamic MRI]]

=Registrants=

Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].

# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA
# Pieper, Steve :: Isomics, Inc., USA
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA
# Spadea, Maria Francesca :: Magna Graecia University, Italy
# Zaffino, Paolo :: Magna Graecia University, Italy
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy
# Pileggi, Giampaolo :: Magna Graecia University, Italy/German Cancer Research Center (DKFZ), Germany
# Rackerseder, Julia :: Technical University of Munich, Germany
# Pinter, Csaba :: Queen's University, Canada
# Kraß, Scheherazade :: University of Bremen, Germany
# Gerig, Guido :: NYU Tandon School of Engineering, USA
# Punzo, Davide :: Kapteyn Astronomical Institute, University of Groningen, The Netherlands
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada
# Lasso, Andras :: School of Computing, Queen's University, Canada
# Favaro, Alberto :: Politecnico di Milano, Italy
# Leger, Etienne :: Concordia University, Canada
# Ziegler, Erik :: Ziegler Consult SAS
# Onken, Michael :: Open Connections GmbH, Germany
# Pinzi, Marlene :: Imperial College, UK
# Nitsch, Jennifer :: University of Bremen, Germany
# Moccia, Sara :: Politecnico di Milano, Italy
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany
# Hansen, Christian :: University of Magdeburg, Germany
# Vegard Solberg, Ole :: Norway
# Heinrich, Florian :: University of Magdeburg, Germany
# Mewes, André :: University of Magdeburg, Germany
# Hatscher, Benjamin :: University of Magdeburg, Germany
# Hettig, Julian :: University of Magdeburg, Germany
# Meyer, Anneke :: University of Magdeburg, Germany
# Gulamhussene, Gino :: University of Magdeburg, Germany
# Cassetta, Roberto :: Politecnico di Milano, Italy
# Fillion-Robin, Jean-Christophe :: Kitware, Inc., USA
# Metzger, Jasmin :: German Cancer Research Center (DKFZ), Germany
# Fishbaugh, James :: NYU Tandon School of Engineering, USA
# Nolden, Marco :: German Cancer Research Center (DKFZ), Germany
# Nehrkorn, Jorge Quintero :: Canary Islands, Spain
# Perez Garcia, Fernando :: ICM Brain & Spine Institute, Paris, France
# De Momi, Elena :: Politecnico di Milano, Italy
# Piantadosi, Gabriele :: DIETI, Federico II di Napoli, Italy
# Pernelle, Guillaume :: Imperial College, UK
# San Jose, Raul :: Brigham and Women's Hospital, Harvard Medical School, USA
# Nardelli, Pietro :: Brigham and Women's Hospital, Harvard Medical School, USA
# Fernandez Vidal, Sara :: ICM Brain & Spine Institute, Paris, France
# Sharp, Gregory :: Massachusetts General Hospital, Harvard Medical School, USA
# Moiraghi, Alessandro :: Università degli Studi di Milano, Italy
# Seco, Joao :: German Cancer Research Center (DKFZ), Germany
# Pumar Carreras, Nayra :: Canary Islands, Spain
# Afonso Suarez, Maria Dolores :: Canary Islands, Spain
# Alzola Ruiz, Juan :: Canary Islands, Spain
# Pujol, Sonia :: Brigham and Women's Hospital, Harvard Medical School, USA

Project Week 25/Surgical Planning In Stereotaxy

2017-06-24T15:47:47Z

Fepegar: Add Slicer developers' affiliations

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Csaba Pinter (Queen's University)
* Andras Lasso (Queen's University)
* Steve Pieper (Isomics, Inc.)

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|

|}

==Illustrations==

[[File:Pydbs module.png|thumb|Post-operative scene in Deep Brain Stimulation (DBS)]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

Project Week 25/Surgical Planning In Stereotaxy

2017-06-24T15:43:28Z

Fepegar: Add project page

__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Csaba Pinter
* Andras Lasso
* Steve Pieper

==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|

|}

==Illustrations==

[[File:Pydbs module.png|thumb|Post-operative scene in Deep Brain Stimulation (DBS)]]

==Background and References==

* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]

File:Pydbs module.png

2017-06-24T15:39:17Z

Fepegar:

Example of a post-operative scene in DBS.

2016 Summer Project Week

2016-07-26T10:14:12Z

Fepegar: Add the rest of the names to the project I worked on

__NOTOC__

[[image:PW-Summer2016.png|300px]]
 

Please fill in the survey about project weeks today!


[https://hms.az1.qualtrics.com/jfe/form/SV_6gK6BFe4Ivfo9RH click here]


 

Please hold January 9-13, 2017 for Project Week#24 at MIT. 

 

Please hold June 16-29 for Project Week#25 in Europe. It will be either right before IPCAI (i.e June ~16-20) or right after CARS! (~June 25-29)

 

 

 Please add photos from this week here: https://goo.gl/photos/Dhx6Fdei27NZe2rX9

 



=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Agenda'''=
Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 [https://goo.gl/maps/e3ZbcsM5KC82 DKFZ]
!style="width:3%" |Tuesday, June 21 IPCAI
!style="width:15%" |Wednesday, June 22 Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Thursday, June 23 Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Friday, June 24 Congress Hall of CARS, Room Trübnersaal
!style="width:15%" |Saturday, June 25 Congress Hall of CARS, Room Trübnersaal
|-
|bgcolor="#ffffdd"|'''9:00am-10:00am'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[{{FULLPAGENAME}}/Workshop_on_Shared_Software_Platform_for_Ultrasound-Guided_Medical_Interventions|Workshop: Ultrasound-guided interventions software platform (all day)]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| 10:30am-12pm: Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"| [[{{FULLPAGENAME}}/Breakout Session Slicer Extensions|Breakout Session: Slicer Extensions]] (JC, Steve)
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

='''Projects'''=

* Note: Please use this [[2016_Summer_Project_Week_Template | template]] to create project pages

=== Worldwide Ultrasound Navigation ===
Over the last several PWs, an international group has emerged for collaborative specification and development of ultrasound-based navigation for surgical and interventional radiology applications. This group represents the leadership of ultrasound navigation technology from Queens University (PERK Lab, PLUS: Andras Lasso, Tamas Ungi, Csaba Pinter, Gabor Fichtinter), Montreal Neurologic Institute (Simon Drouin), Brigham and Women's Hospital/HMS (William Wells, Steve Pieper, Sarah Frisken), Robarts Research Institute, Western University (Terry Peters, Adam Rankin), Trondheim University and SINTEF (CustusX: Christian Askeland, Frank Lindseth).

* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)

=== Simplified Human-Computer Interactions for Intra-Operative Usage===
This theme focuses on infrastructure for simplified human-computer interactions for intra-operative usage. This includes Guidelets, simplified graphical user interfaces that can access the same backend as 3D Slicer; as well as interfaces for virtual reality/augmented reality devices from the consumer market that are that are improving by leaps and bounds and show promise for surgical use.

* [[2016 Summer Project Week/Guidelets | Guidelets (Slicelets for IGT)]] (Tamas Ungi, Andras Lasso, Thomas Vaughan)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper, Anna Roethe)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin, Andras Lasso)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (David García, Javier Pascau)
* [[2016 Summer Project Week/Auditory Display | Auditory Display Integration]] (David Black, Sarah Frisken, Christian Hansen, Longquan Chen)

===Machine Learning for IGT===
This theme applies concepts from machine learning to image-guided therapy, including the application of convolutional neural networks for segmentation of mechanically implanted devices during surgery, and the use of Gaussian processes for estimation of uncertainty in image-fusion.

* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Tina Kapur)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, Christian Hansen, William Wells)

===IGT Other===
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Yannick Suter, Lauren J. O'Donnell)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Rocío López, Javier Pascau, Tamas Ungi)
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI to aid Deep Brain Stimulation]] (Fernando Pérez García, Sara Fernandez Vidal, Sonia Pujol, Steve Pieper, Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Intraoperative Functional Guidance workflows in Neurosurgery | Intraoperative Functional Guidance Workflows in Neurosurgery]] (Prashin Unadkat, Sarah Frisken, Anna Roethe, Christian Hansen)

=== Informatics ===
This theme deals with creating data formats to enable medical image informatics. Led by the [http://qiicr.org/about.html QIICR project], the results will be made available in the DICOM for Quantitative Imaging (DCMQI) Library for sharing quantitative image-processing results in a standardized way.

* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Properties]] (Hans Meine, Andrey Fedorov, Christian Herz, Steve Pieper)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter, Andras Lasso, Marco Nolden, Christian Herz)

=== Infrastructure ===
Improvements to the core functionality of widely used open source tools is an on-going theme.

* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Lauren O'Donnell, Isaiah Norton, Michael Onken)
* [[2016 Summer Project Week/Curve and Surface Creation from Fiducials|Curve and Surface Creation from Fiducials]] (Thomas Vaughan, Junichi Tokuda)
* [[2016 Summer Project WEB and 3D DICOM viewer to the rest of us]] (Koji Kobayashi, Steve Pieper)
* [[2016 Summer Project Week/CommonGL|CommonGL: GPU Rendering and Computation]] (Steve Pieper, Christian Askeland, Andra Lasso, Simon Drouin, Fernando Pérez García)

=== Tutorial===
Creation of tutorials and documentation is an on-going theme.

* [[2016 Summer Project Week/SlicerDMRIDocumentation | Tutorials and Documentation in SlicerDMRI]] (Lauren J. O'Donnell, Fan Zhang, Isaiah Norton)
* [[2016 Summer Project Week/UniversityCourse | Create the basics of a university course about medical image computing]] (Attila Nagy)
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
==Location==
*'''Location:''' Heidelberg, Germany.
**'''Getting to Heidelberg:''' Most will fly into Frankfurt Main International (FRA). At the airport look for "long distance trains". There you can buy a ticket from the machine to Heidelberg Hauptbahnhof (main station), around EUR 25. It usually takes less than an hour, with a change in Mannheim to a regional train. https://www.bahn.de . If you arrive on Sunday you can take a bus from the station to the Old Town or where your hotel is. Heidelberg is pretty small, look for directions on Google Maps. If you arrive on Monday see below on how to get to DKFZ directly.
**'''Monday''' at German Cancer Research Center - DKFZ
*** Enter through the main lobby ( just north of https://goo.gl/maps/e3ZbcsM5KC82, you can't miss it, it's the tallest building on campus with a big "dkfz." on top). The meeting room is on the 8th floor (H824, "Glaskasten", "glass box"). We will leave some instructions how to get there at the reception. The meeting time in the lobby will be 8:45am for those who wish to be at the meeting room by 9am. Official activities will start at noon with lunch.
*** To get to DKFZ in the morning you can use the Google Maps link above, public transport information is available there. For people staying in the Old Town, near Bismarckplatz or coming from the station it will be most likely Bus #32, exit at stop "Chirurgische Klinik", which is the second one after crossing the Neckar river. More detailed timetables at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en the local transportation services VRN]. If you are up early there is also a nice [https://goo.gl/maps/SRRG6x7KDNU2 walk along the river].
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
***Suggested place for meetings is the Marstall student center ([https://www.google.de/maps/place/Zeughaus-Mensa+im+Marstall/@49.4124525,8.7056926,349m/data=!3m1!1e3!4m5!3m4!1s0x0000000000000000:0x8fd41be2e27fc36e!8m2!3d49.412919!4d8.7044381 map])
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
==Preparatory Conference Calls: ==
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

=='''Equipment'''==
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]] '''Updated June 16 2016'''

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

# Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA :: tkapur@bwh.harvard.edu (Mon)
# Ron Kikinis, BWH/HMS, Boston, USA and University of Bremen / Fraunhofer MEVIS, Germany :: kikinis@bwh.harvard.edu (Mon)
# Dženan Zukić, Kitware, USA :: dzenan.zukic@kitware.com
# Ines Prata Machado, MIT Portugal Program, Lisbon, Portugal :: ines7_prata@hotmail.com (Mon)
# Sonia Pujol, BWH/HMS, Boston :: spujol@bwh.harvard.edu (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing] group, Germany :: shery@uni-bremen.de (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy :: mfspadea@unicz.it (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy :: p.zaffino@unicz.it (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy :: salvatorescaramuzzino@gmail.com (Mon)
# Steve Pieper, Isomics, Inc., USA :: pieper@isomics.com (Mon)
# Nicole Aucoin, BWH/HMS, Boston :: nicole@bwh.harvard.edu (Mon)
# Simon Drouin, Montreal Neurological Institute :: simon.drouin@mail.mcgill.ca (Mon)
# Thomas Kirchner, German Cancer Research Center :: t.kirchner@dkfz.de (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada :: chene@imaging.robarts.ca (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada :: arankin@robarts.ca (Mon)
# Christian Askeland, SINTEF, Norway :: christian.askeland@gmail.com (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany :: hans.meine@mevis.fraunhofer.de (Mon)
# Longquan Chen, BWH/HMS, Boston, USA :: lchen@bwh.harvard.edu (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands :: punzodavide@hotmail.it (Mon)
# Lauren O'Donnell, BWH/HMS :: odonnell@bwh.harvard.edu (Mon)
# Yannick Suter, BWH/HMS :: yannicksuter@bluewin.ch (Mon)
# Junichi Tokuda, BWH/HMS :: tokuda@bwh.harvard.edu (Mon)
# Sarah Frisken, BWH/HMS :: sfrisken@bwh.harvard.edu (Mon)
# Prashin Unadkat, BWH/HMS :: punadkat@partners.org
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany :: onken@open-connections.de (Mon)
# Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway :: janne.beate.bakeng@sintef.no
# Ole Vegard Solberg, SINTEF, Norway :: OleVegard.Solberg@sintef.no
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada :: ungi@queensu.ca (Mon)
# Andras Lasso, Queen's University, Canada :: lasso@queensu.ca (Mon)
# Csaba Pinter, Queen's University, Canada :: pinter@cs.queensu.ca (Mon)
# Thomas Vaughan, Queen's University, Canada :: vaughan.thomas.a@gmail.com (Mon)
# Javier Pascau, Universidad Carlos III de Madrid, Spain :: jpascau@hggm.es (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain :: vgarcia@hggm.es (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain :: mgsevilla@hggm.es (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain :: dgmato@hggm.es (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain :: rlopez@hggm.es (Mon)
# Raúl San José, BWH/HMS, Boston :: rsanjose@bwh.harvard.edu
# Pietro Nardelii, BWH/HMS, Boston :: pietro@bwh.harvard.edu
# Andrey Fedorov, BWH/HMS, Boston :: fedorov@bwh.harvard.edu (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston :: cherz1@partners.org (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway :: Frank.Lindseth at sintef.no
# Peter Behringer, Basler AG, Germany :: peterbehringer@gmx.de
# Santhirarajah Mathimugan, Basler AG, Germany :: Santhirarajah.Mathimugan@baslerweb.com
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany :: david.black@mevis.fraunhofer.de (Mon)
# William Wells, BWH/HMS :: sw@bwh.harvard.edu (Mon)
# Attila Nagy, University of Szeged, Hungary :: attila@orl.szote.u-szeged.hu (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany :: bkocev@uni-bremen.de (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France :: sara.fernandez_vidal@upmc.fr (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Marco Nolden, [http://mbi.dkfz-heidelberg.de Medical and Biological Informatics, German Cancer Research Center] (Mon)
# Christian Hansen, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany :: hansen@isg.cs.uni-magdeburg.de (Mon)
# Julian Hettig, [http://isgwww.cs.uni-magdeburg.de/cas/ University of Magdeburg], Germany :: Julian.Hettig@ovgu.de (Mon)
# Jorge Onieva, BWH/HMS, Boston :: jonieva@bwh.harvard.edu
# Caspar Goch, German Cancer Research Center (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-24T15:12:09Z

Fepegar:

<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:Brainstem contours on different images.png|Manually segmented structures of a human brainstem superimposed on a histological slice, a block-face volume and a 11.7 MRI.
Image:Brainstem contours 3D.png|3D visualization of the manually traced contours that have been used to interpolate the masks of the structures.
</gallery>

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sara Fernandez Vidal ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sonia Pujol (BWH)
* Steve Pieper
* Csaba Pinter
* Andras Lasso

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D MRI/histological atlas. Different modules in the extension are used for:
** Contours tracing
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

* A prototype of the "Show unzoomed slice" widget has been developed ([https://youtu.be/VdOux73uWXI YouTube video]). With the help of the Slicer community, it will be improved in order to be more generic and, at some point, be integrated into Slicer's Data Probe module.
* A lot of feedback has been given to the developers of the "Segmentations" and "Segment Editor" modules. This will lead to improvements of these modules and will help us using their features.
|}

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-24T14:37:20Z

Fepegar:

<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:Brainstem contours on different images.png|Manually segmented structures of a human brainstem superimposed on a histological slice, a block-face volume and a 11.7 MRI.
Image:Brainstem contours 3D.png|3D visualization of the manually traced contours that have been used to interpolate the masks of the structures.
</gallery>

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sara Fernandez Vidal ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sonia Pujol (BWH)
* Steve Pieper
* Csaba Pinter
* Andras Lasso

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D histological atlas. Different modules will be used to:
** Trace contours
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

* A prototype of the "Show unzoomed slice" widget has been developed ([https://youtu.be/VdOux73uWXI YouTube video]). With the help of the Slicer community, this might be improved to be more generic and, at some point, be integrated into the DataProbe module.
|}

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-24T09:56:27Z

Fepegar: /* Project Description */

<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:Brainstem contours on different images.png|Manually segmented structures of a human brainstem superimposed on a histological slice, a block-face volume and a 11.7 MRI.
Image:Brainstem contours 3D.png|3D visualization of the manually traced contours that have been used to interpolate the masks of the structures.
</gallery>

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sara Fernandez Vidal ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sonia Pujol (BWH)
* Steve Pieper
* Csaba Pinter
* Andras Lasso

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D histological atlas. Different modules will be used to:
** Trace contours
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

* A prototype of the "Show unzoomed slice" widget has been developed ([https://youtu.be/8CHyhmh7nFk YouTube video]). With the help of the Slicer community, this might be improved to be more generic and, at some point, be integrated into the DataProbe module.
|}

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-24T09:19:22Z

Fepegar:

<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:Brainstem contours on different images.png|Manually segmented structures of a human brainstem superimposed on a histological slice, a block-face volume and a 11.7 MRI.
Image:Brainstem contours 3D.png|3D visualization of the manually traced contours that have been used to interpolate the masks of the structures.
</gallery>

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sara Fernandez Vidal ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sonia Pujol (BWH)
* Steve Pieper
* Csaba Pinter
* Andras Lasso

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D histological atlas. Different modules will be used to:
** Trace contours
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

* A prototype of the "Show unzoomed slice" widget has been developed ([https://www.youtube.com/watch?v=dFlwkYgPiOs YouTube video]). With the help of the Slicer community, this might be improved to be more generic and, at some point, be integrated into the DataProbe module.
|}

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-24T09:10:56Z

Fepegar:

<gallery>
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]
Image:Brainstem contours on different images.png|Manually segmented structures of a human brainstem superimposed on a histological slice, a block-face volume and a 11.7 MRI.
Image:Brainstem contours 3D.png|3D visualization of the manually traced contours that have been used to interpolate the masks of the structures.
</gallery>

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sara Fernandez Vidal ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sonia Pujol (BWH)
* Steve Pieper
* Csaba Pinter
* Andras Lasso

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D histological atlas. Different modules used to:
** Trace contours
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

|}

File:Brainstem contours 3D.png

2016-06-24T09:09:12Z

Fepegar: 3D visualization of the contours used to interpolate the masks of the structures.

3D visualization of the contours used to interpolate the masks of the structures.

File:Brainstem contours on different images.png

2016-06-24T09:03:40Z

Fepegar: Manually traced contours superimposed on a histological slice, a block-face volume and a 11.7 MRI of a human brainstem.

Manually traced contours superimposed on a histological slice, a block-face volume and a 11.7 MRI of a human brainstem.

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-24T08:33:12Z

Fepegar: Edit "key investigators"

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sara Fernandez Vidal ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)
* Sonia Pujol (BWH)
* Steve Pieper
* Csaba Pinter
* Andras Lasso

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D histological atlas. Different modules used to:
** Trace contours
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

|}

File:UnZoomWidget.mov

2016-06-24T08:32:37Z

Fepegar: Demonstration of the "Show unzoomed slice" widget.

Demonstration of the "Show unzoomed slice" widget.

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-15T14:57:40Z

Fepegar: Fepegar moved page 2016 Summer Project Week/Histological Brain Atlas to 2016 Summer Project Week/Brain atlas combining histology and MRI: Wrong title

==Key Investigators==
* Fernando Pérez García ([http://icm-institute.org/en/ Institute of the Brain and Spine], France)

==Project Description==
Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* A Slicer Extension to aid in the creation of a 3D histological atlas. Different modules used to:
** Trace contours
** Count neurons
** Visualize the results
|

* Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
* Create a small preview of the current histological slice (as in [https://www.researchgate.net/profile/Carlos_Ortiz-de-Solorzano/publication/233806662/figure/fig3/AS:299961800511505@1448527874676/Figure-3-Sample-histology-images-corresponding-to-a-lung-lobe-slice-of-a-mouse-17-days.png this image]), so that the user knows where they are in the slice while zooming.
|

|}

2016 Summer Project Week/Histological Brain Atlas

2016-06-15T14:57:40Z

Fepegar: Fepegar moved page 2016 Summer Project Week/Histological Brain Atlas to 2016 Summer Project Week/Brain atlas combining histology and MRI: Wrong title

#REDIRECT [[2016 Summer Project Week/Brain atlas combining histology and MRI]]

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-15T14:56:47Z

Fepegar:

2016 Summer Project Week/Brain atlas combining histology and MRI

2016-06-10T10:18:03Z

Fepegar: Created page with "==Key Investigators== * Fernando Pérez García ==Project Description== Description TODO. {| class="wikitable" ! style="text-align: left; width:27%" | Objective ! style=..."

==Key Investigators==
* Fernando Pérez García

==Project Description==

Description TODO.

{| class="wikitable"
! style="text-align: left; width:27%" | Objective
! style="text-align: left; width:27%" | Approach and Plan
! style="text-align: left; width:27%" | Progress and Next Steps
|- style="vertical-align:top;"
|

* Objectives TODO
|

* Approach TODO
|

|}

2016 Summer Project Week

2016-06-10T10:14:57Z

Fepegar: /* Projects */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
 
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 DKFZ
!style="width:3%" |Tuesday, June 21 IPCAI
!style="width:15%" |Wednesday, June 22 Congress Hall of CARS
!style="width:15%" |Thursday, June 23 Congress Hall of CARS
!style="width:15%" |Friday, June 24 Congress Hall of CARS
!style="width:15%" |Saturday, June 25 Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''8:30am-10:00am'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[Breakout Session/Shared Software Platform for Ultrasound-Guided Medical Interventions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"| TBD
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| [[Breakout Session/Slicer Extensions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

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

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

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

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

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]]

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Andre Mastmeyer, Tina Kapur, Paolo Zaffino)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Lauren J. O'Donnell, Yannick Suter)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper)

=== Infrastructure ===
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Michael Onken)

=== Augmented Reality ===
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (Javier Pascau, David García)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== Atlas construction ===
* [[2016 Summer Project Week/Histological Brain Atlas | Tool for the construction of an integrated brain atlas based on histology and MRI]] (Fernando Pérez García)

=== Informatics ===
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter)

=== Tutorial===
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

#Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
#Gabor Fichtinger, Queen's University, Canada
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week

2016-06-10T10:04:04Z

Fepegar: /* Projects */

__NOTOC__

[[image:PW-Summer2016.png|300px]]
 
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 DKFZ
!style="width:3%" |Tuesday, June 21 IPCAI
!style="width:15%" |Wednesday, June 22 Congress Hall of CARS
!style="width:15%" |Thursday, June 23 Congress Hall of CARS
!style="width:15%" |Friday, June 24 Congress Hall of CARS
!style="width:15%" |Saturday, June 25 Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''8:30am-10:00am'''
|bgcolor="#ffffff"| What does a Neurosurgeon need from technologists? (Alexandra Golby, MD)
|bgcolor="#ffffff"; rowspan="8"|
|bgcolor="#ffffff"|[[Breakout Session/Shared Software Platform for Ultrasound-Guided Medical Interventions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''10:00am-10:30am'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''10:30-12pm'''
|bgcolor="#ffffff"| TBD
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"; rowspan="4"|
|-
|bgcolor="#ffffdd"|'''3:00pm-3:30pm'''
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|bgcolor="#f0e68b"| Coffee Break
|-
|bgcolor="#ffffdd"|'''3:30pm-5:00pm'''
|bgcolor="#ffffff"| [[Breakout Session/Slicer Extensions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|}

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

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

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

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

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

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]]

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the Communications of Robotics Devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Andre Mastmeyer, Tina Kapur, Paolo Zaffino)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in Applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for Data Collection and Prostate Biopsy Support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Lauren J. O'Donnell, Yannick Suter)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells)
* [[2016 Summer Project Week/Slicelet For Ultrasound Acquisition | Slicelet for Ultrasound Acquisition]] (Sarah Frisken, Prashin Unadkat, Steve Pieper)

=== Infrastructure ===
* [[2016 Summer Project Week/3D Lasso Selection | Implementation and Testing Performance of 3-D Lasso Selection within the Segmentation Editor Infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations Infrastructure and Related Modules to Slicer Core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results Implementation in DCMTK for BWH Project]] (Michael Onken)

=== Augmented Reality ===
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a Tablet Device in the Surgical Room]] (Javier Pascau, David García)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== Atlas construction ===
* Tool for the construction of an integrated brain atlas based on histology and MRI (Fernando Pérez García)

=== Informatics ===
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map Implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) Library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter)

=== Tutorial===
* [[2016 Summer Project Week/CameraTutorial | How to use Basler Cameras for Medical Applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

#Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
#Gabor Fichtinger, Queen's University, Canada
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''

2016 Summer Project Week

2016-06-08T14:42:37Z

Fepegar:

__NOTOC__

[[image:PW-Summer2016.png|300px]]
 
=Welcome to the web page for the 23rd Project Week!=
The 23rd Project Week open source hackathon is being held in conjunction with the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS) and the [http://www.ipcai.org/ IPCAI 2016] conferences in Heidelberg, Germany. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].

='''Logistics'''=
*'''Dates:''' Monday June 20th to Saturday June 25th, 2016, with one day break on Tuesday June 21st to attend IPCAI.
*'''Location:''' Heidelberg, Germany.
**'''Monday''' at German Cancer Research Center - DKFZ
**'''Tuesday''' there is '''no''' organized Project Week activity due to IPCAI @ CARS
**'''Wednesday-Saturday''' at the Congress Hall of CARS.
*'''REGISTRATION:''' Please register for the CARS conference at http://www.cars-int.org/cars_2016/registration.html
*'''Registration Fee:''' Euro 650 (after April 26, 2016)
*'''Hotel:''' After registration, you can book hotels using the CARS organization at http://germany.nethotels.com/info/heidelberg/events/cars/default_en.htm or on your own. Please remember that Project Week starts on Monday June 20th, even though the formal CARS/IPCAI program starts a day later, so you will need to pay attention while booking the hotel room.
*Preparatory Conference Calls:
**800-501-8979. The pin is 7327389. ([http://www.windstreambusiness.com/resources/user-guides/international-conferencing International dialing instructions are available here])
**Call #1 Tuesday, May 10, 3pm Boston time.
**Call #2 Tuesday, May 17, 3pm Boston time.
**Call #3 Tuesday, May 31, 9am Boston time.
**Call #4 Tuesday, Jun 7, 9am Boston time.
**Call #5 Tuesday, Jun 14, 9am Boston time.

='''Agenda'''=
Please note that on '''Tuesday''' there is no organized Project Week activity due to IPCAI @ CARS
{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:7%" |Time
!style="width:15%" |Monday, June 20 DKFZ
!style="width:3%" |Tuesday, June 21 IPCAI
!style="width:15%" |Wednesday, June 22 Congress Hall of CARS
!style="width:15%" |Thursday, June 23 Congress Hall of CARS
!style="width:15%" |Friday, June 24 Congress Hall of CARS
!style="width:15%" |Saturday, June 25 Congress Hall of CARS
|-
|bgcolor="#ffffdd"|'''9:00am-12:00pm'''
|bgcolor="#ffffff"| DKFZ Discussions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|[[Breakout Session/Shared Software Platform for Ultrasound-Guided Medical Interventions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"| Progress Review
|-
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffff"|
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch and adjourn
|-
|bgcolor="#ffffdd"|'''1:00pm-3:00pm'''
|bgcolor="#ffffff"| Welcome! Project Introductions
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''3:00pm-5:00pm'''
|bgcolor="#ffffff"| 3:30pm: [[Breakout Session/Slicer Extensions]]
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|bgcolor="#ffffff"|
|-
|bgcolor="#ffffdd"|'''6:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#ffffff"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|
|-
|}

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

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

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

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

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

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

The 23rd Project Week is being held in conjunction with the [http://www.ipcai.org/ IPCAI 2016] conference that is hosted by the [http://www.cars-int.org/ 30th International Conference on Computer Assisted Radiology and Surgery] (CARS).

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

='''Equipment'''=
*[[2016_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)
*[[2016_Summer_Project_Week:Equipment_Requests|Specialized equipment that people would like to have]]

='''Projects'''=
* Use this [[2016_Summer_Project_Week_Template | template]] for project pages

=== IGT ===
* [[2016 Summer Project Week/Integrating/Using OpenIGTLink for the communications of Robotics devices | Integrating/Using OpenIGTLink for the communications of Robotics devices]] (Scheherazade Kraß, Longquan Chen)
* [[2016 Summer Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Guillaume Pernelle, Andre Mastmeyer, Tina Kapur, Paolo Zaffino)
* [[2016 Summer Project Week/Guided Ultrasound Calibration | Guided Ultrasound Calibration]] (Elvis Chen, Inês Prata, Tamas Ungi)
* [[2016 Summer Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization II: The Implementering]] (Andras Lasso, Christian Askeland, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Thomas Kirchner, Janne Beate Bakeng)
* [[2016 Summer Project Week/Integrating PLUS in applications using OpenIGTLink | Integrating PLUS in applications using OpenIGTLink]] (Christian Askeland, Janne Beate Bakeng, Ole Vegard Solberg, Jon Eiesland, Longquan Chen, Simon Drouin)
* [[2016 Summer Project Week/SliceTracker | SliceTracker for data collection and prostate biopsy support ]] (Christian Herz, Peter Behringer, Andrey Fedorov)
* [[2016 Summer Project Week/Sacral Neuromodulation | Sacral Neuromodulation ]] (Javier Pascau, Rocío López, Tamas Ungi)
* [[2016 Summer Project Week/Intra-procedural prostate motion characterization | Prostate Motion Characterization ]] (Peter Behringer, Christian Herz, Andrey Fedorov)
* [[2016 Summer Project Week/Structural-functional measurements | Structural - Functional Relationship Measurements of Tractography Data with fMRI ]] (Lauren J. O'Donnell, Yannick Suter)
* [[2016 Summer Project Week/Uncertainty-aware Information Fusion | Uncertainty-aware Information Fusion for Real-time Soft Tissue Motion Estimation]] (Bojan Kocev, Sarah Frisken, William Wells)

=== Infrastructure ===
* [[2016 Summer Project Week/3D Lasso Selection | Implementation, and testing performance, of 3-D Lasso selection within the segmentation editor infrastructure ]] (Davide Punzo, Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2016 Summer Project Week/Segmentations Integration | Integration of Segmentations infrastructure and related modules to Slicer core]] (Csaba Pinter, Andras Lasso)
* [[2016 Summer Project Week/DICOM Tractography Results | Finalizing DICOM Tractography Results implementation in DCMTK for BWH project]] (Michael Onken)

=== Augmented Reality ===
* [[2016 Summer Project Week/VRPN Integration | VRPN Integration]] (Dženan Zukić)
* [[2016 Summer Project Week/OpenVR_integration | OpenVR Integration]] (Adam Rankin)
* [[2016 Summer Project Week/AR with a tablet device in the surgical room | AR with a tablet device in the surgical room]] (Javier Pascau, David García)

=== Cloud ===
* [[2016 Summer Project Week/medical imaging webapp | Medical Imaging WebApp Software]] (Steve Pieper, Marco Nolden, Hans Meine)

=== Informatics ===
* [[2016 Summer Project Week/DICOM Parametric Maps | Finalizing DICOM Parametric Map implementation in DCMTK for QIICR project]] (Michael Onken, Jan Schlamelcher, Andrey Fedorov, Christian Herz)
* [[2016 Summer Project Week/dcmqi | DICOM for Quantitative Imaging (dcmqi) library]] (Andrey Fedorov, Christian Herz, Marco Nolden, Hans Meine, Csaba Pinter, Steve Pieper, et al)
* [[2016 Summer Project Week/MeVisLab SEG Colors | Support Reading and Writing DICOM Tags for SEG Colors]] (Hans Meine)
* [[2016 Summer Project Week/Segmentation Editor and Terminology | Segmentation Editor and Terminology]] (Nicole Aucoin, Andrey Fedorov, Csaba Pinter)

=== Tutorial===
* [[2016 Summer Project Week/CameraTutorial | How to use Basler cameras for medical applications]] (Peter Behringer, Santhirarajah Mathimugan, Steve Pieper)

= '''Registrants''' =

'''REGISTRATION:''' Please add your name to this list if you are definitely planning to attend. If you are not already on it, please add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]. We need to know the number of people at DKFZ, so if you are there on Monday, please add "(Mon)" next to your name. Official registration for the event is through the CARS conference at http://www.cars-int.org/cars_2016/registration.html -- which you can do now or onsite.

#Tina Kapur, Brigham and Women's Hospital, Harvard Medical School (BWH/HMS), Boston, USA (Mon)
# Dženan Zukić, Kitware, USA
# Ines Prata Machado, MIT Portugal Program (PhD Student), Lisbon, Portugal. (Mon)
# Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School (Mon)
# Scheherazade Kraß, PhD Student, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Maria Francesca Spadea [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Paolo Zaffino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Salvatore Scaramuzzino [http://www.imagenglab.com ImagEngLab], Italy (Mon)
# Steve Pieper, Isomics, Inc., USA (Mon)
# Nicole Aucoin, Brigham and Women's Hospital (Mon)
# Simon Drouin, Montreal Neurological Institute (Mon)
# Thomas Kirchner, German Cancer Research Center (Mon)
# Elvis Chen, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Adam Rankin, [http://www.imaging.robarts.ca/petergrp/Research Robarts Research Institute], Canada (Mon)
# Christian Askeland, SINTEF, Norway (Mon)
# Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany
# Longquan Chen, BWH/HMS, Boston, USA (Mon)
# Davide Punzo, Kapteyn Astronomical Institute, Netherlands (Mon)
# Lauren O'Donnell, BWH/HMS
# Yannick Suter, BWH/HMS (Mon)
# Junichi Tokuda, BWH/HMS (Mon)
# Sarah Frisken, BWH/HMS (Mon)
# Prashin Unadkat, BWH/HMS
# Anna Roethe, Charite, Berlin
# Michael Onken, Open Connections, Germany (Mon)
#Jan Schlamelcher, Open Connections/OFFIS, Germany
# Janne Beate Bakeng, SINTEF, Norway
# Ole Vegard Solberg, SINTEF, Norway
# Jon Eiesland, SINTEF, Norway
# Tamas Ungi, Queen's University, Canada (Mon)
# Andras Lasso, Queen's University, Canada (Mon)
# Csaba Pinter, Queen's University, Canada (Mon)
# Thomas Vaughan, Queen's University, Canada (Mon)
#Gabor Fichtinger, Queen's University, Canada
# Javier Pascau, Universidad Carlos III de Madrid, Spain (Mon)
# Verónica García-Vazquez, Universidad Carlos III de Madrid, Spain (Mon)
# Mónica García-Sevilla, Universidad Carlos III de Madrid, Spain (Mon)
# David García-Mato, Universidad Carlos III de Madrid, Spain (Mon)
# Rocío López-Velazco, Universidad Carlos III de Madrid, Spain (Mon)
# Raúl San José, BWH/HMS, Boston
# Pietro Nardeli, BWH/HMS, Boston
# Andrey Fedorov, BWH/HMS, Boston (Mon, Wed, Thu)
# Christian Herz, BWH/HMS, Boston (Mon)
# Frank Lindseth, NTNU/SINTEF, Norway
# Peter Behringer, Basler AG, Germany
# Santhirarajah Mathimugan, Basler AG, Germany
# Koji Kobayashi, Vocsis Corporation, Japan
# David Black, University of Bremen / Fraunhofer MEVIS, Germany (Mon)
#William Wells, BWH/HMS (Mon)
# Attila Nagy, University of Szeged, Hungary (Mon)
# Bojan Kocev, [http://www.uni-bremen.de/ University of Bremen], [http://www.mic.uni-bremen.de/ Medical Image Computing]group, Germany (Mon)
# Sara Fernández Vidal, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)
# Fernando Pérez García, [http://icm-institute.org/en/ Institute of the Brain and Spine], France (Mon)

'''Please don't forget to add yourself to the [http://public.kitware.com/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list].'''