Mbirn: Visualization Tools

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UPDATES

November 18, 2005 (S. Pieper)

  • FreeSurfer visualization modules in 3D Slicer are being migrated into the main branch of slicer in preparation for the release of version 2.6 around the end of 2005. This will support integrated viewing and analysis of freesurfer data together with VETSA DTI data. Research on integration of Susumu's DTI-based atlas through a tensor-based registration method is still ongoing.

October 3, 2005 (N. Aucoin)

  • Additions to 3D Slicer to better integrate FreeSurfer visualisation:
    • Fully integrated reading of MGZ volume format (N. Aucoin)
    • Added another model overlay file format, .w (K. Teich, N. Aucoin)
    • Implemented a port for the Heat colour scale (N. Aucoin, K. Teich)
    • Allow switching between various overlays on surface models, with appropriate colour look up tables (N. Aucoin)
    • Support for plotting statistical data from FreeSurfer group descriptor files (N. Aucoin)
    • Run time reading of colour definition text files (N. Aucoin)
  • Build multiple jointly smoothed models at once from a segmented volume (B. Lorensen, S. Pieper, N. Aucoin)
  • 3D Slicer workshop held at MGH on September 16th, with a large segment focussed on using the FreeSurfer data visualization capabilities: Training:User_Workshop_MGH_Summer_2005
  • 3D Slicer workshop held at BWH on September 30 to accommodate overflow students from the workshop at MGH: Training:User_Workshop_SPL_Fall_2005

July 27, 2005

  • FreeSurfer-related QA and visualization techniques are being tested and documented in preparation for a slicer workshop for FreeSurfer users to be held at MGH in mid-September.

May 17, 2005

  • 3D Slicer expanded for tractography analysis using J. Fallon's feedback
  • 3D Slicer expanded by N. Aucoin to facilitate quality assurance test of automated segmentation results using feedback from C. Fennema-Notestine and B. Dickerson
  • 3D Slicer (version 2.5) distributed in Spring 2005 includes EM Segmentation used in MIRIAD analysis. Next release will include the optimized Expectation Maximization code from Kilian Pohl (which has a unified approach for what used to be two separate steps: first, registration of data to an atlas, then segmentation).

March 21, 2005 (J. Sacks)

  • Slice Launcher Aim: To prototype various methods of using Java Web Start to launch Slicer from a remote server to the local desktop with image data selected by the user. Further, to investigate how such a tool can be used together with both XML and relational databases to make visual inspection of raw and derived images based on database queries.
  • A. Initial development on the SPL network.
    • 1. December 15, 2004: Start of project
    • 2. December 31, 2004: Understand BIRN Slicer launch and diagnose problems (Completed)
    • 3. January 15, 2005: Test of launcher on simple Java program (Completed)
    • 4. January 31, 2005: Test Java implementation of Scp outside launcher (Completed)
    • 5. February 15, 2005: Test of Scp integrated in launcher on a sample image volume from the Server (URL, no GUI) (Completed, but not adopted as part of download)
    • 6. February 28, 2005: Add basic web GUI for username, password and directory tree browser (In progress)
    • 7. March 2 – 8, 2005: mBIRN Spring Meeting
    • 8. March 15, 2005: Add deployment of Slicer to client, including version control (Completed)
    • 9. March 31, 2005: Add session control (single sign on), enable other formats (COR, analyze etc)
    • 9. April 15: Test overlays
    • 10. April 30: Investigate and implement other deployment and launch methods e.g. FTP
    • 11. May 15: Test in other client/server and security environments (across, inside firewalls), and with different browsers
    • 13 May 31: Proposed prototype integration in XNAT Pipeline
    • 14. June15: Proposed test integration in XNAT Pipeline


  • B. Try out on XNAT testbed (proposed)
    • Create a plan based on experience with the project proposing how we can best provide working examples of Slicer/database interactions in order to meet the BWH mBIRN Grant commitments. Identify unknowns and suggest how they can be resolved.
    1. . March 31, 2005: Initial draft
    2. . April 15, 2005: First review completed
    3. . June 1, 2005: Incorporate experience with XNAT
    4. . June 15, 2005: Final plan reviewed

February 14, 2005 (J. Jovicich)

  • Steve Pieper needs to characterize diffusion MRI format variability across mBIRN & fBIRN so that he can extend 3D Slicer to allow flexible data importing and DTI visualization. Jorge sent out request for mBIRN and fBIRN sites (see also Acquisition/analysis of test-retest DTI, Updates from Feb 14, 2005).
  • This week Steve and Raul Estepar will be at UCI assisting James & Michelle with their use of 3D Slicer to load DTI data and build track atlas efficiently.
  • Movie generation to facilitate QA of automated segmentation results: Silvester & Steve are working to have 3D Slicer generate movies that overlay the aseg labels on structural image data. These movies will be automatically generated as part of the processing stream.

Februrary 3, 2005 (S. Pieper, J. Sacks)

  • Continued close interaction between J. Fallon, M. Perry, S. Pieper, and R. Estepar on using the DTMRI module in slicer for creating white matter atlases from scans obtained using the MGH protocol.
  • The issue of security is being taken care of by utilizing some internal security capabilities of Java Web Start (use keytool together with jarsigning). This avoids the necessity for certificates initially. File transfer will be done with a purely Java version of Scp, which is therefore includable in the launch process. There are several versions of Scp written in Java. After some experimentation, a suitable, open source, implementation has been chosen and is being included in the launch program.
  • J. Grethe has reported that the Portal/SRB Java interface (called Jargon) does not allow for client initiated downloads, only those initiated by servers. The BIRN Portal group is fixing this, but is not sure how this enhancement will work with the current Portal app launchers. Until this is fixed, it will not be feasible to use Slicer launch (or any other app that requires downloading files to the local site) from the Portal.

January 20, 2005 (J. Sacks)
A local environment for testing and enhancing Slicer launch has been created at BWH. The current goal is to create a local modified version of the Portal Slicer launch. It is now possible to download a Java Web Start configuration file from the local server to the desktop.