NAMIC Wiki - User contributions [en]

2013 Summer Project Week:WMQL Integration in Slicer

2013-06-21T12:40:06Z

Demian:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:DW-WMQL2013.png|[[WMQL#QueryResults|Query Results]]
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Carl-Fredrik Westin

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

<h3>Objective</h3>
Integrating the White Matter Query Language, a system for automatical definition and extraction of white matter tracts into 3D Slicer

</div>

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

<h3>Approach, Plan</h3>

We already have a pure-python toolkit to perform this. The approach would be to integrate it as a python modules

</div>

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

<h3>Progress</h3>
The GUI and the loadable scripted module are in place. A python console needs to be implemented in order to provide access to the interactive features of the system

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- Python

==References==
*Wassermann, et al. "On Describing White Matter Anatomy", MICCAI 2013
*[http://demianw.github.io/tract_querier WMQL Python implementation page]

2013 Summer Project Week:MRML Infrastructure Airway Inspector

2013-06-21T12:31:21Z

Demian: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:EmphysemaGUI.png|Emphysema Analysis Tool
Image:AIScreenshot.png|Airway Analysis Tool
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Raul San Jose, Rola Harmouche (BWH)

<h3>Background</h3>
Airway Inspector (www.airwayinspector.org) is a tool for CT-based image quantitative analysis of the lung to allow the exploration of airway morphology and desitometric characteristics [1]. In order to become a part of 3D Slicer 4, the Airway inspector needs to have a consistent MRML representation of data and visualization

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
To develop a MRML Infrastructure for the airway inspector
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We will base the developement in the current infrastructure for tractography in 3D slicer. This is well modularized and encompasses data representation, I/O and GUI
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
A Loadable module with the MRML nodes for storage, data representation and visualization has been created. The next steps are to create the Logic and GUI components.
</div>

</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension — loadable modules

==References==
* San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302. Available on-line: www.lulu.com/content/3507981.

File:ProstateResylt-MIT2013.png

2013-06-21T12:30:09Z

Demian: Result of prostate processing. Summer project week 2013

Result of prostate processing. Summer project week 2013

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-21T12:29:26Z

Demian:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:ProstateBarrat-MIT2013.png|[[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI|Prostate Model from Hu et al. 2013]]
Image:ProstateResylt-MIT2013.png|[[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI|Results of the prostate processing]]

</gallery>

==Key Investigators==

* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

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

<h3>Objective</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image. Our goal is to develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.

</div>

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

<h3>Approach, Plan</h3>

We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.

</div>

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

<h3>Progress</h3>
After careful discussion in the IGT breakout and interaction with Claire Tempany, we devised how to present results for the surgeons performing image guided biopsies. We were able to obtain results in this format. The next step is to develop a slicer module that can perform this work within the 3D Slicer platform.
</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- loadable

==References==

* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-21T12:25:07Z

Demian: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:ProstateBarrat-MIT2013.png|[[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI|Prostate Model from Hu et al. 2013]]
</gallery>

==Key Investigators==

* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

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

<h3>Objective</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image. Our goal is to develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.

</div>

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

<h3>Approach, Plan</h3>

We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.

</div>

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

<h3>Progress</h3>
After careful discussion in the IGT breakout and interaction with Claire Tempany, we devised how to present results for the surgeons performing image guided biopsies. We were able to obtain results in this format. The next step is to develop a slicer module that can perform this work within the 3D Slicer platform.
</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- loadable

==References==

* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:WMQL Integration in Slicer

2013-06-17T18:34:46Z

Demian: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:DW-WMQL2013.png|[[WMQL#QueryResults|Query Results]]
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Carl-Fredrik Westin

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

<h3>Objective</h3>
Integrating the White Matter Query Language, a system for automatical definition and extraction of white matter tracts into 3D Slicer

</div>

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

<h3>Approach, Plan</h3>

We already have a pure-python toolkit to perform this. The approach would be to integrate it as a python modules

</div>

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

<h3>Progress</h3>

TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- Python

==References==
*Wassermann, et al. "On Describing White Matter Anatomy", MICCAI 2013
*[http://demianw.github.io/tract_querier WMQL Python implementation page]

2013 Summer Project Week:WMQL Integration in Slicer

2013-06-17T17:38:38Z

Demian: /* References */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:DW-WMQL2013.png|[[WMQL#QueryResults|Query Results]]
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Carl-Fredrik Westin

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

<h3>Objective</h3>
Integrating the White Matter Query Language, a system for automatical definition and extraction of white matter tracts into 3D Slier

</div>

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

<h3>Approach, Plan</h3>

We already have a pure-python toolkit to perform this. The approach would be to integrate it as a python modules

</div>

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

<h3>Progress</h3>

TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- Python

==References==
*Wassermann, et al. "On Describing White Matter Anatomy", MICCAI 2013
*[http://demianw.github.io/tract_querier WMQL Python implementation page]

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-17T17:26:56Z

Demian:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:ProstateBarrat-MIT2013.png|[[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI|Prostate Model from Hu et al. 2013]]
</gallery>

==Key Investigators==

* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

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

<h3>Objective</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image. Our goal is to develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.

</div>

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

<h3>Approach, Plan</h3>

We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.

</div>

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

<h3>Progress</h3>
TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- loadable

==References==

* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

File:ProstateBarrat-MIT2013.png

2013-06-17T17:25:18Z

Demian: 3D Illustration of prostate modelling from Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10

3D Illustration of prostate modelling from Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:WMQL Integration in Slicer

2013-06-17T17:22:22Z

Demian:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:DW-WMQL2013.png|[[WMQL#QueryResults|Query Results]]
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Carl-Fredrik Westin

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

<h3>Objective</h3>
Integrating the White Matter Query Language, a system for automatical definition and extraction of white matter tracts into 3D Slier

</div>

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

<h3>Approach, Plan</h3>

We already have a pure-python toolkit to perform this. The approach would be to integrate it as a python modules

</div>

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

<h3>Progress</h3>

TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- Python

==References==
*Wassermann, et al. "On Describing White Matter Anatomy", MICCAI 2013

File:DW-WMQL2013.png

2013-06-17T17:21:57Z

Demian: Automatic tract segmentations obtained with WMQL from 70 healthy subjects

Automatic tract segmentations obtained with WMQL from 70 healthy subjects

2013 Summer Project Week:WMQL Integration in Slicer

2013-06-17T17:19:47Z

Demian:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:DW_WMQL.png|[[WMQL#QueryResults|Query Results]]
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Carl-Fredrik Westin

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

<h3>Objective</h3>
Integrating the White Matter Query Language, a system for automatical definition and extraction of white matter tracts into 3D Slier

</div>

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

<h3>Approach, Plan</h3>

We already have a pure-python toolkit to perform this. The approach would be to integrate it as a python modules

</div>

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

<h3>Progress</h3>

TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- Python

==References==
*Wassermann, et al. "On Describing White Matter Anatomy", MICCAI 2013

2013 Summer Project Week:WMQL Integration in Slicer

2013-06-17T15:07:54Z

Demian: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * BWH: Demian Wassermann, Carl-Fredrik Westin <div…'

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

==Key Investigators==
* BWH: Demian Wassermann, Carl-Fredrik Westin

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

<h3>Objective</h3>
Integrating the White Matter Query Language, a system for automatical definition and extraction of white matter tracts into 3D Slier

</div>

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

<h3>Approach, Plan</h3>

We already have a pure-python toolkit to perform this. The approach would be to integrate it as a python modules

</div>

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

<h3>Progress</h3>

TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- Python

==References==
*Wassermann, et al. "On Describing White Matter Anatomy", MICCAI 2013

2013 Summer Project Week

2013-06-17T15:05:05Z

Demian: /* Additional Collaborations */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Using ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, ?)

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)

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

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo, Dave, Hans)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Hans Johnson, Dave Welch, Brad Lowekamp)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter Hierarchy]] (Adam Rankin, ??)

== '''Background''' ==

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

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

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

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

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

== '''Registrants''' ==

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

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

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-17T15:03:41Z

Demian:

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

==Key Investigators==

* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

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

<h3>Objective</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image. Our goal is to develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.

</div>

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

<h3>Approach, Plan</h3>

We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.

</div>

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

<h3>Progress</h3>
TBD

</div>
</div>

==Delivery Mechanism==

#Slicer Module
##Extension -- loadable

==References==

* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-17T14:47:52Z

Demian: /* Key Investigators */

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

==Key Investigators==
* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

<h3>Background</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image.

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>.
Develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.
</div>

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

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension — loadable modules

==References==
* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-17T14:47:04Z

Demian: /* Key Investigators */

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

==Key Investigators==
* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

<h3>Background</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image.

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

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>.
Develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.
</div>

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

</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension — loadable modules

==References==
* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-17T14:45:50Z

Demian: /* Key Investigators */

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

==Key Investigators==
* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

<h3>Background</h3>
A difficult problem in image-guided therapy is to be able to overlay pre-operative plannign with intra-operative imaging for surgical guidance. In this project we implement an algorithm to do that in the case of prostate surgery. We do that through biophysical simulation of the intra-operative tissue dynamics and registration on top of the intra-operative US image.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>.
Develop a module which taking a set of artificially deformed prostate volumes extracted from MRI infers the deformation modes and uses them to register the planning over the US intra-op images.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We have a prototype version of the algorithm in Python, the idea is to assess the interactive needs and plugging it into Slicer.
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
TBD
</div>

</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension — loadable modules

==References==
* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week:3D prostate registration of Ultrasound image using MRI

2013-06-17T12:16:45Z

Demian: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * BWH: Demian Wassermann, Andriy Fedorov, Tina Kapu…'

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

==Key Investigators==
* BWH: Demian Wassermann, Andriy Fedorov, Tina Kapur, Sandy Wells (BWH)

<h3>Background</h3>

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>.
Develop a module which taking a set of artificially deformed prostate volumes extracted from MRI will generate a .......
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
...
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
TBD
</div>

</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension — loadable modules

==References==
* Hu, Y., Ahmed, H. U., Taylor, Z., Allen, C., Emberton, M., Hawkes, D., & Barratt, D. (2012). MR to ultrasound registration for image-guided prostate interventions. Medical Image Analysis, 16(3), 687–703. doi:10.1016/j.media.2010.11.003

2013 Summer Project Week

2013-06-17T12:13:41Z

Demian: /* IGT and Device Integration with Slicer */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] (Steve Pieper) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans Johnson, Brad Lowekamp)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina Kapur)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|<br>----------------------------------------<br>'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

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

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

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

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

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: Dicom-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, Kevin Wang, Andrey Fedorov, anyone else?)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Using ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)

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

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[Plastimatch in NiPype]] (Paolo, Dave, Hans)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Hans Johnson, Dave Welch, Brad Lowekamp)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter Hierarchy]] (Adam Rankin, ??)

== '''Background''' ==

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

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

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

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

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

== '''Registrants''' ==

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

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

2013 Summer Project Week:MRML Infrastructure Airway Inspector

2013-06-17T12:11:53Z

Demian:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:EmphysemaGUI.png|Emphysema Analysis Tool
Image:AIScreenshot.png|Airway Analysis Tool
</gallery>

==Key Investigators==
* BWH: Demian Wassermann, Raul San Jose, Rola Harmouche (BWH)

<h3>Background</h3>
Airway Inspector (www.airwayinspector.org) is a tool for CT-based image quantitative analysis of the lung to allow the exploration of airway morphology and desitometric characteristics [1]. In order to become a part of 3D Slicer 4, the Airway inspector needs to have a consistent MRML representation of data and visualization

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
To develop a MRML Infrastructure for the airway inspector
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We will base the developement in the current infrastructure for tractography in 3D slicer. This is well modularized and encompasses data representation, I/O and GUI
</div>

<div style="width: 40%; float: left;">
<h3>Progress</h3>
TBD
</div>

</div>

==Delivery Mechanism==
This work will be delivered to the NA-MIC Kit as a

#Slicer Module
##Extension — loadable modules

==References==
* San Jose Estepar R, Washko GG, Silverman EK, Reilly JJ, Kikinis R, Westin CF. Airway inspector: An open source application for lung morphometry. In First International Workshop on Pulmonary Image Processing. New York City, USA, 2008;293-302. Available on-line: www.lulu.com/content/3507981.

Slicer-4.1

2012-04-07T16:30:33Z

Demian: /* Bug fixes targeted for this release */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget (done)
**pop up reorganization (done)
**Lollipop (implemented and available for testing)
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp](resolved)
**[http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor](resolved)
* View controller cosmetics: J2
**[http://www.na-mic.org/Bug/view.php?id=1750 redesign](resolved)
**[http://www.na-mic.org/Bug/view.php?id=1751 mouse gesture for foreground/labelmap opacity] ([http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Slice_Viewer resolved])
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling](resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies](resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import](resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1783 crash on scene close](resolved) - Nicole
*OpenIGTLink IF module: Junichi

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian, checked it out. It seems that it is a limitation of the Otsu strategy in this case due to the lack of padding, probably we need a real brain extraction tool)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian fixed)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) is due to extreme values in the data - can this be clamped in the scalar estimation module? (assigned to Demian, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue] (fixed by Julien Finet)
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: Jim)
* Suggested Reorganization of the Diffusion menu (assigned to Demian, Done)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian, done)

* Use new Slicer4 QTtesting functionalities for cross-platform [[Tests of Iowa Workshop tutorials]] (Benjamin/Sonia)

* Editor memory leaks and performance issues (Steve)

= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole
* [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-04-07T16:30:10Z

Demian: /* Bug fixes targeted for this release */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget (done)
**pop up reorganization (done)
**Lollipop (implemented and available for testing)
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp](resolved)
**[http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor](resolved)
* View controller cosmetics: J2
**[http://www.na-mic.org/Bug/view.php?id=1750 redesign](resolved)
**[http://www.na-mic.org/Bug/view.php?id=1751 mouse gesture for foreground/labelmap opacity] ([http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Slice_Viewer resolved])
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling](resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies](resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import](resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1783 crash on scene close](resolved) - Nicole
*OpenIGTLink IF module: Junichi

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian, checked it out. It seems that it is a limitation of the Otsu strategy in this case due to the lack of padding, probably we need a real brain extraction tool)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian fixed)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) is due to extreme values in the data - can this be clamped in the scalar estimation module? (assigned to Demian, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue] (fixed by Julien Finet)
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: Jim)
* Suggested Reorganization of the Diffusion menu (assigned to Demian, Done)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform [[Tests of Iowa Workshop tutorials]] (Benjamin/Sonia)

* Editor memory leaks and performance issues (Steve)

= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole
* [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer4 Diffusion tutorial

2012-03-12T16:26:25Z

Demian:

Feb.14 Diffusion meeting - Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian, checked it out. It seems that it is a limitation of the Otsu strategy in this case due to the lack of padding, probably we need a real brain extraction tool)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex, fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module (assigned to Demian, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]] (fixed by Julien Finet)

* Suggested Reorganization of the Diffusion menu (assigned to Demian, Done)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* DicomToNrrdConverter should be DICOM To NRRD Converter, and make the parameters of the Output sections visible on the GUI (assigned to Demian, done)
* Slicer crashes when saving the DTI tutorial Scene on Mac (assigned to Steve)

* Tutorial dataset: [[media:DiffusionMRI_tutorialData.zip‎| Slicer4 DTI dataset]]
* '''Suggested dead-line March 12, 2012''' ( preparation for the Iowa Workshop March 20-21)

Slicer4 Diffusion tutorial

2012-03-11T11:58:40Z

Demian:

Feb.14 Diffusion meeting - Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex, fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module (assigned to Demian, fixed, not committed yet)
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]] (fixed by Julien Finet)

* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* DicomToNrrdConverter should be DICOM To NRRD Converter, and make the parameters of the Output sections visible on the GUI (assigned to Demian)
* Slicer crashes when saving the DTI tutorial Scene on Mac (assigned to Steve)

* Tutorial dataset: [[media:DiffusionMRI_tutorialData.zip‎| Slicer4 DTI dataset]]
* '''Suggested dead-line March 12, 2012''' ( preparation for the Iowa Workshop March 20-21)

Slicer4 Diffusion tutorial

2012-03-11T11:57:34Z

Demian:

Feb.14 Diffusion meeting - Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex, fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module (assigned to Demian, fixed, not committed yet)
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]]

* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* DicomToNrrdConverter should be DICOM To NRRD Converter, and make the parameters of the Output sections visible on the GUI (assigned to Demian)
* Slicer crashes when saving the DTI tutorial Scene on Mac (assigned to Steve)

* Tutorial dataset: [[media:DiffusionMRI_tutorialData.zip‎| Slicer4 DTI dataset]]
* '''Suggested dead-line March 12, 2012''' ( preparation for the Iowa Workshop March 20-21)

Whole-Brain-Tractography-Wizard

2012-01-10T16:59:44Z

Demian: /* API support for workflows */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step
* Provide the user with the appropriate information about errors in the processing and/or missing data

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* [http://www.commontk.org/docs/html/classctkWorkflow.html ctkWorkflow]: State machine for the workflow
* [http://www.commontk.org/docs/html/classctkWorkflowStackedWidget.html ctkWorkflowStackedWidget]: UI class for the workflow
* [http://www.commontk.org/docs/html/classctkWorkflowWidgetStep.html ctkWorkflowWidgetStep]: Base class for each step of the workflow

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit. The class ctkWorkflow is a state machine that controls the sequence of steps that are to be executed. The next figure gives an example of a non-linear workflow that can be implemented through this method:
[[File:workflow_scheme.jpg | thumb | Example fo non-linear workflow]]

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

File:Workflow scheme.jpg

2012-01-10T16:57:34Z

Demian:

Whole-Brain-Tractography-Wizard

2012-01-10T16:57:19Z

Demian: /* API support for workflows */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step
* Provide the user with the appropriate information about errors in the processing and/or missing data

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* [http://www.commontk.org/docs/html/classctkWorkflow.html ctkWorkflow]: State machine for the workflow
* [http://www.commontk.org/docs/html/classctkWorkflowStackedWidget.html ctkWorkflowStackedWidget]: UI class for the workflow
* [http://www.commontk.org/docs/html/classctkWorkflowWidgetStep.html ctkWorkflowWidgetStep]: Base class for each step of the workflow

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit. The class ctkWorkflow is a state machine that controls the sequence of steps that are to be executed. The next figure gives an example of a non-linear workflow that can be implemented through this method:
[[File:workflow_scheme.jpg]]

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T16:13:57Z

Demian: /* API support for workflows */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step
* Provide the user with the appropriate information about errors in the processing and/or missing data

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* [http://www.commontk.org/docs/html/classctkWorkflow.html ctkWorkflow]: State machine for the workflow
* [http://www.commontk.org/docs/html/classctkWorkflowStackedWidget.html ctkWorkflowStackedWidget]: UI class for the workflow
* [http://www.commontk.org/docs/html/classctkWorkflowWidgetStep.html ctkWorkflowWidgetStep]: Base class for each step of the workflow

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T16:09:19Z

Demian: /* API support for workflows */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step
* Provide the user with the appropriate information about errors in the processing and/or missing data

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* [http://www.commontk.org/docs/html/classctkWorkflowStackedWidget.html ctkWorkflowStackedWidget]
* [http://www.commontk.org/docs/html/classctkWorkflowWidgetStep.html ctkWorkflowWidgetStep]

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T16:07:55Z

Demian: /* The Idea of a Wizard */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step
* Provide the user with the appropriate information about errors in the processing and/or missing data

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* ctkWorkflowStackedWidget
* ctkWorkflowWidgetStep

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T16:06:53Z

Demian: /* Obtaining the input from the Interface */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* ctkWorkflowStackedWidget
* ctkWorkflowWidgetStep

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T15:38:34Z

Demian: /* Obtaining the input from the Interface */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* ctkWorkflowStackedWidget
* ctkWorkflowWidgetStep

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
* The validation for each step to be implemented

====Declaring the Modules====
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

====Declaring Each Module's Fields====
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

====Validating Data for a Field====

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T15:36:15Z

Demian: /* API support for workflows */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* ctkWorkflowStackedWidget
* ctkWorkflowWidgetStep

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows:
WorkflowConfiguration

===Declaring the Modules===
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

===Declaring Each Module's Fields===
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

===Validating Data for a Field===

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T15:32:54Z

Demian: /* The Idea of a Wizard */

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* ctkWorkflowStackedWidget
* ctkWorkflowWidgetStep

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at
Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

===Declaring the Modules===
step_widget_files = [
'dicom2nrrd',
'dwi2dti',
'dti2fibers',
'done',
]

===Declaring Each Module's Fields===
step_widget_fields = {
'dicom2nrrd':[
('DICOMRadioButton', 'checked'),
('NRRDDWIRadioButton', 'checked'),
('inputDicomDirectory', 'directory'),
('outputVolume', 'currentPath'),
('useBMatrixGradientDirections','checked'),
('inputNRRDVolume','currentPath'),
],
'dwi2dti':[
('leastSquaresEstimation', 'checked'),
('weightedLeastSquaresEstimation', 'checked'),
('thresholdParameter', 'value'),
('removeIslands', 'checked'),
('applyMask', 'checked'),
],
'dti2fibers':[
('seedSpacing','value'),
('stoppingFAValue','value'),
('minimumFAValueSeed','value'),
('stoppingTrackCurvature','value'),
],
'done':[],
}

===Validating Data for a Field===

def validate_dicom2nrrd(self, step_object, data):
if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
data[step_object.id()],
wait_for_completion = True)
Validating the result of a CLI module
if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
file_path = data[step_object.id()]['outputVolume']
result_status, node = slicer.util.loadVolume(
file_path,
True
)
else:
result_status = False
Setting data for the next module
if result_status:
self.dwi_node = node
self.dwi_node_name = node.GetID()
Output errors if needed
if not result_status:
display_error("Error in DICOM to NRRD conversion, please see log")
return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
def onEntry(self, comingFrom, transitionType):
comingFromId = "None"
if comingFrom: comingFromId = comingFrom.id()
super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
if hasattr(self, 'onEntryCallback'):
self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
def onExit(self, goingTo, transitionType):
goingToId = "None"
if goingTo: goingToId = goingTo.id()
super(GeneralizedStep, self).onExit(goingTo, transitionType)
if hasattr(self, 'onExitCallback'):
self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
def validate(self, desiredBranchId):
validationSuceeded = True
if hasattr(self, 'validateCallback'):
validationSuceeded = self.validateCallback(self, desiredBranchId)
super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)

Whole-Brain-Tractography-Wizard

2012-01-10T15:24:56Z

Demian: /* Obtaining the input from the Interface */

Whole-Brain-Tractography-Wizard

2012-01-10T15:22:49Z

Demian: /* The Idea of a Wizard */

Whole-Brain-Tractography-Wizard

2012-01-10T15:05:29Z

Demian: /* The Idea of a Wizard */

Whole-Brain-Tractography-Wizard

2012-01-10T15:04:32Z

Demian: Created page with '=The Idea of a Wizard= Make a simple set of steps that will guide the user through a complex process <gallery> Image:dicom2dti.png|[DICOM to DWI] Image:dwi2dti.png|[DWI to DTI] …'

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>

AHM2012-Slicer-Overview-and-Migration

2012-01-10T14:57:04Z

Demian: /* Module Creation and Migration */

[[AHM_2012#Agenda|Back to AHM Schedule]]

'''Tuesday, January 10, 2012 8 to 10am'''
This session is for all developers planning to migrate existing slicer3 modules to slicer4 or start a new project from scratch in slicer4.

==Overview and Architecture==
* Steve (10 minutes) [[AHM2012-Slicer-Introduction|Introduction]]
** Capabilities
** Release Schedule
** Goals
** Ongoing Slicer4 projects and collaborations (NAC, NCIGT, CTK, Supplements...)
* Jc (10 minutes) [[AHM2012-Slicer-Architecture|Architecture]]
** Modularization Object Specialization
*** Qt Widgets <- CTK Widgets <- MRML Widgets <- Slicer Widgets
*** vtkObject <- MRMLLogic <- Module Logic
** Displayable Managers
** Views and Layouts

== Module Creation and Migration ==
* Steve (5 minutes) [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/ModuleWizard Module Wizard]
* Jim (10 minutes)
** [[Media:Slicer4 CLI.ppt|CLI Modules]]
** Creating a CLI from existing C++ code
** Migrating CLI Modules to ITK version 4
* J2: Loadable Modules (20 minutes)
** Structure of a Loadable Module
** Specialization of Module Classes
** Integration with Designer
* Steve: [[AHM2012-Slicer-Python|Scripted Modules and Python Console]] (20 minutes)
** What is accessible via python
** Using the console (See [http://vimeo.com/33236047 J2's excellent demo video])
** Writing a Scripted Module
*** PythonQt interface
*** Logic with vtk/vtkITK/CLI Modules
*** Accessing MRML Data via numpy
** Refining the code and UI with slicerrc
** Limitations of python
* Demian: [[Whole-Brain-Tractography-Wizard|Whole Brain Tractography]] (10 minutes)
** Python wizard example
** Discussion of interactions among modules
** How to build on the dMRI module

== Testing Infrastructure ==
* Benjamin (20 minutes)
** Writing and Running Module Tests
** Creating GUI Tests
** What your modules/widgets need to do in order to support automated UI testing
== Documentation ==
* Jc (10 minutes) [[AHM2012-Slicer-Documentation|Documentation]]
** How to write end user documentation for your module
** Source code naming and documentation style
** CMake documentaiton

== Extensions ==
* Jc (20 minutes) [[AHM2012-Slicer-Extension|Extension]]
** Writing an s4ext file
** Testing your extension
** How users will access your extension

File:Fibers.png

2011-06-24T14:40:33Z

Demian:

2011 Summer Project Week Finishing details on the workflows DICOM full brain tractography peritumoral

2011-06-24T14:40:06Z

Demian:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>

==Key Investigators==
* BWH: Demian Wasserman

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

<h3>Objective</h3>
Finishing details on the workflows: DICOM->Full brain tractography / peritumoral
</div>

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

<h3>Approach, Plan</h3>
Start by finishing the DICOM->Full brain tractography workflow. Evaluate improvements on the interface and coding on the workflow. Then move to the peritumoral use-cases and its implementation

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

<h3>Progress</h3>
The DICOM to Full brain tractography is almost ready. There are issues to be solved with object lifetime in the python-embedded in slicer.
</div>

2011 Summer Project Week Nifti Support for Diffusion Tensor Images

2011-06-24T14:09:44Z

Demian:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Demian Wasserman, Nicole Aucoin, Sonia Pujol

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

<h3>Objective</h3>
Add support for reading and writing DTI files in Nifti format
</div>

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

<h3>Approach, Plan</h3>
The format I/O is already implemented in ITK, change the calls to the vtkNRRDReader and vtkNRRDWriter to the corresponding ITK ones in the pertinent slicer files.

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

<h3>Progress</h3>
Worked with Nicole on the support of slicer, however the inner structure is not simple to figure out. Sonia, independently developed a CLI application for NIFTI<->NRRD DTI conversion
</div>

2011 Summer Project Week Finishing details on the workflows DICOM full brain tractography peritumoral

2011-06-24T14:08:21Z

Demian:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
</gallery>

==Key Investigators==
* BWH: Demian Wasserman

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

<h3>Objective</h3>
Finishing details on the workflows: DICOM->Full brain tractography / peritumoral
</div>

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

<h3>Approach, Plan</h3>
Start by finishing the DICOM->Full brain tractography workflow. Evaluate improvements on the interface and coding on the workflow. Then move to the peritumoral use-cases and its implementation

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

<h3>Progress</h3>
The DICOM to Full brain tractography is almost ready. There are issues to be solved with object lifetime in the python-embedded in slicer.
</div>

2011 Summer Project Week Finishing details on the workflows DICOM full brain tractography peritumoral

2011-06-24T14:07:16Z

Demian:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
</gallery>

==Key Investigators==
* BWH: Demian Wasserman

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

<h3>Objective</h3>
Finishing details on the workflows: DICOM->Full brain tractography / peritumoral
</div>

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

<h3>Approach, Plan</h3>
Start by finishing the DICOM->Full brain tractography workflow. Evaluate improvements on the interface and coding on the workflow. Then move to the peritumoral use-cases and its implementation

</div>

File:Dti2fibers.png

2011-06-24T14:07:01Z

Demian:

2011 Summer Project Week Finishing details on the workflows DICOM full brain tractography peritumoral

2011-06-24T14:05:34Z

Demian:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fiers.png|[DTI to Fibers]
</gallery>

==Key Investigators==
* BWH: Demian Wasserman

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

<h3>Objective</h3>
Finishing details on the workflows: DICOM->Full brain tractography / peritumoral
</div>

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

<h3>Approach, Plan</h3>
Start by finishing the DICOM->Full brain tractography workflow. Evaluate improvements on the interface and coding on the workflow. Then move to the peritumoral use-cases and its implementation

</div>

2011 Summer Project Week Nifti Support for Diffusion Tensor Images

2011-06-24T14:04:56Z

Demian:

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Demian Wasserman

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

<h3>Objective</h3>
Add support for reading and writing DTI files in Nifti format
</div>

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

<h3>Approach, Plan</h3>
The format I/O is already implemented in ITK, change the calls to the vtkNRRDReader and vtkNRRDWriter to the corresponding ITK ones in the pertinent slicer files.

</div>

File:Dwi2dti.png

2011-06-24T14:02:41Z

Demian: