Difference between revisions of "RSNA2011 Planning"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(75 intermediate revisions by 5 users not shown)
Line 1: Line 1:
−
PAGE UNDER CONSTRUCTION
+
==Quantitative Imaging Reading Room==
−
 
 
 
Tentative list of demonstrations for the RSNA 2011 Slicer booth. Needs further development and testing
 
Tentative list of demonstrations for the RSNA 2011 Slicer booth. Needs further development and testing
−
 
+
'''Note: RSNA demo machines will need nvidia graphics cards to get GPU Volume Rendering'''
 
{| border="1"
 
{| border="1"
 
|- bgcolor="#abcdef"
 
|- bgcolor="#abcdef"
−
! DEMO !! Datasets !! Notes !! Tools
+
!Nb !!DEMO !! Datasets !! Notes !! Tools !! Slicer Modules
 +
|-
 +
||1 ||Data Loading and Visualization || [https://www.slicer.org/wiki/Documentation/4.1/Training#Slicer4_Data_Loading_and_3D_Visualization  3D Visualization data ] || [[media:Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf‎‎ ‎ | Slicer3Visualization Tutorial]]|| Compare View, Clipping, Save, Restore, Scene Views, Dicom studies sorting, Dicom networking (?) || Data, Volumes, Models, Scene Views
 +
|-
 +
||2||MRI-based topographic parcellation of human brain || [[Media:RSNA2010_EMS.zip | EM Segmenter Data]] || registration, segmentation [https://www.slicer.org/wiki/EMSegmenter-Tasks EMSegmenter Tasks] || EM Segmenter || EMSegmenter
 +
|-
 +
||3|| Volume Rendering #1 Head || [[Media:RSNA2010_OsirixManixDataset.zip  |  Head CT Scan (Osirix Manix Dataset)]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations || Volume Rendering, Annotations, Scene Views
 +
|-
 +
||4|| Volume Rendering #2 Abdomen|| [[Media:RSNA2010_OsirixPanoramixDataset.zip | Abdominal CT scan with AAA (Osirix Panoramix Dataset)]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations || Volume Rendering, Annotations, Scene Views
 
|-
 
|-
−
| Data Loading and Visualization || [http://www.slicer.org/slicerWiki/images/6/61/Slicer3VisualizationDataset.zip Slicer3Visualization Data]|| [[media:Slicer3_DataLoadingAndVisualization_UCSF2010_SoniaPujol.pdf‎‎ ‎ | Slicer3Visualization Tutorial]]|| Compare View, Clipping, Save, Restore, Scene Views, Dicom studies sorting, Dicom networking (?)
+
||5|| Volume Rendering #3 Thorax|| [[Media:RSNA2010_Lungs_Dataset.zip | Thoracic CT scan]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations || Volume Rendering, Annotations, Scene Views
 
|-
 
|-
−
| MRI-based topographic parcellation of human brain || [[Media:RSNA2010_EMS.zip | EM Segmenter Data]] || registration, segmentation [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks EMSegmenter Tasks] || EM Segmenter
+
||6|| Traumatic Brain Injury Case Analysis || [[Media:TBI-DemoScene-RSNA2011.zip | TBI Demo Data (UCLA)]] || [http://wiki.na-mic.org/Wiki/index.php/File:TBISegmentation_TutorialContestSummer2011.pdf TBI tutorial] || ABC Segmentation, Model Maker, Editor, Annotations || Data, ABC Segmentation, Model Maker, Editor, Annotations, Scene Views
 
|-
 
|-
−
| Volume Rendering #1 Head || [[Media:RSNA2010_OsirixManixDataset.zip  | Head CT Scan (Osirix Manix Dataset)]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations
+
||7|| Radiotherapy || [http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1828/popi-plan.tar.gz Plastimatch Dose Warping Data (MGH)] || [http://wiki.na-mic.org/Wiki/index.php/File:PlastimatchDoseWarping_TutorialContestSummer2011.pdf Plastimatch Tutorial] || Plastimatch, DVH extension (Csaba) || Data, Plastimatch Extension: DICOM/DICOM-RT Import, DICOM/DICOM-RT Export, B-Spine Deformable Registration,XFORMWARP Warping with transform Transforms,  
 
|-
 
|-
−
| Volume Rendering #2 Abdomen|| [[Media:RSNA2010_OsirixPanoramixDataset.zip | Abdominal CT scan with AAA (Osirix Panoramix Dataset)]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations
+
||8|| White matter exploration for neurosurgical planning || [[media:WhiteMatterExplorationData.zip‎| White Matter Exploration dataset]]  || [[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ |Neurosurgical planning Tutorial]] || Diffusion ( Estimation, Tractography, Fiducial Seeding), Editor, Model Maker || Data, Volumes, Editor, Fiducials, Diffusion Tensor Estimation, Diffusion Tensor Scalar Measurements, Labelmap Seeding, Tractography Fiducial Seeding, Tractography Display
 
|-
 
|-
−
| Volume Rendering #3 Thorax|| [[Media:RSNA2010_Lungs_Dataset.zip | Thoracic CT scan]] || show cropping, transfer functions, GPU, slice composite view, Annotations || Volume Rendering and Annotations
+
||9|| Longitudinal analysis of meningioma growth||  Change Tracker Data are part of the tutorial || [http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf Change Tracker Tutorial] || Change Tracker, Compare Views, Volume Rendering, CropVolume, Crosshairs, BRAINSFit || Change Tracker, Volume Rendering, BRAINSFit, CropVolume
 
|-
 
|-
−
| Traumatic Brain Injury Case Analysis || [http://wiki.na-mic.org/Wiki/index.php/File:TBISegmentationData_TutorialContestSummer2011.zip TBI data (UCLA)] || [http://wiki.na-mic.org/Wiki/index.php/File:TBISegmentation_TutorialContestSummer2011.pdf TBI tutorial] || ABC Segmentation, Model Maker, Editor, Annotations
+
||10||Image-guided prostate interventions || [[media:RSNA2011_Prostate.zip | Prostate Data updated for Slicer4, in progress]] ''Can load RSNA2010 demo scene, mostly working, see [http://www.na-mic.org/Bug/view.php?id=1523]''|| Pre-op/Intra-op registration; [http://www.na-mic.org/Wiki/index.php/Slicer4:Prostate_mpMRI_review_use_case Use Case Demo] [[media:RSNA2010_Prostate.zip | Prostate Data]]  || Linked Viewing || Annotations, Models, Crosshairs, CompareViews
 
|-
 
|-
−
| Radiotherapy || [http://wiki.na-mic.org/Wiki/index.php/File:PlastimatchDoseWarpingData_TutorialContestSummer2011.tar.gz Plastimatch Dose Warping Data (MGH)]|| [http://wiki.na-mic.org/Wiki/index.php/File:PlastimatchDoseWarping_TutorialContestSummer2011.pdf Plastimatch Tutorial] || Plastimatch, DVH extension (Csaba)
+
||11|| Brain Atlas || [http://www.na-mic.org/publications/item/view/2037 NAC Multi-modality MRI-based Atlas of the Brain] || Work in progress  - atlases are being updated|| Linked Viewing || Data, Volumes, Models, Scene Views
 
|-
 
|-
−
| White matter exploration for neurosurgical planning || [[media:WhiteMatterExplorationData.zip‎| White Matter Exploration dataset]]  || [[media:WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf‎ |Neurosurgical planning Tutorial]] || Diffusion ( Estimation, Tractography, Fiducial Seeding), Editor, Model Maker
+
||12||  Abdomen Atlas|| [http://www.slicer.org/publications/item/view/1953 Knee Atlas] || Work in progress  - atlases are being updated|| Linked Viewing || Data, Volumes, Models, Scene Views
 
|-
 
|-
−
| Longitudinal analysis of meningioma growth (tentative)|| Change Tracker Data are part of the tutorial || [http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf Change Tracker Tutorial] || Change Tracker, Compare Views, Volume Rendering
+
||13|| Knee Atlas Atlas || [http://www.slicer.org/publications/item/view/1918 Abdominal Atlas]|| Work in progress  - atlases are being updated|| Linked Viewing || Data, Volumes, Models, Scene Views
 
|-
 
|-
−
|Image-guided prostate interventions || TBD || Pre-op/Intra-op registration; [http://www.na-mic.org/Wiki/index.php/Slicer4:Prostate_mpMRI_review_use_case Use Case Demo] || Linked Viewing
 
−
|
 
 
|}
 
|}
 +
 +
== Some of the issues found with the demos ==
 +
* EMS: use without atlas only
 +
* Manix VR: minor issues with VR [http://www.na-mic.org/Bug/view.php?id=1576]
 +
* Prostate dataset demo: not ready yet
 +
* Radiotherapy: where are Plastimatch tools ? They used to be extensions in Slicer3, I don't think they are available in Slicer4
 +
 +
== List of Slicer Modules involved in RSNA tutorials & demos==
 +
 +
*Data
 +
*Welcome to Slicer
 +
*Volumes
 +
*Models
 +
*Scene Views
 +
*Annotations
 +
*Volume Rendering
 +
*Editor
 +
*Model Maker
 +
*Diffusion Tensor Estimation
 +
*Diffusion Tensor Scalar Measurements
 +
*Tractography Labelmap Seeding
 +
*Tractography Fiducial Seeding
 +
*Tractography Display
 +
*BRAINSTools
 +
*Change Tracker
 +
*CropVolume
 +
*Extensions:
 +
**ABC
 +
**Plastimatch
 +
**EMSegmenter
 +
**Skull Stripper
 +
 +
==Slicer4 Punchlist==
 +
*Unresolved
 +
**em segmenter: task simple brain segmentation works, but slowly.
 +
**ctkDICOMwidget
 +
**skull stripper
 +
**DWI to full brain tractography still does not work on mac
 +
**Data module does not refresh after drag and drop. [http://www.na-mic.org/Bug/view.php?id=1510]
 +
*Volume rendering: We have a plan
 +
*Resolved
 +
**brainsfit
 +
**changetracker
 +
**Center 3D view does not work properly [http://www.na-mic.org/Bug/view.php?id=1490]
 +
**Render performance [http://www.na-mic.org/Bug/view.php?id=1519]: This is a big issue
 +
 +
 +
*Documentation: We need all [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0#Core_Modules core modules] reasonably well documented.
 +
*Download pages: We do not have a lot of time left.
 +
*See the [[Events:Slicer4-Review-07-2011#RSNA_2011_Targeted_Objectives|plan in July 2011]]
 +
 +
==Additional Material==
 +
(under development)
 +
* [[File:RSNA2010QIRRPoster.ppt]] poster 2010  (ppt)
 +
* [[File:RSNA2010QIRRPoster.pdf]] poster 2010  (pdf)
 +
* [[File:RSNA2011QIRR-LoopSlides.ppt]] Looping slide FINAL (ppt)
 +
* [[File:RSNA2011QIRR-LoopSlides.pdf]] Looping slide FINAL (pdf)
 +
* [[File:RSNA2011QIRRHandout.pptx]] handouts FINAL (pptx)
 +
* [[File:RSNA2011QIRRHandout.pdf]] handouts FINAL (pdf)
 +
* [[File:RSNA2011_16x9_slides_template.ppt]] 16x9 wide-screen slides template (courtesy Mike Halle) (ppt)
 +
 +
==People==
 +
* Ron Kikinis (Sunday through Tuesday)
 +
* Sonia Pujol (Saturday through Friday)
 +
* Samira Farough (Saturday-Friday)
 +
* Andriy Fedorov  (Saturday-Friday)
 +
* Steve Pieper (Sunday through Wednesday?)
 +
* Randy Gollub (Sunday-Monday)
 +
* Valerie Humblet (Sunday-Tuesday)
 +
* Kitware ( Julien Finet)
 +
 +
[http://www.cdash.org/slicer4/viewFiles.php?buildid=5120 Slicer4RSNA Windows]
 +
 +
[[RSNA2011_Slicer4| RSNA2011 material]]
  
 
[http://www.na-mic.org/Wiki/index.php?title=Events:Slicer4-Review-07-2011 Back to Slicer4 Review]
 
[http://www.na-mic.org/Wiki/index.php?title=Events:Slicer4-Review-07-2011 Back to Slicer4 Review]

Latest revision as of 17:15, 10 July 2017

Home < RSNA2011 Planning

Quantitative Imaging Reading Room

Tentative list of demonstrations for the RSNA 2011 Slicer booth. Needs further development and testing Note: RSNA demo machines will need nvidia graphics cards to get GPU Volume Rendering

Nb DEMO Datasets Notes Tools Slicer Modules
1 Data Loading and Visualization 3D Visualization data Slicer3Visualization Tutorial Compare View, Clipping, Save, Restore, Scene Views, Dicom studies sorting, Dicom networking (?) Data, Volumes, Models, Scene Views
2 MRI-based topographic parcellation of human brain EM Segmenter Data registration, segmentation EMSegmenter Tasks EM Segmenter EMSegmenter
3 Volume Rendering #1 Head Head CT Scan (Osirix Manix Dataset) show cropping, transfer functions, GPU, slice composite view, Annotations Volume Rendering and Annotations Volume Rendering, Annotations, Scene Views
4 Volume Rendering #2 Abdomen Abdominal CT scan with AAA (Osirix Panoramix Dataset) show cropping, transfer functions, GPU, slice composite view, Annotations Volume Rendering and Annotations Volume Rendering, Annotations, Scene Views
5 Volume Rendering #3 Thorax Thoracic CT scan show cropping, transfer functions, GPU, slice composite view, Annotations Volume Rendering and Annotations Volume Rendering, Annotations, Scene Views
6 Traumatic Brain Injury Case Analysis TBI Demo Data (UCLA) TBI tutorial ABC Segmentation, Model Maker, Editor, Annotations Data, ABC Segmentation, Model Maker, Editor, Annotations, Scene Views
7 Radiotherapy Plastimatch Dose Warping Data (MGH) Plastimatch Tutorial Plastimatch, DVH extension (Csaba) Data, Plastimatch Extension: DICOM/DICOM-RT Import, DICOM/DICOM-RT Export, B-Spine Deformable Registration,XFORMWARP Warping with transform Transforms,
8 White matter exploration for neurosurgical planning White Matter Exploration dataset Neurosurgical planning Tutorial Diffusion ( Estimation, Tractography, Fiducial Seeding), Editor, Model Maker Data, Volumes, Editor, Fiducials, Diffusion Tensor Estimation, Diffusion Tensor Scalar Measurements, Labelmap Seeding, Tractography Fiducial Seeding, Tractography Display
9 Longitudinal analysis of meningioma growth Change Tracker Data are part of the tutorial Change Tracker Tutorial Change Tracker, Compare Views, Volume Rendering, CropVolume, Crosshairs, BRAINSFit Change Tracker, Volume Rendering, BRAINSFit, CropVolume
10 Image-guided prostate interventions Prostate Data updated for Slicer4, in progress Can load RSNA2010 demo scene, mostly working, see [1] Pre-op/Intra-op registration; Use Case Demo Prostate Data Linked Viewing Annotations, Models, Crosshairs, CompareViews
11 Brain Atlas NAC Multi-modality MRI-based Atlas of the Brain Work in progress - atlases are being updated Linked Viewing Data, Volumes, Models, Scene Views
12 Abdomen Atlas Knee Atlas Work in progress - atlases are being updated Linked Viewing Data, Volumes, Models, Scene Views
13 Knee Atlas Atlas Abdominal Atlas Work in progress - atlases are being updated Linked Viewing Data, Volumes, Models, Scene Views

Some of the issues found with the demos

  • EMS: use without atlas only
  • Manix VR: minor issues with VR [2]
  • Prostate dataset demo: not ready yet
  • Radiotherapy: where are Plastimatch tools ? They used to be extensions in Slicer3, I don't think they are available in Slicer4

List of Slicer Modules involved in RSNA tutorials & demos

  • Data
  • Welcome to Slicer
  • Volumes
  • Models
  • Scene Views
  • Annotations
  • Volume Rendering
  • Editor
  • Model Maker
  • Diffusion Tensor Estimation
  • Diffusion Tensor Scalar Measurements
  • Tractography Labelmap Seeding
  • Tractography Fiducial Seeding
  • Tractography Display
  • BRAINSTools
  • Change Tracker
  • CropVolume
  • Extensions:
    • ABC
    • Plastimatch
    • EMSegmenter
    • Skull Stripper

Slicer4 Punchlist

  • Unresolved
    • em segmenter: task simple brain segmentation works, but slowly.
    • ctkDICOMwidget
    • skull stripper
    • DWI to full brain tractography still does not work on mac
    • Data module does not refresh after drag and drop. [3]
  • Volume rendering: We have a plan
  • Resolved
    • brainsfit
    • changetracker
    • Center 3D view does not work properly [4]
    • Render performance [5]: This is a big issue


Additional Material

(under development)

People

  • Ron Kikinis (Sunday through Tuesday)
  • Sonia Pujol (Saturday through Friday)
  • Samira Farough (Saturday-Friday)
  • Andriy Fedorov (Saturday-Friday)
  • Steve Pieper (Sunday through Wednesday?)
  • Randy Gollub (Sunday-Monday)
  • Valerie Humblet (Sunday-Tuesday)
  • Kitware ( Julien Finet)

Slicer4RSNA Windows

RSNA2011 material

Back to Slicer4 Review

Retrieved from "https://www.na-mic.org/w/index.php?title=RSNA2011_Planning&oldid=97170"