Difference between revisions of "Dissemination:Workshop May 26"

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Feedback from Users about clinical use cases, and feature requests for Slicer:
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== Some Pictures from the Workshop ==
  
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Steve et al, please divide this list into two separate lists- one for Slicer development and one for tutorial/training development (e.g. the functionality is already there, just needs to be taught).
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* [[Media:Panorama1.jpg| a "stitched" mosaic]]
  
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# Streamline process of MaskStat/Cast for Scalar Volumes (rewrite VolumeMath)
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== Workshop Goals ==
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# Compute FA along fiber
 
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# Telegraphing markers along orthogonal views (Brains feature)
 
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# Analyze step editor (can save set of steps for future use)
 
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# Distortion correction of DWI (do it and be able to preview/verify it) - might belong in the pre-slicer space
 
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# Segmentation: missing the ability to backup (undo)
 
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# Keyboard shortcuts should be made available in tutorial
 
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# Synchronization of the three planes when you draw
 
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# Lots of interest in incorporating Brains Editor functionality in Slicer which is already being explored as a collaboration (nca@unm.edu, vincent_magnotta@uiowa.edu)
 
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# DTIStudio (S. Mori) program at JHU is worth looking at
 
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# Unify UI: EMSeg seeding is done using C-LMB, while in most other modules Fiducials feature is used for this (press P).
 
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# Fiducial feature appears only in 3D window.
 
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# Registration GUI needs to be made more uniform
 
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# NIfTI readers needed in ITK (format experts to possibly contact: John Ashburner at Dartmouth)
 
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# fmri module: discrepancy between 0 indexed (in the configuration parameters) vs. 1 indexed slices (in slicer)
 
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# fmri: can we load statistical maps (tmaps) from SPM and threshold it in Slicer? Note that t values can be positive/negative. Typically colorscales (cool/hot) are used. Slicer is most likely to be used for visualization/registration of these tmaps.
 
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# fmri: While displaying a tmap, the t-value should show up in the window, not the scaled value.
 
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# fmri: want to be able to click on a blob, and get stats on it (SPM gives max and eigenvectors of cluster).
 
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# visualization of fmri: be able to show Brodman areas
 
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# visualization: how to visualize aggregate data from multiple subjects
 
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# add information about slicer contact info to the tutorial slides
 
  
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== ''From Dartmouth Users:'' ==
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* To provide hands-on training in NAMIC Toolkit applications to clinical researchers.
 +
* To establish contact between NAMIC Tookit experts (users and developers) and clinical researchers of the NAMIC community.
 +
* To obtain feedback on how the NAMIC Toolkit applications satisfy the needs of the clinical research being carried out in NAMIC
  
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==== Slicer: Suggestions for Features/Functionality ====
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<br />
  
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# would be to have friendly data output format, e.g., deposit volume measures in an excel spreadsheet with ID
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== Workshop Logistics ==
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# "loop" modules for processing multiple subjects in the same way
 
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# Paint function for volumetrics
 
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# Lesions to normal tissue, visualizations that would be helpful, tools used in structure tracing, features from other programs that are desireable.
 
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# group data?
 
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# more streamlined as far as memory and processing to prevent crashes
 
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# the website specifies the minimum requirements for the computer system, but we would like you to specify "recommended" specs as well
 
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# time series analysis - SPM & Slicer
 
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# shrink wrap (from Alice)
 
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#* [John MacDonald prefers brush system below to this feature - it doesn't work well]
 
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# macros
 
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# scripting language
 
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# group data?
 
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# header checking (automatic parameters)
 
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# coronal scrolling
 
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# output animations as mp4, avi
 
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# option to browse and mark all 3 planes to update the others OR lock any one of the planes
 
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# T1 and T2 on the same time (2 registers) -- to get one volume
 
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# bump margins -- automatically changes the overlap for structures next to each other
 
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# Add manual "paint-brush" editor, with
 
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#* Various sized "brushes" (typically circles, smallest is 1-pixel); these are bi-modal: default mode paints, alt-mode erases. Brush size selected by function or number keys.
 
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#* Brushes should be adjustably translucent; painted color should also be adjustably translucent
 
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#* Modal paint-to-ROI, paint over ROI switch [probably multi paint overlays required to avoid conflicts; eg, if I start tracing lesions I create a lesion overlay space that does not conflict with other overlays; but another time I access an automated model overlay to edit]
 
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#* Modal intensity-capture: a) capture all under brush, b) capture only between threshhold levels
 
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#* Auto-smoothing command key/button
 
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#* Command to auto-close current ROI color, if fully encircled
 
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#* 3-D model build option for visualisation
 
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#* Calculations of ROI areas, dimensions, overall volumes step in tabed text format.
 
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#* Fine brush doubles as drawing tool???
 
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#* Hide/show toggle
 
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#* Requires _large_ interpolated views
 
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#* Ideally, user-definable presets of color groups with names, intensity approximations (later ability to correlate with other objects?).
 
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#* Output options: analyze file if bitmapped overlays, open-GL views and/or quicktime movie, built-in screen/window captures?
 
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#* Outer fringe stuff
 
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#*# ability to segment everyother slice and iterpolate slices in between?
 
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#* Questions:
 
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#*# Is there a need to differentiate a "mask" from an ROI?
 
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# Is there a way to do skull-stripping in Slicer at this point? We probably need in the future.
 
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# Could use function that would normalize image intensity ranges in irregular scans (esp. FLAIRS).
 
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# Would like to be able to place "marks" and see them in all three views
 
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# We presently have a realignment phase where several alignments are made (using Brains); would like to be able to do this in slicer with precision, and set origin point at the same time. Output as analyze files.
 
  
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==== Dissemination Event: Likes and Improvements/Additions ====
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* [[Dissemination:Workshop_May26-27_2005_Logistics|Location, Hotels, Airport Information, and Driving Directions]]
 +
* [[Dissemination:Workshop_May26-27_2005_Feedback|Attendee Feedback -- Attendees, please provide feedback here.]]
  
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===== ''Likes'' =====
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== Workshop Participants ==
  
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# We thought there would be problems with the different ability levels but they made it really easy for everyone to participate at an advanced level.
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* [[Dissemination:Workshop_May26-27_2005_Attendee_List|List of Participants]]
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# RAs from Marty Shenton's lab were very helpful in getting everyone caught up/solving problems
 
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# The slides were extremely helpful, especially with the screen captures so that everyone could see what the menus look like, etc.
 
  
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===== ''Suggestions'' =====
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== Preparation for Workshop -- ''Important Information for all attendees'' ==
  
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# Could have been more clear about what we actually needed for the session -- it took 2-3 hours over the workshop that people were getting data, that could have been used for the actual workshop. Need very detailed instructions as to where to put things, in what folder, etc.
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All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.
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# Would have been nice to have a smaller group -- especially in the future for more advanced workshops, and maybe the advanced workshops could focus on one area (fMRI vs DTI vs structural)
+
 
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# The feature about bringing your problems and data is desireable, perhaps data with problems so everyone can work through the problem-solving
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# Mailing List: Please ensure that you are on the mailing list [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-dissemination namic-dissemination].
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# "Behind-the-scenes" workshop (soon) to understand what is happening, why certain parameters are chosen
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# Software Installation: Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to the computer you will be bringing to the workshop, the tutorial guide for Slicer, the generic sample data set. This material is located in [[Slicer:Slicer2.5_Getting_Started|Slicer 2.5 Getting Started: Software & Sample Data ]].
 +
# Also, go to this link [[Training:Resources_and_Information|Loading-Dartmouth-NAMIC-DTI]] and download the powerpoint presentation that will guide you through the process of accessing Dartmouth specific data sets from the BIRN portal.
 +
 
 +
* '''The documentation refers to a protocol file to be obtained from Dartmouth - this available here. Save [[Media:NAMIC-Dartmouth-2b12g-Volume.doc| this protocol file]] as slicer2/Modules/vtkDTMRI/data/NAMIC-Dartmouth-2b12g-Volume''' in your slicer distribution.
 +
 
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# Data to Download:
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## Get the Tutorial Data with Dicom pointed to at the getting started page [http://share.spl.harvard.edu/share/birn/public/software/tutorial-with-dicom.zip [1]]
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## Get this extra set of interoperative data [[Media:Mrt-images.zip| mrt-images.zip]]
 +
## Get this data for testing registrations [[Media:Reg-sample.zip|reg-sample.zip]]
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## Get this data for fMRI demonstrations: [[Media:FMRI-demo-short.zip|short sequence for small memory machines]] [[Media:FMRI-demo-long.zip|longer data sequence.]]
 +
## Get this data for DTI demonstrations: [http://slicerl.bwh.harvard.edu/tmp/dtiviz.tar.gz dtiviz.tar.gz ]
 +
 
 +
<br /> We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by NAMIC Tookit experts. We will focus on how to use the application(s) during the workshop, so please do the install before you arrive.
 +
 
 +
== Agenda ==
 +
 
 +
Note: The computer room does not permit food, so we will be wandering downstairs to the [[http://www.dartmouth.edu/~dds/text/novackcafe.shtml|Novak Cafe]] for lunch and coffee breaks.
 +
 
 +
=== '''Day 1:noon-6pm''' ===
 +
 
 +
* 12:00 - 12:15 Goals of Workshop, Introduction to the NAMIC Kit, and People-Introductions (Ron Kikinis)
 +
* 12:15 - 1:00 Lunch (If you had trouble downloading and/or installing Slicer 2.5 or the sample data sets, we will help you- but don't come hungry because you will miss lunch!)
 +
* Confirm user accounts and data download
 +
* '''1pm-5pm End-User Slicer Training'''
 +
** Introduction (Steve Pieper) [[Media:Slicer-Overview.ppt| Overview Slides for Background (will not be presented in detail)]]
 +
** 1:00 - 2:00 Hands-on Session 1 (Sonia Pujol, RLG-B/U) [[Media:SlicerTraining-NAMIC-1.ppt|Hands-on Session 1 Slides]], ([[Media:Laura_NAMIC_slide.ppt|Laura intro]],[[Media:AdamCohenNAMIC.ppt|Adam intro]], [[Media:Mark_NAMIC_slide.ppt|Mark intro]])
 +
*** User Interface Overview
 +
*** Loading Data (Volumes, Models, Scenes)
 +
*** Viewing Images and Models (Structural MRI)
 +
* 2:00 - 2:15 User Experiences and Applications - Segmentation (Sylvain Bouix) [[Media:01-IntroSegmentation.ppt|(slides)]]
 +
* Hands-on Session 2 (Steve Pieper and Sylvain Bouix) [[Media:Slicer_Segmentation_Tutorial.ppt|(slides)]]
 +
** Manual Segmentation with the Editor (SP)
 +
** Model Making (SP)
 +
* 3:00 - 3:15 Break
 +
* 3:15 - 4:45 Break
 +
** Segmentation Foundations (Sandy Wells) [[Media:NAMICSegFoundations.ppt|(slides)]]
 +
** Voxel Classification with EMSegment (SB) [[Media:02-EMmanual.ppt|(slides)]]
 +
** Level Set Segmentation (SB) [[Media:03-LevelSet.ppt|(slides)]]
 +
* 4:45 - 6:15 Hands-on Session 3 (Steve Pieper) [[Media:Volume-Registration.ppt|Registration Slides]]
 +
** Manual Registration (SP)
 +
** Registration Foundations (Sandy Wells) [[Media:NAMICSReg-IntroEtc-sw.ppt|(slides)]]
 +
** Automatic Registration (SP)
 +
*** ITK-based Rigid Registration, Resampling Volumes (SP)
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*** vtkAG - nonrigid Registration (SP)
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** Atlas Based Segmentation with vtkAG and EMSegment (SB) [[Media:04-AtlasEMSeg.ppt|(slides)]]
 +
** Measuring Image Statistics (SB) [[Media:05-MeasureVol.ppt|(slides)]]
 +
 
 +
=== ''' Day 2:8am-3pm ''' ===
 +
 
 +
* 8:00 - 8:15 Review and Questions
 +
* 8:15 - 8:45 Introduction to DTI (Sylvain Bouix, Mark Dreusicke) [[Media:06-IntroDTI.ppt|(slides)]]
 +
* 8:45 - 9:15 White Matter Neuroanatomy using Tractography (Jim Fallon)[[Media:NAMIC_Fallon_Dartmouth_post.ppt|(slides)]]
 +
* 9:15 - 11:30 Hands on DTI Analysis Using Slicer(Tina Kapur) [[Media:Slicer_DTMRI_Tutorial_Dartmouth_Data.ppt| Slicer DTMRI Module Slides]]
 +
** Loading Data
 +
** Tensor Conversion
 +
** Scalar Fields (FA, ColorByOrientation)
 +
** 10:00 - 10:15 Break
 +
** Tractography
 +
** ROI Analysis (Mark D.)
 +
* 11:30 - noon DTI Use Cases and User Experiences Discussion (Tina Kapur)
 +
** Harvard Schiz Group
 +
** Dartmouth Feedback / Needs
 +
** University of Toronto
 +
* noon - 1:00 Lunch
 +
* 1:00 - 2:00 fMRI in Slicer (Steve Pieper and Sandy Wells)
 +
** Statistical Foundations (SW)[[Media:NAMICfMRIintro.ppt|(slides)]]
 +
** Interval Browser (SP) [[Media:IbrowserAndFMRIengine-03-23-05.ppt|IBrowser and fMRI Engine Design Slides]]
 +
** fMRIEngine (SP) [[Media:Analyzing-fMRI-Data-Short.ppt|Small Data Version Slides]], [[Media:Analyzing-fMRI-Data.ppt|Large Data Version Slides]]
 +
*** Block Design (detailed discussion)
 +
*** Event Related (overview)
 +
* 2:00 - 3:00 Discuss Results Wrap up (Ron Kikinis)
 +
** End User Needs / Priorities
 +
** Ideas for Future Dissemination and Training Activities
 +
 
 +
== [[Dissemination:Workshop_May_26-27_2005UseCaseDiscussion|User Feedback Discussion]] ==

Revision as of 14:06, 18 December 2006

Home < Dissemination:Workshop May 26

Some Pictures from the Workshop

Workshop Goals

  • To provide hands-on training in NAMIC Toolkit applications to clinical researchers.
  • To establish contact between NAMIC Tookit experts (users and developers) and clinical researchers of the NAMIC community.
  • To obtain feedback on how the NAMIC Toolkit applications satisfy the needs of the clinical research being carried out in NAMIC


Workshop Logistics

Workshop Participants

Preparation for Workshop -- Important Information for all attendees

All attendees are required to complete the following items prior to the workshop. Support will be provided as requested.

  1. Mailing List: Please ensure that you are on the mailing list namic-dissemination.
  2. Software Installation: Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to the computer you will be bringing to the workshop, the tutorial guide for Slicer, the generic sample data set. This material is located in Slicer 2.5 Getting Started: Software & Sample Data .
  3. Also, go to this link Loading-Dartmouth-NAMIC-DTI and download the powerpoint presentation that will guide you through the process of accessing Dartmouth specific data sets from the BIRN portal.
  • The documentation refers to a protocol file to be obtained from Dartmouth - this available here. Save this protocol file as slicer2/Modules/vtkDTMRI/data/NAMIC-Dartmouth-2b12g-Volume in your slicer distribution.
  1. Data to Download:
    1. Get the Tutorial Data with Dicom pointed to at the getting started page [1]
    2. Get this extra set of interoperative data mrt-images.zip
    3. Get this data for testing registrations reg-sample.zip
    4. Get this data for fMRI demonstrations: short sequence for small memory machines longer data sequence.
    5. Get this data for DTI demonstrations: dtiviz.tar.gz


We will be happy to assist anybody who may encounter difficulties in the installation process. As first point of contact, send an email to the NAMIC-developers mailing list which will be closely monitored by NAMIC Tookit experts. We will focus on how to use the application(s) during the workshop, so please do the install before you arrive.

Agenda

Note: The computer room does not permit food, so we will be wandering downstairs to the [Cafe] for lunch and coffee breaks.

Day 1:noon-6pm

  • 12:00 - 12:15 Goals of Workshop, Introduction to the NAMIC Kit, and People-Introductions (Ron Kikinis)
  • 12:15 - 1:00 Lunch (If you had trouble downloading and/or installing Slicer 2.5 or the sample data sets, we will help you- but don't come hungry because you will miss lunch!)
  • Confirm user accounts and data download
  • 1pm-5pm End-User Slicer Training
  • 2:00 - 2:15 User Experiences and Applications - Segmentation (Sylvain Bouix) (slides)
  • Hands-on Session 2 (Steve Pieper and Sylvain Bouix) (slides)
    • Manual Segmentation with the Editor (SP)
    • Model Making (SP)
  • 3:00 - 3:15 Break
  • 3:15 - 4:45 Break
    • Segmentation Foundations (Sandy Wells) (slides)
    • Voxel Classification with EMSegment (SB) (slides)
    • Level Set Segmentation (SB) (slides)
  • 4:45 - 6:15 Hands-on Session 3 (Steve Pieper) Registration Slides
    • Manual Registration (SP)
    • Registration Foundations (Sandy Wells) (slides)
    • Automatic Registration (SP)
      • ITK-based Rigid Registration, Resampling Volumes (SP)
      • vtkAG - nonrigid Registration (SP)
    • Atlas Based Segmentation with vtkAG and EMSegment (SB) (slides)
    • Measuring Image Statistics (SB) (slides)

Day 2:8am-3pm

  • 8:00 - 8:15 Review and Questions
  • 8:15 - 8:45 Introduction to DTI (Sylvain Bouix, Mark Dreusicke) (slides)
  • 8:45 - 9:15 White Matter Neuroanatomy using Tractography (Jim Fallon)(slides)
  • 9:15 - 11:30 Hands on DTI Analysis Using Slicer(Tina Kapur) Slicer DTMRI Module Slides
    • Loading Data
    • Tensor Conversion
    • Scalar Fields (FA, ColorByOrientation)
    • 10:00 - 10:15 Break
    • Tractography
    • ROI Analysis (Mark D.)
  • 11:30 - noon DTI Use Cases and User Experiences Discussion (Tina Kapur)
    • Harvard Schiz Group
    • Dartmouth Feedback / Needs
    • University of Toronto
  • noon - 1:00 Lunch
  • 1:00 - 2:00 fMRI in Slicer (Steve Pieper and Sandy Wells)
  • 2:00 - 3:00 Discuss Results Wrap up (Ron Kikinis)
    • End User Needs / Priorities
    • Ideas for Future Dissemination and Training Activities

User Feedback Discussion

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