Plans and Goals

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Revision as of 20:40, 2 February 2010 by Cagatay Demiralp (talk | contribs)
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On this page the members of the VRL record and refine their goals for the current semester. This is a living document in which dhl will provide feedback. See the bottom of the page for links to past plans & goals documents.

Current Schedule

Meetings are on Tuesdays.

  • 1:50 - jadrian
  • 2:00 - wenjin
  • 2:10 - eni
  • 2:20 - jadrian
  • 2:30 - bb
  • 2:40 - dtr
  • 2:50 - trevor
  • 3:00 - cad
  • 3:10 - steve
  • 3:20 - radu

Current Plans and Goals (Spring '10)

Brad

Projects

  • Support the ongoing projects including collaborators. Active projects are wrist, brain, adviser, and protein.
  • Assist Radu to integrate a test and any recent code.
  • Contribute to the design and development of the new cave. This includes integrating g3d, vrpn and hosting vrg3d. Once the software is running simplify the configuration and provide a quick start path for student projects.
  • Set up a distribution of diffusion imaging data.

Infrastructure

  • Continue to write Wiki entries as needed.
  • Continue setting up external software for students to use. Current imported packages are: blitz, cg, g3d, qt, camino, dtk, vrpn, glut, and sdl.
  • Finish extending make files for local installs and kits for source and binary distributions.
  • Continue to make improvements to the make files so they are easier to use.
  • Upgrade migrated Linux code to work with gcc 4.3.
  • Continue to integrate any new tests written by students into nightly test runs.


  • Finish integrating the new version of the Nag libraries.


Knowledge

  • Learn more about the cave; particularly vrg3d software development.
  • Meet (SciVis talk) with students to address any integration issues.
  • Learn how to manage a project using Source Forge.

Çağatay

  1. Stay alive through the military service.
  2. Focus on realizing the proposal timeline milestones.
  3. Submit 'On Coloring' to vis'10 and/or siggraph.
  4. Submit '2D Brain Maps' to vis'10 w/ Radu.
  5. Submit the non-parametric tract-based statistics paper to miccai'10.
  6. Submit the improved surface deformation paper to sgp'10 or siggraph asia'10.
  7. Develop new collaborations.
  8. Do not waste time on insignificant problems/collaborations.
  9. Add a 4th person (outside Brown) to the committee.
  10. Arrange an internship with someone who is the best in his field (get help from the committee members; consider MSR in Cambridge, UK (vision group), MSR in Richmond, US (graphics group) or in IST, Austria (topology group).

David

  1. get diffusion normals, one library, and one executable distributed
  2. wrist proposal submission (check with Trey?)
  3. support 5 phd students' + trevor's progress
  4. write a plan for HCI modeling work
  5. minimize professional service

Jadrian

  1. Further refine the thesis proposal in response to new information
  2. Create a list of papers to spawn from the proposal
  3. Present the proposal formally to the department
  4. Implement a macrostructure model and derive it from diffusion data (by clustering or otherwise, with possible manual adjustment)
  5. Create a 3D surface rendering of a macrostructure model instance
  6. Continue working with Ed Walsh, et al. to settle on some HARDI parameters
  7. Take at least one HARDI scan, even if parameters have not been finalized
  8. Get preliminary histological data of some kind, either by doing it in-house, working with collaborators, or outsourcing
  9. Continue working with DifSim/MCell developers to get source access and a working install here
  10. Derive a minimal set of microstructure measurements from histological data
  11. Make a plan for a future summer industry or academic internship
  12. Make a plan for completing the outside minor requirements


Radu

  1. deploy my current work (as application or google maps) to: Christophe, Hardy, Art, and Neuroscience
  2. gather structured feedback from the above mentioned labs
  3. write "Related Work" section of dissertation and updated thesis proposal.
  4. submit to Vis:
    • one paper on large map-like visualizations to InfoVis (100% submission probability),
    • one on comparing clusterings to VAST (50% submission probability)
    • one on 2D brain visualizations with Cagatay to Vis (25%).
  5. finalize my course requirements

Steve

  1. Staying on track for candidacy
    1. Complete programming comp (late January)
    2. Complete research comp proposal and presentation to committee (mid April)
    3. Do well in courses
  2. Research goals
    1. Explore current research in HCI related to creativity, and user interaction modeling
    2. Identify significant, well-scoped research project in this area for the research comp proposal
    3. Develop research skills, including paper reading/analysis and learning to communicate effectively
  3. Other academic goals
    1. Work on collaboration skills (finding and communicating with colleagues in or outside of CS)
    2. Work on time management and project planning
    3. Learn what working with DHL is like, his expectations, etc.
    4. Plan for the summer

Trevor

  1. I3D poster & demo
    1. Revised abstract: January 29
    2. Conference: February 19th (poster complete by February 17)
  2. Vis Papers - Iterate often
    1. Abstract: March 21
    2. Full paper: March 31
      1. Gene visualization paper
      2. Confocal microscopy paper
  3. Genome Research paper
  4. Grad TA for CS224
  5. Paper with Paul Kulesa
    1. Define goals contributions from Vis perspective
  6. Look for themes between work with Paul, Trey, and maybe Ben
    1. Coordinate spaces? (Tensor invariances?)
    2. Morphometrics? (Non-dimensionalization)
    3. Other feature detection?
  7. Organize code, papers, tools, other resources to be backed up, handed off

Wenjin

  1. Submit to MICCAI (March 11th) + good collaboration with Matt
  2. Prepare histology data - do homework about the right path to choose, acquire, and prepare the tissue
  3. Derive and test optimal double-PGSE imaging on Brown 3T scanner
  4. Propose by 10/15
  5. Submit MRM/TMI journal paper

Eni

  1. Process and analyze data from subjects that are currently being scanned for the cmc study
  2. Write an abstract for the American Society of Biomechanincs Meeting (August 2010 in Prov.)on the TPM & MC1 surface curvatures and joint congruency
  3. Write a short paper that compares capitate/lunate/scaphoid movement in old and young subjects during dart thrower’s motion
  4. Learn algo & data structures
  5. Think about the direction of my work


Current Plans and Goals (Fall '09)

Andy

  1. mri/wrist
    1. tools
      1. registration, classification, distance-field calculation, bone proximity calc.
      2. graphical visualization/verification?
    2. modeling?
  2. $G (nightly tests, architecture, outside test-case = ADVISER)
  3. future funding candidates
    1. volume data visualization/analysis
    2. flow visualization w/ leopold/GK
    3. other?

Brad

Projects

  • Support the ongoing projects including collaborators. Active projects are wrist, brainapp, adviser, and protein.
  • Assist Radu to integrate a test and any recent code.
  • Contribute to the design of the new cave.


Infrastructure

  • Continue to write Wiki entries as needed.
  • Continue setting up external software for students to use. Current imported packages are: blitz, cg, g3d, qt, and xerces
  • Extend make files for local installs and kits for source and binary distributions.
  • Continue to make improvements to the make files so they are easier to use and to provide Windows support.
  • Upgrade migrated Linux code to work with gcc 4.3.
  • Continue to integrate any new tests written by students into nightly test runs.
  • Integrate the new version of the Nag libraries.


Knowledge

  • Learn more about the cave; particularly software development.
  • Meet (SciVis talk) with students to address any integration issues.


Çağatay

  1. Incorporate feedback from the committee into the proposal
  2. Start working realizing the finalized proposal.
  3. Submit the histogram embedding work to ISMRM.
  4. Submit the surface deformation work to SIGGRAPH.

David

  1. figure out software and data dissemination and get implemented with bb's help [some progress, more next semester]
  2. wrist proposal submission [not sure where this went with Trey]
  3. harvard stuff moving; read Janeway? [good meeting in Boston]
  4. support 6 phd students' progress [all proposals done!]
  5. write a plan for HCI modeling work (draft by 10/23, rev by 11/20) [not enough structure]
  6. minimize professional service [less successful than hoped]
  7. vis2011 sited, early committee defined after Vis by 10/16 [contract signed, delaying committee]

Eni

  • submit tract integrity vs. cognitive tests abstract and histograms abstract to ismrm
  • possibly write a paper on the wrist comparison study (old/new subjects)
  • while working on different wrist problems, think of a problem I might want to focus on
  • do well in the courses I'm taking

Jadrian

Initial thesis proposal, submitted 2009-06-22

  1. Incorporate committee's comments into my proposal by 2009-10-15
    • Revision complete 2009-10-15
  2. Make a list of papers to spawn from the proposal by 2009-10-15
    • Incomplete
  3. Decide with dhl on the role of animal models in the proposal
    • Histological "wetwork" will play an important role in the research; significant planning and collaboration-building took place this semester
  4. Finish clustering code sufficient for an initial version of the backsolving system
    • Incomplete
  5. Find or build implementations of a more sophisticated tractography technique (Q-ball or Gordon's multi-tensor)
    • DTK & Trackvis installed and working with current data as of 2009-11-04
  6. Work with Ed Walsh, dhl, and wzhou to settle on some HARDI parameters
    • Scan parameters have not been decided but ongoing work with Steve's group is teaching us all more about parameter tradeoffs
  7. Take one HARDI scan by 2009-11-24
    • No new scan was acquired this fall, pending a decision about scan parameters
  8. Get DifSim (the MCell-based UCSD diffusion simulator) installed and working here
    • Not installed due to ongoing license issues, but I'm in communication with the developers and confident that it'll work out

Radu

  1. Deploy existing visualization tools by Oct 15 (in Labs and in CVS - Protein-version2, Clustering apps)
  2. Migrate BrainApp functionality to the new framework by Nov 1 (help from Cagatay and Eni)
  3. Test usefulness of the QT vis framework (on Cagatay); if useful deploy by Nov 1
  4. Advance Immgen
    1. Write report for next year
    2. Daphne-data vis prototype by Nov 1
    3. Genome-google maps operation by Oct1
    4. Broad display operational
    5. Paper on analyzing and disseminating large visualizations?
  5. Gather vis tools usage data
  6. Proposal
    1. Gather, read and summarize cogsci and linked visualization literature
  7. 2D interaction on stream-tubes study? Paper?
  8. Successful Vis talk
  9. Proposal is here

Trevor

  1. Research comps!
  2. Review and address EuroVis reviews for cell paper.
    1. Submit to PacVis?
  3. Research comps work --> i3d submission.
  4. Narrow long term focus.
  5. Foster collaborations:
    1. Paul Kulesa
    2. Trey Crisco
    3. Sharon Swartz
  6. Finish course requirements.

Wenjin

  • Finalize Proposal: incorporate feedback from committee in NIH format
  • Survive NEUR 1650
  • Analytical model tested on simulation data to accomplish 1-2 of the following (based on current limitations):
    • estimate axon parameter for unknown fiber direction
    • recover small axon radii < 4 micrometer
    • estimation with clinically achievable acquisitions
    • build and evaluate 4-compartment model with water exchange vs. 2-compartment
  • Derive and test optimal imaging parameters on Brown 3T scanner
  • submit to ISMRM (Nov. 10th) or MICCAI in March
  • prepare for MRM/TMI journal submission

Steve

Course work

  • Explore courses that may be relevant to research interests, or may help me think more outside-the-box
  • Use project classes to explore interests in graphics, vis, hci

Research

  • Draft R&R plan for spring semester by 11/15
  • Start thinking about research comp ideas and proposal by 11/15
  • Contribute to the VRL however I can
  • Search through past ideas/projects worth investigating more by 10/1
    • Online raytracing with voronoi diagrams?
    • Interfaces that learn?

Personal

  • Get adjusted to Brown, Providence, graduate school
    • Work on time management, organization
  • Pass programming comp in January

Past Plans and Goals

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