Difference between revisions of "Iowa-March-20-2012-Slicer-Workshop"

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Note: not all steps of the tutorials can be completed on 32bit operating systems due to memory limitations.
 
Note: not all steps of the tutorials can be completed on 32bit operating systems due to memory limitations.
  
== Data Instructions ==
+
== Workshop Instructions ==
 
* Step 1: (On the USB) Delete the directory Home->Data
 
* Step 1: (On the USB) Delete the directory Home->Data
 
* Step 2: Create a new directory called 'workshopData' in your home directory
 
* Step 2: Create a new directory called 'workshopData' in your home directory
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***To see when the downloads are complete, go to Firefox->Downloads to monitor the progress
 
***To see when the downloads are complete, go to Firefox->Downloads to monitor the progress
 
* Step 5: Unzip all archive datasets into 'workshopData'  
 
* Step 5: Unzip all archive datasets into 'workshopData'  
* Step 6: (Personal laptop) If not done already, download the correct Slicer4 binary file (see above)
+
* Step 6: (Personal laptop) If not done already, download the correct Slicer4 binary file (see '''Laptop Instructions''' above)
  
 
'''For USB participants''':  
 
'''For USB participants''':  
All tutorials except [[SimpleITK with Slicer]], will be using the 'Slicer' icon.
+
All tutorials except the SimpleITK tutorial, will be using the 'Slicer' icon.
The [[SimpleITK with Slicer]] will be using the 'Slicer-ITKv4' icon.
+
The SimpleITK tutorial will be using the 'Slicer-ITKv4' icon.
  
 
== Agenda  ==
 
== Agenda  ==
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|-
 
|-
 
| style="background:#efefef; color:#663300"| '''9:00-9:10 AM'''
 
| style="background:#efefef; color:#663300"| '''9:00-9:10 AM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Welcome (Ron Kikinis)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:2012-03-20-Iowa.pptx|3D Slicer, a Platform for Medical Image Computing]]  (Ron Kikinis)
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''9:10-9:55 AM'''
 
| style="background:#efefef; color:#663300"| '''9:10-9:55 AM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Slicer Basics (Sonia Pujol)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf |‎ Data Loading and 3D Visualization (Sonia Pujol)]]
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''9:55-10:45 AM'''
 
| style="background:#efefef; color:#663300"| '''9:55-10:45 AM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| DTI Tutorial: From DWI images to tracts (Sonia Pujol)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:DTI_Analysis_Tutorial_Slicer4.1_SoniaPujol.pdf‎ |DTI Tutorial: From DWI images to tracts (Sonia Pujol)]]
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''10:45-11:00 AM'''
 
| style="background:#efefef; color:#663300"| '''10:45-11:00 AM'''
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|-
 
|-
 
| style="background:#efefef; color:#663300"| '''11:00-12:15 PM'''
 
| style="background:#efefef; color:#663300"| '''11:00-12:15 PM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Neurosurgical Workflow (Sonia Pujol)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:WhiteMatterExplorationNeurosurgicalPlanning_Iowa_SoniaPujol.pdf ‎| Neurosurgical Workflow (Sonia Pujol)]]
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''12:15-1:30 PM'''
 
| style="background:#efefef; color:#663300"| '''12:15-1:30 PM'''
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|-
 
|-
 
| style="background:#efefef; color:#663300"| '''1:30-3:00 PM'''
 
| style="background:#efefef; color:#663300"| '''1:30-3:00 PM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| XNAT, Registration (Hans Johnson)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[Media:XNAT Tutorial Iowa HansJohnson.pdf|XNAT]], [[Media:Registration Tutorial Iowa HansJohnson.pdf|Registration]] (Hans Johnson)
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''3:00-3:30 PM'''
 
| style="background:#efefef; color:#663300"| '''3:00-3:30 PM'''
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|-
 
|-
 
| style="background:#efefef; color:#663300"| '''3:30-5:00 PM'''
 
| style="background:#efefef; color:#663300"| '''3:30-5:00 PM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| BWH QIN project: Quantitiative MRI of prostate cancer as a biomarker and guide for treatment: Presentation and Slicer demo (Andrey Fedorov)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[Media:Fedorov-QIN BWH use case.pdf|BWH QIN project: Quantitiative MRI of prostate cancer as a biomarker and guide for treatment: Presentation and Slicer demo (Andrey Fedorov)]]
 
|-
 
|-
 
| style="background:#FFFFFF; height:35px" colspan="3" |  
 
| style="background:#FFFFFF; height:35px" colspan="3" |  
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|-
 
|-
 
| style="background:#efefef; color:#663300"| '''09:00-10:30 AM'''
 
| style="background:#efefef; color:#663300"| '''09:00-10:30 AM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Programming in Slicer4: The Hello Python tutorial (Sonia Pujol/Andrey Fedorov/Demian Wassermann)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf‎| Programming in Slicer4 (Sonia Pujol)]] (Andriy Fedorov.Demian Wassermann)
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''10:30-10:45 AM'''
 
| style="background:#efefef; color:#663300"| '''10:30-10:45 AM'''
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|-
 
|-
 
| style="background:#efefef; color:#663300"| '''10:30 AM-11:30 AM'''
 
| style="background:#efefef; color:#663300"| '''10:30 AM-11:30 AM'''
| style="background:#FBF7BB; color:#522200" colspan="2"| SimpleITK with Slicer (Hans Johnson)
+
| style="background:#FBF7BB; color:#522200" colspan="2"| [[Media:SimpleITK with Slicer HansJohnson.pdf|SimpleITK with Slicer]] (Hans Johnson)
 
|-
 
|-
 
| style="background:#efefef; color:#663300"| '''11:30-12:00 PM'''
 
| style="background:#efefef; color:#663300"| '''11:30-12:00 PM'''
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|}
 
|}
  
[http://www.biomed-imaging.uiowa.edu/events.html Additional information]
+
*[http://www.biomed-imaging.uiowa.edu/events.html Additional information]
 
+
*[http://wiki.na-mic.org/Wiki/index.php/DTI_Tractography_Challenge_MICCAI_2012 DTI Challenge 2012]
'''Note''': 3rd Tuesday of the month 11AM until 1PM Iowa time is the time of monthly QIN working group TCONs (Image Analysis and Bioinformatics WGs). Some of the Iowa QIN members and Andrey Fedorov (BWH QIN) will need to attend those calls.
 
 
 
===BWH/Iowa QIN/AIM meeting (March 22)===
 
 
 
'''Agenda to be finalized by Milan Sonka, based on email communication of BWH and Iowa teams'''
 
  
Items of interest (Reinhard Beichel):
+
== Slicer4 Training Survey ==
*AIM - general overview + discussion (~1 h)
+
[http://www.surveymonkey.com/s/GZDXKXQ Click here to take the Slicer4 Training Survey]
* Discussion of BWH QIN use-case (~30 min)
 
* Discussion of Iowa QIN use-case - H&N (~1-2 h)
 
* Discussion of Iowa bioinformatics infrastructure setup: XNAT, databases, application to Iowa use cases (~30 min)
 
* AIM/Slicer project - overview + discussion: 2D/3D/4D objects, AIM toolkit concept vs. specific use-case implementation, ...  (~2h)
 
* Slicer 4 - module development, GUI design, future directions, development support, etc. (~1-2h; I'm not sure if this will be covered by other presentations and who would be the right person for this)
 
  
Andrey's sugested items
+
==BWH/Iowa QIN/AIM meeting==
<pre>
+
*Wednesday 3/21
1) Slicer 4.0 status and future (~30 min -- beyond what will be
+
** 1:00 pm - 5:00pm - 4016 SC, 1501-B SC - Informal discussions: It would be great to arrive at some consensus what to present as a preferred future steps to the U01 group on Th
covered by the general workshop program, Fedorov)
+
** 1:00pm - 4016 SC - get together, fine-tune schedule – ALL (Bauer, Beichel, Braun, Brown, Fedorov, Kikinis (?), Sonka, Wahle, Watharkar)
* what is currently available
+
** 1:15pm - AIM/Slicer - technical description, toolkit, DICOM SR relationships, status and plans – Fedorov, Beichel, Bauer + whoever else wants to participate. Slides: [[Image:Fedorov-Reporting-Slicer-Technical_description.pdf]]
* what is being actively developed and should be available soon
+
** 2:00pm - Slicer 4.0 status – Fedorov, BeichelBauer + whoever else wants to participate
  * it would help if Iowa collect specific set of questions according
+
** 2:40pm – 1501-B SC - Demo of Iowa Slicer usage – Beichel,  Bauer, Fedorov + whoever else wants to participate
to your needs
+
** 3:20pm - Slicer/AIM integration plans and status - Fedorov, Beichel, Bauer + whoever else wants to participate
2) AIM 3.0 overview (~1 hr, Fedorov + Iowa AIM experts)
+
**  4:00pm – 4016 SC - XNAT at Iowa – Wahle, Fedorov, Beichel, Braun, Brown + whoever else wants to participate
  * concepts and motivation for structured reporting
+
** 6:00 – dinner
  * AIM
 
* alternatives (e.g., DICOM SR)
 
* available support: user-level tools, toolkits
 
  * limitations
 
3) Slicer/AIM integration plans and status (~30 min, Fedorov)
 
* connection with the existing Slicer functionality
 
* supported annotation types
 
  * user-level workflow
 
  * limitations
 
  
4) BWH QIN use case (~30-45 min, Fedorov)
+
*Thursday 3/22
* research questions of our interest
+
** 9:00am – Radiation Oncology tour - Bayouth
* kinds of data being analyzed
+
**  9:30am -  Radiation Oncology conf. room 01600 PFP - Overview of Slicer, Overview of AIM, DICOM SR, linkages, etc. – Recommendation to Iowa U01 which way to go è outcome of Wed technical discussion – Fedorov (DICOM-SR and the role of Siemens?)
* processing workflows
+
**  10:15am - Discussion of BWH QIN use-case – Fedorov, Kikinis. Slides: [[Image:Fedorov-QIN_BWH_use_case.pdf]]. SlicerRt slides: [[Image:Lasso-SlicerRt-2012.pptx]]
* use of Slicer
+
**        10:45am - [http://wiki.na-mic.org/Wiki/index.php/Projects:QIN:3D_Slicer_Annotation_Image_Markup:Use_cases#Iowa:_Head_and_Neck_cancer Iowa QIN use-case] - H&N – Buatti, Beichel, Bayouth, Sunderland
  * applicability of AIM
+
**        11:30am – XNAT infrastructure, bioinformatics – outcomes of Wed discussions in light of the BWH and Iowa use cases – Braun, Brown
5) Iowa QIN use case (~1 hr, Iowa)
+
**        12:00            Lunch
* I would like to learn specifically about Iowa bioinformatics
+
**      1:00pm    AIM/DICOM-SR/Slicer project - more general overview + discussion - Fedorov
infrastructure (use of XNAT, other components)
+
**      2:00pm    Strategy for sharing data with BWH, Stanford – web page?, XNAT? - Fedorov, Beichel, Sunderland. Link to the QIN use cases summary page:
 +
**       3:00pm    Conclusions and next steps – Buatti, all
 +
**      3:30pm    Focused discussion for developers – address remaining and newly occurred problems based on Th program – Beichel, Fedorov
 +
**      4:30pm    Leave for airport
 +
**      6:20pm    Flight from CID
  
6) Brainstorming/discussion of AIM applicability, alternatives (~1hr)
 
  
6) Focused discussion for developers, as Reinhard suggested (~1-2 hr),
+
Slicer/AIM integration project main page: http://wiki.na-mic.org/Wiki/index.php?title=AIM_Annotations_integration_with_3DSlicer
need to coordinate with the general program events to avoid
 
duplication)
 
</pre>
 
  
 
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]
 
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]

Latest revision as of 15:12, 10 May 2012

Home < Iowa-March-20-2012-Slicer-Workshop
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Training Faculty

  • Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA
  • Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA
  • Demian Wasserman, Ph.D., Brigham and Women's Hospital, Boston, MA
  • Andrey Fedorov, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA
  • Hans Johnson, Ph.D., University of Iowa, Iowa City, IA
  • Vince Magnotta, Ph.D., University of Iowa, Iowa City, IA
  • David Welch, University of Iowa, Iowa City, IA
  • Eric Axelson, University of Iowa, Iowa City, IA
  • Joy Matsui, University of Iowa, Iowa City, IA

Logistics

Laptop Instructions

If you are bringing a laptop to the training session, please download and install the correct Slicer binary before the event. Also, consider downloading the datasets in the Data Instructions section below before the session.

You can find the correct pre-built executable for your system below:

Note: not all steps of the tutorials can be completed on 32bit operating systems due to memory limitations.

Workshop Instructions

  • Step 1: (On the USB) Delete the directory Home->Data
  • Step 2: Create a new directory called 'workshopData' in your home directory
  • Step 3: Download the 4 archive datasets on the workshop workstation (Right-click->Save Link As->Choose 'workshopData' directory->Okay)
  • Step 5: Unzip all archive datasets into 'workshopData'
  • Step 6: (Personal laptop) If not done already, download the correct Slicer4 binary file (see Laptop Instructions above)

For USB participants: All tutorials except the SimpleITK tutorial, will be using the 'Slicer' icon. The SimpleITK tutorial will be using the 'Slicer-ITKv4' icon.

Agenda

Time Tuesday, March 20, 2012
9:00-9:10 AM 3D Slicer, a Platform for Medical Image Computing (Ron Kikinis)
9:10-9:55 AM ‎ Data Loading and 3D Visualization (Sonia Pujol)
9:55-10:45 AM DTI Tutorial: From DWI images to tracts (Sonia Pujol)
10:45-11:00 AM Coffee Break
11:00-12:15 PM Neurosurgical Workflow (Sonia Pujol)
12:15-1:30 PM Lunch
1:30-3:00 PM XNAT, Registration (Hans Johnson)
3:00-3:30 PM Coffee Break
3:30-5:00 PM BWH QIN project: Quantitiative MRI of prostate cancer as a biomarker and guide for treatment: Presentation and Slicer demo (Andrey Fedorov)
Time Wednesday, March 21, 2012
09:00-10:30 AM Programming in Slicer4 (Sonia Pujol) (Andriy Fedorov.Demian Wassermann)
10:30-10:45 AM Coffee Break
10:30 AM-11:30 AM SimpleITK with Slicer (Hans Johnson)
11:30-12:00 PM Concluding Remarks and Feedback
1:00-5:00 PM DWI Discussion (Demian Wassermann) (By invitation only) QIN Discussion (Andriy Fedorov) (By invitation only)

Slicer4 Training Survey

Click here to take the Slicer4 Training Survey

BWH/Iowa QIN/AIM meeting

  • Wednesday 3/21
    • 1:00 pm - 5:00pm - 4016 SC, 1501-B SC - Informal discussions: It would be great to arrive at some consensus what to present as a preferred future steps to the U01 group on Th
    • 1:00pm - 4016 SC - get together, fine-tune schedule – ALL (Bauer, Beichel, Braun, Brown, Fedorov, Kikinis (?), Sonka, Wahle, Watharkar)
    • 1:15pm - AIM/Slicer - technical description, toolkit, DICOM SR relationships, status and plans – Fedorov, Beichel, Bauer + whoever else wants to participate. Slides: File:Fedorov-Reporting-Slicer-Technical description.pdf
    • 2:00pm - Slicer 4.0 status – Fedorov, Beichel, Bauer + whoever else wants to participate
    • 2:40pm – 1501-B SC - Demo of Iowa Slicer usage – Beichel, Bauer, Fedorov + whoever else wants to participate
    • 3:20pm - Slicer/AIM integration plans and status - Fedorov, Beichel, Bauer + whoever else wants to participate
    • 4:00pm – 4016 SC - XNAT at Iowa – Wahle, Fedorov, Beichel, Braun, Brown + whoever else wants to participate
    • 6:00 – dinner
  • Thursday 3/22
    • 9:00am – Radiation Oncology tour - Bayouth
    • 9:30am - Radiation Oncology conf. room 01600 PFP - Overview of Slicer, Overview of AIM, DICOM SR, linkages, etc. – Recommendation to Iowa U01 which way to go è outcome of Wed technical discussion – Fedorov (DICOM-SR and the role of Siemens?)
    • 10:15am - Discussion of BWH QIN use-case – Fedorov, Kikinis. Slides: File:Fedorov-QIN BWH use case.pdf. SlicerRt slides: File:Lasso-SlicerRt-2012.pptx
    • 10:45am - Iowa QIN use-case - H&N – Buatti, Beichel, Bayouth, Sunderland
    • 11:30am – XNAT infrastructure, bioinformatics – outcomes of Wed discussions in light of the BWH and Iowa use cases – Braun, Brown
    • 12:00 Lunch
    • 1:00pm AIM/DICOM-SR/Slicer project - more general overview + discussion - Fedorov
    • 2:00pm Strategy for sharing data with BWH, Stanford – web page?, XNAT? - Fedorov, Beichel, Sunderland. Link to the QIN use cases summary page:
    • 3:00pm Conclusions and next steps – Buatti, all
    • 3:30pm Focused discussion for developers – address remaining and newly occurred problems based on Th program – Beichel, Fedorov
    • 4:30pm Leave for airport
    • 6:20pm Flight from CID


Slicer/AIM integration project main page: http://wiki.na-mic.org/Wiki/index.php?title=AIM_Annotations_integration_with_3DSlicer

Back to NA-MIC Events