Difference between revisions of "RSNA2011 Planning"
From NAMIC Wiki
(→People) |
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/") |
||
| (45 intermediate revisions by 4 users not shown) | |||
| Line 6: | Line 6: | ||
!Nb !!DEMO !! Datasets !! Notes !! Tools !! Slicer Modules | !Nb !!DEMO !! Datasets !! Notes !! Tools !! Slicer Modules | ||
|- | |- | ||
| − | ||1 ||Data Loading and Visualization || [ | + | ||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 [ | + | ||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 | ||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 | ||
| Line 16: | Line 16: | ||
||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 | ||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 | ||
|- | |- | ||
| − | ||6|| Traumatic Brain Injury Case Analysis || [ | + | ||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 |
|- | |- | ||
| − | ||7|| Radiotherapy || [ | + | ||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, |
|- | |- | ||
||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 | ||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 | ||
|- | |- | ||
| − | ||9|| Longitudinal analysis of meningioma growth | + | ||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 |
|- | |- | ||
| − | ||10||Image-guided prostate interventions || | + | ||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 |
| + | |- | ||
| + | ||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 | ||
| + | |- | ||
| + | ||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 | ||
| + | |- | ||
| + | ||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 | ||
|- | |- | ||
| − | |||
| − | |||
|} | |} | ||
| + | |||
| + | == 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== | ==Additional Material== | ||
(under development) | (under development) | ||
| − | * [[File:RSNA2010QIRRPoster.ppt]] poster | + | * [[File:RSNA2010QIRRPoster.ppt]] poster 2010 (ppt) |
| − | * [[File:RSNA2010QIRRPoster.pdf]] poster | + | * [[File:RSNA2010QIRRPoster.pdf]] poster 2010 (pdf) |
| − | * [[File: | + | * [[File:RSNA2011QIRR-LoopSlides.ppt]] Looping slide FINAL (ppt) |
| − | * [[File: | + | * [[File:RSNA2011QIRR-LoopSlides.pdf]] Looping slide FINAL (pdf) |
| − | * [[File: | + | * [[File:RSNA2011QIRRHandout.pptx]] handouts FINAL (pptx) |
| − | * [[File: | + | * [[File:RSNA2011QIRRHandout.pdf]] handouts FINAL (pdf) |
| + | * [[File:RSNA2011_16x9_slides_template.ppt]] 16x9 wide-screen slides template (courtesy Mike Halle) (ppt) | ||
==People== | ==People== | ||
* Ron Kikinis (Sunday through Tuesday) | * Ron Kikinis (Sunday through Tuesday) | ||
| − | * Sonia Pujol ( | + | * Sonia Pujol (Saturday through Friday) |
* Samira Farough (Saturday-Friday) | * Samira Farough (Saturday-Friday) | ||
* Andriy Fedorov (Saturday-Friday) | * Andriy Fedorov (Saturday-Friday) | ||
| − | * Steve Pieper (Wednesday | + | * Steve Pieper (Sunday through Wednesday?) |
* Randy Gollub (Sunday-Monday) | * Randy Gollub (Sunday-Monday) | ||
* Valerie Humblet (Sunday-Tuesday) | * 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 PlanningContents
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
- Documentation: We need all core modules reasonably well documented.
- Download pages: We do not have a lot of time left.
- See the 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)
