VrlWiki - User contributions [en]

Plans and Goals

2012-05-11T22:45:43Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2012-01-24T17:08:40Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2012-01-24T16:34:36Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2012-01-24T16:34:17Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2012-01-24T16:33:52Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-09-13T16:42:12Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-09-13T16:23:55Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-06-28T17:20:41Z

Wenjin Zhou: /* Wenjin */

Plans and Goals/Summer-Fall 2010

2011-06-15T17:13:36Z

Wenjin Zhou: /* Wenjin */

== Summer and Fall 2010 Plans and Goals ==

=== Beth ===

* Update web
** refresh text for projects and themes, add/delete some (maybe "active" as a theme)
** ensure pubs are all correctly attributed to projects/themes/people
** identify other areas to improve

----

=== [[User:Brad Berg|Brad]] ===

Projects

* Support the ongoing VRL Group projects:
** Jadrian's brain research.
** Radu's Protein project: 
::Assist Radu to integrate a test and any recent code.

* Support collaborative projects.
** Wrist cartilage support for Eni and Michael.
** Migrate Win's mri pipeline to run in CIT.
** Andy Loomis and Andy Forsberg's Adviser program.

* Contribute to the design and development of the new cave. Integrate changes to vrg3d. Simplify the configuration and provide a quick start path for student projects.

* Set up public distribution of diffusion imaging data.

Infrastructure

* Manage the migration to the new file system.

* Continue to write Wiki entries as needed.

* Continue setting up third party software for students to use. Current imported packages are: blitz, cg, g3d, qt, camino, dtk, afni, nifti, vivro, vrpn, glut, and sdl.

* Extend the build system to make kits for public source and binary distributions.

* Improve support for remote development.

* Launch the Windows test system.

* Continue extend the make files to support new features such as additional third party packages.

* Upgrade migrated Linux code to work with gcc 4.3 in conjunction with the summer Debian upgrade.

* 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.

----

=== [[User:Cagatay Demiralp|Çağatay]] ===

# Resolve crossings w/ Geman and Erik (submit the results to cvpr by 11/11)
# Count cycles w/ Mumford
# Submit the ToG paper and explore the follow up ideas w/ Gabriel
# Submit the optimization on mesh graphs (to where? )
# Finalize the revision of the 2d map paper
# Solidify the ideas on metric learning through interaction
# Minimize the ta'ship workload of c. topology class by preparing course material aeap.

----

=== [[User:Caroline Ziemkiewicz|Caroline]] ===

Explore cognitive modeling for assessing multiview visualization interfaces
* Literature review: guidelines for multiview design, evaluations of multiview visualization, cognitive science perspective on problem solving with multiple perspectives etc.
* Identify an application area (brain circuits, proteins, etc.)
* Identify tasks for user study / modeling
* Identify ways to define the similarity of models between two different visual representations
* Build a model of multiview context-switching given a certain type of task, to predict response times (and accuracy?)
* Test the model's predictions against a user study
* Aim for VisWeek publication?

Identify potential modeling projects based on visual structure for future work...
* Intrinsic quality measures of visual representations
* How decision-making is affected by visualization design
* Simple ways to define and measure the mental model of a visualization

----

=== David ===
#get diffusion normals, one library, and one executable distributed
#good TBI talk in Chicago
#support 5 phd students' + trevor's progress
#si^2 proposal for 6/14, then expedition?
#wrist proposal possibilities, w/eni (check with Trey?)
#keep Vis '11 on track

----

=== Eni ===

* Make progress in the surface analysis/congruency problem
* Draft a proposal for my work
* Read more literature that’s related to my work
* Submit a paper to MRM on tracts

----

=== [[User:Jadrian Miles|Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

# Write up dissertation table of contents, outline, and some hole-filled chapters by July 31st
#* Done.
# Write up departmental proposal document by September 1st
#* Initial submission on September 10th.
# Present the proposal formally to the department in October
#* Proposal presentation on October 7th.
# Define a macrostructure model and cost function
#* The committee has been very involved in refining the idea of the "cost functions" for various fitting steps. The macrostructure model has gone through several revisions and is almost done.
# Implement curve clustering using the macrostructure model; write up for ISMRM
#* {{red|Not done.}} Intended ISMRM submission on Rician noise correction turned out not to be novel, though I did learn about a ton of related work that has been quite successful.
# Extend the macrostructure cost function to include DWI values
#* {{red|Not done.}}
# Implement macrostructure adjustment from DWIs; write up for an MRM paper
#* {{red|Not done.}}
# Get preliminary histological data of some kind, either by doing it in-house, working with collaborators, or outsourcing
#* {{red|Not done.}}
# Derive a minimal set of microstructure measurements from histological data
#* {{red|Not done.}}
# Copy South Africa data from DVDs and work with Amanda to import and process it
#* All data are organized on the data server but not processed.

----

=== [[User:Nathan Malkin|Nathan]] ===
# <s>[[Job_Jar/Streamline_boolean_ROI_selection_program|Streamline ROI selection program]]</s> → [[roi_select]]
# [[Job_Jar/Streamline_statistics_program|Streamline stats program]]
#* <s>Line lengths and general statistics</s>
#* Density: # of lines per mm2 — ''cancelled?''
#* Calculate FA/MD along the entire length of the line
# Culling algorithm
# Try to replicate previous paper results using culling and ROI selection programs
# ...

----

=== Radu ===

# Learning distance metrics from users (with Cagatay)
# Finalize(revision)/Resubmit maps paper
# Analysis "nudge" pilot study
# Prepare thesis proposal talk
# Create a daphne-module map
# Deploy existent maps at Immgen
# Design collaborative module for maps + instrumentation

----

=== Wenjin ===

* Neuroimage paper - submit asap even just with simulation results.
* Axon application on real data: human/pig/macaque
* IACUC - work with David on submission
* IRB - work with David and Ed on submission
* CV ready for job search in fall
----

=== [[User:Steven Gomez|Steve]] ===

Comps progress
# Receive brain+code dump from Trevor re: interaction histories (meet to discuss before 6/7)
# Application integration for interaction histories
#* Get G3D history library from Trevor asap, and implement sample app and some basic interactions w/ history collection by 6/20
#* BrainApp, Brain circuit vis?
# LCS algorithm over histories for required interaction patterns
#* first draft, test on synthetic data by 6/25
# Algorithm for remaining time estimation from pattern
#* first pass by 7/1

ImmGen
# Build Radu's code and look for contribution to extend tools (6/15) - meet with Radu?

Misc
# [http://www.eis.mdx.ac.uk/vass VASS] Application/Registration
#* draft of app materials (essay, cv) by 6/1 (deadline: 7/23)
# Work on poster submission for vis (deadline: 7/1)
# Learn more about Caroline's work before she gets here (read her "Implied Dynamics" and "Visual Metaphors" papers)
# NSF Grad Fellowship application -- first draft on all parts by 8/30
#* search other fellowships
...

----

=== Ryan ===

* Get oriented in lab and on campus
* Progress with coursework
* Work on NSF GRFP Application and Research Comps projects
** Cortical connectivity (vis)
** Surface registration (vis and modeling)
** Surface descriptors (algo and applications)

Plans and Goals

2011-01-11T21:52:08Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-01-11T21:47:18Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-01-11T21:44:47Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-01-11T21:28:19Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-01-11T21:27:48Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2011-01-04T20:32:55Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2010-06-01T17:35:13Z

Wenjin Zhou:

Plans and Goals

2010-03-25T02:31:19Z

Wenjin Zhou: /* Wenjin */

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) ==

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

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

----
=== [[Jadrian]] ===

* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]
* [[:Image:Jadrian Miles PhD Proposal rev2 2009-10-15.pdf|Proposal second revision, prepared 2009-10-15]]

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



----
=== Radu ===
#deploy my current work (as application or google maps) to: Christophe, Hardy, Art, and Neuroscience
#gather structured feedback from the above mentioned labs
#write "Related Work" section of dissertation and updated thesis proposal.
#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%).
#finalize my course requirements

----

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

=== [[User:Trevor O'Brien|Trevor]] ===

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

----

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

-----

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

-----

=== Fuyi ===
# Familiarize the working environment and check out any progress about vrg3d.
# Play with the vrg3d demo for a while and figure out what it does and how it works.
# Write a tutorial describing the way I have been using the demo to let others understand what it does.
# Define a feature that the demo needs in order to be more useful as an example to our group.
# Add the new feature to the demo.
# Think of an application that the vrg3d may be used on and try to construct a basic structure.

== Current Plans and Goals (Fall '09) ==

=== [[User:Andy Forsberg|Andy]] ===
# mri/wrist
## tools
### registration, classification, distance-field calculation, bone proximity calc.
### graphical visualization/verification?
## modeling?
# $G (nightly tests, architecture, outside test-case = ADVISER)
# future funding candidates
## volume data visualization/analysis
## flow visualization w/ leopold/GK
## other?

----

=== [[User:Brad Berg|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 ===
# Incorporate feedback from the committee into the[[:Image:Çağatay's_thesis_ideas.pdf | proposal]]
# Start working realizing the finalized proposal.
# Submit the histogram embedding work to ISMRM.
# Submit the surface deformation work to SIGGRAPH.
----

=== David ===
#figure out software and data dissemination and get implemented with bb's help [some progress, more next semester]
#wrist proposal submission [not sure where this went with Trey]
#harvard stuff moving; read Janeway? [good meeting in Boston]
#support 6 phd students' progress [all proposals done!]
#write a plan for HCI modeling work (draft by 10/23, rev by 11/20) [not enough structure]
#minimize professional service [less successful than hoped]
#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

----

=== [[User:Jadrian Miles|Jadrian]] ===
[[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]

# Incorporate committee's comments into my proposal by 2009-10-15
#* Revision complete 2009-10-15
# Make a list of papers to spawn from the proposal by 2009-10-15
#* {{red|Incomplete}}
# 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
# Finish clustering code sufficient for an initial version of the backsolving system
#* {{red|Incomplete}}
# 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
# Work with Ed Walsh, dhl, and wzhou to settle on some HARDI parameters
#* {{red|Scan parameters have not been decided}} but ongoing work with Steve's group is teaching us all more about parameter tradeoffs
# Take one HARDI scan by 2009-11-24
#* {{red|No new scan was acquired this fall}}, pending a decision about scan parameters
# Get DifSim (the MCell-based UCSD diffusion simulator) installed and working here
#* {{red|Not installed}} due to ongoing license issues, but I'm in communication with the developers and confident that it'll work out

----

=== Radu ===
# Deploy existing visualization tools by Oct 15 (in Labs and in CVS - Protein-version2, Clustering apps)
# Migrate BrainApp functionality to the new framework by Nov 1 (help from Cagatay and Eni)
# Test usefulness of the QT vis framework (on Cagatay); if useful deploy by Nov 1
# Advance Immgen
## Write report for next year
## Daphne-data vis prototype by Nov 1
## Genome-google maps operation by Oct1
## Broad display operational
## Paper on analyzing and disseminating large visualizations?
# Gather vis tools usage data
# Proposal
## Gather, read and summarize cogsci and linked visualization literature
# 2D interaction on stream-tubes study? Paper?
# Successful Vis talk
# Proposal is [http://cs.brown.edu/people/jr/proposal_jr.pdf here]

----

=== Trevor ===

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

----

=== Wenjin ===

* Finalize [http://cs.brown.edu/~wzhou/proposal_wzhou.pdf 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

=== [[User:Steven Gomez|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 ==
* [[/Summer 2009|Summer '09]]
* [[/Spring 2009|Spring '09]]
* [[/Fall 2008|Fall '08]]
* [http://sites.google.com/a/vis.cs.brown.edu/collaboravis/Home/summer-08-group-goals Summer '08]

[[Category:VRL]]

Plans and Goals

2010-01-13T16:10:25Z

Wenjin Zhou: /* Wenjin */

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) ==

=== [[User:Brad Berg|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.

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

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

=== [[User:Trevor O'Brien|Trevor]] ===

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

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

== Current Plans and Goals (Fall '09) ==

=== Çağatay ===
# Incorporate feedback from the committee into the[[:Image:Çağatay's_thesis_ideas.pdf | proposal]]
# Start working realizing the finalized proposal.
# Submit the histogram embedding work to ISMRM.
# Submit the surface deformation work to SIGGRAPH.
----

=== [[User:Andy Forsberg|Andy]] ===
# mri/wrist
## tools
### registration, classification, distance-field calculation, bone proximity calc.
### graphical visualization/verification?
## modeling?
# $G (nightly tests, architecture, outside test-case = ADVISER)
# future funding candidates
## volume data visualization/analysis
## flow visualization w/ leopold/GK
## other?

----

=== [[User:Brad Berg|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 ===
# Incorporate feedback from the committee into the[[:Image:Çağatay's_thesis_ideas.pdf | proposal]]
# Start working realizing the finalized proposal.
# Submit the histogram embedding work to ISMRM.
# Submit the surface deformation work to SIGGRAPH.
----

=== David ===
#figure out software and data dissemination and get implemented with bb's help [some progress, more next semester]
#wrist proposal submission [not sure where this went with Trey]
#harvard stuff moving; read Janeway? [good meeting in Boston]
#support 6 phd students' progress [all proposals done!]
#write a plan for HCI modeling work (draft by 10/23, rev by 11/20) [not enough structure]
#minimize professional service [less successful than hoped]
#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

----

=== [[User:Jadrian Miles|Jadrian]] ===
[[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Initial thesis proposal, submitted 2009-06-22]]

# Incorporate committee's comments into my proposal by 2009-10-15
#* Revision complete 2009-10-15
# Make a list of papers to spawn from the proposal by 2009-10-15
#* {{red|Incomplete}}
# 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
# Finish clustering code sufficient for an initial version of the backsolving system
#* {{red|Incomplete}}
# 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
# Work with Ed Walsh, dhl, and wzhou to settle on some HARDI parameters
#* {{red|Scan parameters have not been decided}} but ongoing work with Steve's group is teaching us all more about parameter tradeoffs
# Take one HARDI scan by 2009-11-24
#* {{red|No new scan was acquired this fall}}, pending a decision about scan parameters
# Get DifSim (the MCell-based UCSD diffusion simulator) installed and working here
#* {{red|Not installed}} due to ongoing license issues, but I'm in communication with the developers and confident that it'll work out

----

=== Radu ===
# Deploy existing visualization tools by Oct 15 (in Labs and in CVS - Protein-version2, Clustering apps)
# Migrate BrainApp functionality to the new framework by Nov 1 (help from Cagatay and Eni)
# Test usefulness of the QT vis framework (on Cagatay); if useful deploy by Nov 1
# Advance Immgen
## Write report for next year
## Daphne-data vis prototype by Nov 1
## Genome-google maps operation by Oct1
## Broad display operational
## Paper on analyzing and disseminating large visualizations?
# Gather vis tools usage data
# Proposal
## Gather, read and summarize cogsci and linked visualization literature
# 2D interaction on stream-tubes study? Paper?
# Successful Vis talk
# Proposal is [http://cs.brown.edu/people/jr/proposal_jr.pdf here]

----

=== Trevor ===

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

----

=== Wenjin ===

* Finalize [http://cs.brown.edu/~wzhou/proposal_wzhou.pdf 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

=== [[User:Steven Gomez|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 ==
* [[/Summer 2009|Summer '09]]
* [[/Spring 2009|Spring '09]]
* [[/Fall 2008|Fall '08]]
* [http://sites.google.com/a/vis.cs.brown.edu/collaboravis/Home/summer-08-group-goals Summer '08]

[[Category:VRL]]

Work With Histology Data

2010-01-11T17:37:08Z

Wenjin Zhou:

12/17/09 
Goal: Reveal microstructure information of size around 1 micrometer from a 1 mm slab of tissue.

* Using 1 mm slab, only the top 10-15 micrometers will be clear enough for analysis.
Suggested solutions:
* Cut into 10-15 micrometer tissue. Pretty easy to achieve with instrument.
* Two-photon microscopy (very expansive, only 1 group in Brown own it. Possible collaboration)
* todo: check about the most suitable fluorescent dye for brain tissue with Prof. Berson.

 12/30/09 from David 
talked to Paul Kulesa about microscopy stuff for brain tissue. He thinks that the requesting histology and imaging are not too tricky and can probably be outsourced. He believes, also, that the tissue can be "cleared" in a way that will let confocal (as opposed to 2-photon) imaging work. He mentioned a particular stain TUJ1 that labels axons and neurons (he thinks). He thought that with clearing, even wide-field imaging could work. He sent a pointer to a paper presented by Glen MacDonald at the Stowers meeting we attended (Trevor and I). It may have been about clearing or just a pointer to that group. He thought that that UW group might be willing to collaborate, since it would be quite easy for them to do the imaging and possibly the prep. They do human stuff, which Paul doesn't handle as much.

 Paper reference from the Rubel lab that Glen MacDonald presented at the Stowers microscopy workshop. 
'''Three-dimensional imaging of the intact mouse cochlea by fluorescent laser scanning confocal microscopy.'''
 <http://www.ncbi.nlm.nih.gov/pubmed/18573326?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=10> 
MacDonald GH, Rubel EW.
Hear Res. 2008 Sep;243(1-2):1-10. Epub 2008 Jun 6.

Plans and Goals

2010-01-11T01:59:28Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2010-01-11T01:59:15Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2010-01-11T01:58:28Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2010-01-11T01:39:03Z

Wenjin Zhou: /* Current Plans and Goals (Spring '10) */

Plans and Goals

2010-01-11T01:38:05Z

Wenjin Zhou: /* Current Schedule */

Work With Histology Data

2009-12-17T00:31:09Z

Wenjin Zhou: New page: Goal: Reveal microstructure information of size around 1 micrometer from a 1 mm slab of tissue. * Using 1 mm slab, only the top 10-15 micrometers will be clear enough for analysis. Sugges...

Goal: Reveal microstructure information of size around 1 micrometer from a 1 mm slab of tissue.

* Using 1 mm slab, only the top 10-15 micrometers will be clear enough for analysis.
Suggested solutions:
* Cut into 10-15 micrometer tissue. Pretty easy to achieve with instrument.
* Two-photon microscopy (very expansive, only 1 group in Brown own it. Possible collaboration)
* todo: check about the most suitable fluorescent dye for brain tissue with Prof. Berson.

Diffusion MRI

2009-12-17T00:24:08Z

Wenjin Zhou: /* See Also */

''Diffusion-weighted magnetic resonance imaging'' ('''DW-MRI''') is a radiological technique that measures water diffusion in living tissue in order to infer microstructural details of fibrous textured tissues like brain [[w:white matter|white matter]]. The information that comes from a DW-MRI scan sequence generally requires extensive processing before it is useful for brain scientists --- see the article on [[diffusion MRI techniques]] for more details. Our research group collaborates with scientists around the world to help make medical discoveries while developing novel techniques to process, quantify, and visualize diffusion MRI data.

You may also want to check the [[/Glossary|diffusion MRI glossary]] page to learn some jargon, or the [[brain anatomy]] page.

== Neuroscience Collaborations ==
The following is a table of all the projects on which we're collaborating, the data we've received from our collaborators, information about the data, and our progress in processing them.

Entries in the "Dataset Date Received" column may include a "[more]" link. This drops down more detail, including the path to the data and additional notes.

In the "Status" column, the rule of thumb is to only mark a particular stage completed if it's completed for all scans (usually corresponding to patients) in the dataset. Sometimes a step will be marked complete if it's known to work for all scans but has not been completed on a minority of them, but this practice is discouraged.

In the "Resolution" and "Voxel Size" columns, dimensions are ordered XxYxZ.

In the "Orientation" columns, "L" stands for "left side of patient from an anterior view", or "patient's right". "R" stands for "right side of patient from an anterior view", or "patient's left". "A" stands for "anterior" (front), "P" for "posterior" (back), "I" for "inferior" (bottom), and "S" for "superior" (top). See the [[w:Anatomical terms of location#Medical (human) directional terms|wikipedia page on anatomical coordinate systems]] for more information. Ordinarily you will see these pairs in order as "LR", "AP", and "IS"; if they are in the opposite order it indicates a [[Diagnose tensor orientation problems|direction flip]].

=== Collaboration Table ===


{| {{Prettytable}}
|-
! {{Hl2}} rowspan="2" | Project
! {{Hl2}} rowspan="2" | Location
! {{Hl2}} rowspan="2" | Collaborators
! {{Hl2}} rowspan="2" | Dataset Date Received
! {{Hl2}} colspan="8" | Status
! {{Hl2}} colspan="2" | Scanner
! {{Hl2}} rowspan="2" | Format
! {{Hl2}} rowspan="2" | # Scans
! {{Hl2}} rowspan="2" | Resolution (voxels)
! {{Hl2}} rowspan="2" | # DWIs
! {{Hl2}} rowspan="2" | Voxel Size (mm)
! {{Hl2}} colspan="6" | DWI Orientation
! {{Hl2}} colspan="6" | bvec Orientation
|-
! {{Hl2}} | <abbr title="Scans collected by collaborator?">C</abbr>
! {{Hl2}} | <abbr title="Scans uploaded to our FTP by collaborator?">U</abbr>
! {{Hl2}} | <abbr title="Scans downloaded from our FTP?">D</abbr>
! {{Hl2}} | <abbr title="Scans filed in $G/data/diffusion?">F</abbr>
! {{Hl2}} | <abbr title="DWIs converted to MriImage?">M</abbr>
! {{Hl2}} | <abbr title="Tensors fit?">F</abbr>
! {{Hl2}} | <abbr title="Tubes generated?">T</abbr>
! {{Hl2}} | <abbr title="Works in Brainapp?">B</abbr>
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
|-
| {{Hl2}} | Cognitive Aging
| St. Louis
| Rob Paul ([[Wikipedia:UMSL|UMSL]]), Tom Conturo ([[Wikipedia:WUSTL|WUSTL]])
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-20
| content = <code>$G/data/diffusion/st_louis/cognitive_aging.2008.07.20</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| [[Interfile]]
| 1
| 83x110x64
| 36
| 2.0x2.0x2.0
| L || R || {{no|P}} || {{no|A}} || I || S
| L || R || A || P || I || S
|-
| {{Hl2}} rowspan="2" | [[Fibers at Risk]]
| Colorado
| Jack Simon
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-08-28
| content = Longitudinal data collected a long while ago, mailed to us on DVD.
}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| Portland
| Jack Simon ([[wikipedia:VA Hospital|VA]]), Bill Rooney ([[wikipedia:OHSU|OHSU]] <abbr title="Advanced Imaging Research Center">AIRC</abbr>)
| {{?}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 7T
| GE
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{Hl2}} rowspan="4" | HIV
| Memorial Hospital
| rowspan="4" | Steve Correia, Ron Cohen
| {{?}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| Siemens
| [[DICOM]]
| {{?}}
| 256x256x90
| {{?}}
| 0.8477x0.8477x1.667
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| rowspan="3" | Brown Life Sci
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-11-30
| content = <code>$G/data/diffusion/brown3t/302CK.2007.11.30</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| rowspan="3" | 3T
| rowspan="3" | Siemens
| [[DICOM]]
| 1
| 256x256x180
| 74
| .8828x.8828x.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-21
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study.2007.02.07</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| [[NIfTI]]
| 13
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-10-09
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study_registered.2007.02.07</code>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| [[NIfTI]]
| 8
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| L || R || A || P || I || S
| {{no|R}} || {{no|L}} || A || P || I || S
|-
| {{Hl2}} | Macaques
| Caltech
| Jason Kaufman
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-21
| content = <code>$G/data/diffusion/caltech/macaque.2008.05.21</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Bruker
| [[Analyze]]
| 1
| 98x110x130
| 36
| 0.6x0.6x0.6
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{Hl2}} rowspan="3" | SA HIV
| rowspan="3" | Cape Town
| rowspan="3" | Rob Paul (PI), Bruce Spottiswoode, Paul Carey, John Joska
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-10-22
| content = <code>$G/data/diffusion/south_africa/normal.2007.10.22</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Siemens
| [[DICOM#Mosaic|DICOM Mosaic]]
| 1
| 127x128x70
| 40
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-09
| content = <code>$G/data/diffusion/south_africa/normal.2008.05.06.average1</code> <code>$G/data/diffusion/south_africa/normal.2008.05.06.average2</code> <code>$G/data/diffusion/south_africa/hiv.2008.05.09</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| Siemens
| [[DICOM#Mosaic|DICOM Mosaic]]
| 3
| 127x127x75
| 66
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 85ex;
| header = 2008-07-24
| content = <code>$G/data/diffusion/south_africa/hiv_positive_apathy_negative_15patients.2008.07.24</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| Siemens
| 4-D [[NIfTI]]
| 15
| 128x128x75
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 9ex; | contentcss = font-size: 90%; width: 25ex;
| header = 65
| content = For each patient, there are 5 acquisitions in 13 directions each, all registered to each other. Each acquisition is a separate 4-D [[NIfTI]] file.
}}
| 1.875x1.875x1.9
| L || R || A || P || I || S
| L || R || A || P || I || S
|-
| {{Hl2}} rowspan="3" | [[Tumors]]
| rowspan="3" | Edinburgh
| rowspan="3" | Mark Bastin
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-11-06
| content = <code>$G/data/diffusion/edinburgh/tumor.2007.11.06</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| 1
| 128x128x72
| 71
| 2.0x2.0x2.0
| colspan="6" {{?}}
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-24
| content = <code>$G/data/diffusion/edinburgh/tumor_pilot.2008.07.24</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{some}}
| {{some}}
| {{some}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 9ex; | contentcss = font-size: 90%; width: 25ex;
| header = 29
| content = 1 scan each of 5 tumor patients, plus 3 scans each of 8 healthy volunteers.
}}
| 128x128x72
| 71
| 2.0x2.0x2.0
| L || R || A || P || I || S
| L || R || {{no|P}} || {{no|A}} || I || S
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2009-11-23
| content = <code>$G/data/diffusion/edinburgh/tumor_fullstudy.2009.11.23</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{some}}
| {{some}}
| {{some}}
| {{some}}
| 1.5T
| GE
| [[DICOM#Tar|DICOM tarball]]
| 17
| 128x128x72
| 71
| 2.0x2.0x2.0
| L || R || A || P || I || S
| L || R || {{no|P}} || {{no|A}} || I || S
|}

== Software ==
The principle pieces of software we use for research now are:
* [[Diffusion Processing Pipeline]] --- a series of small programs that turns data we get from collaborators into tensor models, scalar measures, tractograms, etc.
* [[Brainapp]] --- a GUI program for viewing tractograms and computing scalar statistics on them.
* <code>$G/bin/mriatlas</code> --- generates a PDF of slices of [[MRIimage]] files.
* [[Diffusion MRI Matlab Scripts]] --- Matlab scripts to read, write, view, and manipulate MRI data (especially in [[MRIimage]] format)

You may also be interested in the exhaustive list of [[In-House Diffusion MRI Software|diffusion MRI software we've developed in-house]], or that of [[3rd Party Diffusion MRI Software|3rd-party software]].

== File Formats ==
{| {{Prettytable | width = 40%}}
|-
! {{Hl2}} | Format
! {{Hl2}} | Extension
|-
| [[DICOM]]
| <tt>.ima</tt>; <tt>.dcm</tt>
|-
| [[Analyze]]
| <tt>.hdr</tt> / <tt>.img</tt>
|-
| [[NIfTI]]
| <tt>.nii</tt>; <tt>.nii.gz</tt>; <tt>.hdr</tt> / <tt>.img</tt>
|-
| [[Interfile]]
| <tt>.ifh</tt> / <tt>.img</tt>; <tt>.i33</tt> / <tt>.h33</tt>
|-
| [[MRIimage]]
| ''none''
|}

== HOWTOs ==
* [[Run the diffusion processing pipeline at low resolution]]
* [[Diagnose tensor orientation problems]]
* [[Compute apparent diffusion coefficient]]

== See Also ==
* [[/Introductory Reading List|Introductory Reading List]] --- a minimal guide of good references for understanding the background of this project
* [[Diffusion MRI techniques]] --- technical information about the diffusion MRI process
* [[Brain anatomy]]
* [[/Glossary|Diffusion MRI glossary]]
* [[Work With Histology Data]]

[[Category:Projects]][[Category:Diffusion MRI]]

Plans and Goals

2009-11-22T21:07:28Z

Wenjin Zhou: /* Wenjin */

Propose your PhD

2009-10-14T18:26:01Z

Wenjin Zhou: /* Examples */

{{stub}}

In the past, PhD proposals in our department have come rather late in the PhD process; often they were balanced more toward reporting extensive thesis work so far than toward actually proposing work to be done. It may be useful to model PhD proposals that truly ''propose'' work after grant proposals. This page collects references, guidelines, and examples for crafting a PhD proposal document early on in the thesis work. David's vision for the proposal process is for the student's committee to be involved in three evaluations of the research:
# Review the proposal document before most of the work it proposes has begun; due by the end of third academic year
# Review the student's progress at a formal CS department-style "proposal" presentation; due by the end of fourth academic year
# Sign off on the student's research at the public thesis defense presentation; due by the end of fifth academic year

The goal for timing of these events would be one year between each pair.

== NIH-Style PhD Proposals ==
There are five sections in the NIH grant proposal format relevant to PhD propsals:
# Vision / Introduction / Summary
#* A (strictly) one-page summary of the context of your work, the "hole in the web of knowledge" that you perceive in this area, and what you plan to do to fill it. The page limit seems short but you only need enough background to give a general picture; arguments to establish novelty and significance go in the ''Significance'' section, accompanied with any more specific background required to make those arguments.
# Contributions
#* An approximately one-page summary of the specific contributions you intend to make; in other words, deliverables. Each one needs only a short blurb to describe it, but it should include a sketch of how you intend to "prove" your contribution.
# Significance
#* A longer section explaining the significance and novelty of your proposed work, along with any further background you need to provide in order to argue these points. You need not refer to individual contributions, though that might be useful. This section should be chock-full of references to back up your arguments. The level of detail in the descriptions of your proposed work in this section should be between the ''Contributions'' section (where everything's high-level and you only have a page to fit it all in) and the ''Research Design'' section (where you get into the specifics of each proposed experiment); the emphasis is on impact and context rather than mechanics.
# Preliminary Work
#* For a PhD proposal, this may include published work, informal feasibility studies for your various contributions, established relationships with collaborators, or unpublished (and perhaps even unpublishable) work demonstrating your familiarity with the field. You should try to cover everything that's relevant at all to your ability to complete the proposed research.
# Research Design
#* Talk about the specific experiments you will perform and arrange them into a timeline. This will likely be a quite long section.
# References

The ''Contributions'' section should be about one page long, and in total the ''Contributions'', ''Significance'', ''Preliminary Work'', and ''Research Plan'' sections should total no more than ten pages---the NIH is strict about this, and David intends to be, too. You may take as much space as you need for references.

== NIH-Style Revised PhD Proposals ==

Unless you get your proposal perfect the first time around, feedback from your committee is likely to require changes at a number of levels. You are expected to produce a revised proposal based on this feedback. It should differ from your initial proposal as follows:

# It will have an additional one-page introduction outlining the major criticisms together with how and where you addressed them in the revised proposal. Typically, this introduction should not argue against a critique, but rather state how it is addressed in the revision. Sometimes that may mean that a description in the revision is clarified. Sometimes it means that a piece of the proposal is removed. Sometimes it means that significant new work must be added to the proposal. Some interaction with your committee is likely to help in crafting this introduction.
# The other proposal sections will be revised as outlined in the introduction.
# Some mechanism for distinguishing changes (text color, change bars, etc.) must be used to show where any substantive changes were made.

Note that the revised proposal is still subject to the 10-page limit (plus the single introduction page).

NIH has a very similar revision process. Their guides to writing proposals describe this, if you would like further reading. This revision process is also very similar to the revision process at many journals. Example of journal-paper response letters from your colleagues may be enlightening.

=== Evaluation Rubric ===
David's rubric for this proposal format follows:
# Vision
#* concise
#* convincing
# Contributions
#* contributions clear
#* evaluations of contributions clear
# Significance
#* well established
#* assertions cited
#* related well to the literature
# Research Plan
#* clear
#* concise
#* appropriate scale
#* no wasted effort
#* risks identified and sized
#* contingencies

=== LaTeX Templates ===
You can copy the files <tt>nih.cls</tt> and <tt>prop.tex</tt> in <tt>/pro/graphics/proposals/nih/bisti</tt> to serve as templates for your proposal, but please don't modify the originals.

=== Examples ===
* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Jadrian Miles's initial diffusion MRI proposal]], submitted to his committee summer 2009
* [http://cs.brown.edu/~wzhou/proposal_wzhou.pdf Wenjin Zhou's initial diffusion MRI proposal], submitted to his committee summer 2009

== Grant Proposals ==

Since this brave new world of authentic PhD research proposals is supposed to be modeled after the grant proposal and review process, here are guidelines and examples for two major granting agencies to which the VRL has applied in the past.

=== NIH ===

* [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2001-PHS.pdf NIH guide to proposals]
* Example proposal: ''DTI+MRI-based Tools for Analyzing White Matter Variation'' by Laidlaw, Ahrens, Allman, and Bastin
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DTI.pdf First submission]
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DTI.pdf NIH Reviews]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DA1.pdf Revision A1], in response to the first round of reviews
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DRV.PDF NIH Reviews of the revised proposal]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2005-DA2.pdf Revision A2], in response to the second round of reviews

=== NSF ===
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPG.pdf NSF grant proposal guide]
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPW.pdf NSF guide to proposal writing]

== Older PhD Proposal Examples ==

Most of these example PhD "proposals" from previous years are proposals in the CS department sense: they report on a large body of completed work and propose the completion of the dissertation research. Some are from biomed, where the format is more similar to David's.

* [[:Image:Dan Keefe PhD proposal.pdf|Dan Keefe's visualization PhD proposal]] from 2006
* [[:Image:Tomer Moscovich PhD proposal.pdf|Tomer Moscovich's graphics PhD proposal]] from 2006
* [[:Image:Daf phd proposal.pdf|Daniel Acevedo's visualization PhD proposal]] from 2006 ([[:Image:Daf phd proposal presentation.ppt|presentation PPT]])
* [[:Image:Dana Tenneson phd proposal.pdf|Dana Tenneson's graphics PhD proposal]] from 2007 ([[:Image:Dana Tenneson phd proposal talk.ppt|presentation PPT]])
* [[:Image:Example biomed-eng PhD proposal by awald.pdf|Andy Wald's biomedical engineering PhD proposal]] from 2007
* [[:Image:Evan Leventhal PhD proposal.pdf|Evan Leventhal's biomedical engineering PhD proposal]] from 2008
* [[:Image:Pepe's proposal.pdf|Pepe's ecology & evolutionary biology PhD proposal]]

[[Category:HOWTO]][[Category:The PhD Process]]

Propose your PhD

2009-10-14T18:25:18Z

Wenjin Zhou: /* Examples */

{{stub}}

In the past, PhD proposals in our department have come rather late in the PhD process; often they were balanced more toward reporting extensive thesis work so far than toward actually proposing work to be done. It may be useful to model PhD proposals that truly ''propose'' work after grant proposals. This page collects references, guidelines, and examples for crafting a PhD proposal document early on in the thesis work. David's vision for the proposal process is for the student's committee to be involved in three evaluations of the research:
# Review the proposal document before most of the work it proposes has begun; due by the end of third academic year
# Review the student's progress at a formal CS department-style "proposal" presentation; due by the end of fourth academic year
# Sign off on the student's research at the public thesis defense presentation; due by the end of fifth academic year

The goal for timing of these events would be one year between each pair.

== NIH-Style PhD Proposals ==
There are five sections in the NIH grant proposal format relevant to PhD propsals:
# Vision / Introduction / Summary
#* A (strictly) one-page summary of the context of your work, the "hole in the web of knowledge" that you perceive in this area, and what you plan to do to fill it. The page limit seems short but you only need enough background to give a general picture; arguments to establish novelty and significance go in the ''Significance'' section, accompanied with any more specific background required to make those arguments.
# Contributions
#* An approximately one-page summary of the specific contributions you intend to make; in other words, deliverables. Each one needs only a short blurb to describe it, but it should include a sketch of how you intend to "prove" your contribution.
# Significance
#* A longer section explaining the significance and novelty of your proposed work, along with any further background you need to provide in order to argue these points. You need not refer to individual contributions, though that might be useful. This section should be chock-full of references to back up your arguments. The level of detail in the descriptions of your proposed work in this section should be between the ''Contributions'' section (where everything's high-level and you only have a page to fit it all in) and the ''Research Design'' section (where you get into the specifics of each proposed experiment); the emphasis is on impact and context rather than mechanics.
# Preliminary Work
#* For a PhD proposal, this may include published work, informal feasibility studies for your various contributions, established relationships with collaborators, or unpublished (and perhaps even unpublishable) work demonstrating your familiarity with the field. You should try to cover everything that's relevant at all to your ability to complete the proposed research.
# Research Design
#* Talk about the specific experiments you will perform and arrange them into a timeline. This will likely be a quite long section.
# References

The ''Contributions'' section should be about one page long, and in total the ''Contributions'', ''Significance'', ''Preliminary Work'', and ''Research Plan'' sections should total no more than ten pages---the NIH is strict about this, and David intends to be, too. You may take as much space as you need for references.

== NIH-Style Revised PhD Proposals ==

Unless you get your proposal perfect the first time around, feedback from your committee is likely to require changes at a number of levels. You are expected to produce a revised proposal based on this feedback. It should differ from your initial proposal as follows:

# It will have an additional one-page introduction outlining the major criticisms together with how and where you addressed them in the revised proposal. Typically, this introduction should not argue against a critique, but rather state how it is addressed in the revision. Sometimes that may mean that a description in the revision is clarified. Sometimes it means that a piece of the proposal is removed. Sometimes it means that significant new work must be added to the proposal. Some interaction with your committee is likely to help in crafting this introduction.
# The other proposal sections will be revised as outlined in the introduction.
# Some mechanism for distinguishing changes (text color, change bars, etc.) must be used to show where any substantive changes were made.

Note that the revised proposal is still subject to the 10-page limit (plus the single introduction page).

NIH has a very similar revision process. Their guides to writing proposals describe this, if you would like further reading. This revision process is also very similar to the revision process at many journals. Example of journal-paper response letters from your colleagues may be enlightening.

=== Evaluation Rubric ===
David's rubric for this proposal format follows:
# Vision
#* concise
#* convincing
# Contributions
#* contributions clear
#* evaluations of contributions clear
# Significance
#* well established
#* assertions cited
#* related well to the literature
# Research Plan
#* clear
#* concise
#* appropriate scale
#* no wasted effort
#* risks identified and sized
#* contingencies

=== LaTeX Templates ===
You can copy the files <tt>nih.cls</tt> and <tt>prop.tex</tt> in <tt>/pro/graphics/proposals/nih/bisti</tt> to serve as templates for your proposal, but please don't modify the originals.

=== Examples ===
* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Jadrian Miles's initial diffusion MRI proposal]], submitted to his committee summer 2009
* [[http://cs.brown.edu/~wzhou/proposal_wzhou.pdf | Wenjin Zhou's initial diffusion MRI proposal]], submitted to his committee summer 2009

== Grant Proposals ==

Since this brave new world of authentic PhD research proposals is supposed to be modeled after the grant proposal and review process, here are guidelines and examples for two major granting agencies to which the VRL has applied in the past.

=== NIH ===

* [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2001-PHS.pdf NIH guide to proposals]
* Example proposal: ''DTI+MRI-based Tools for Analyzing White Matter Variation'' by Laidlaw, Ahrens, Allman, and Bastin
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DTI.pdf First submission]
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DTI.pdf NIH Reviews]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DA1.pdf Revision A1], in response to the first round of reviews
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DRV.PDF NIH Reviews of the revised proposal]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2005-DA2.pdf Revision A2], in response to the second round of reviews

=== NSF ===
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPG.pdf NSF grant proposal guide]
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPW.pdf NSF guide to proposal writing]

== Older PhD Proposal Examples ==

Most of these example PhD "proposals" from previous years are proposals in the CS department sense: they report on a large body of completed work and propose the completion of the dissertation research. Some are from biomed, where the format is more similar to David's.

* [[:Image:Dan Keefe PhD proposal.pdf|Dan Keefe's visualization PhD proposal]] from 2006
* [[:Image:Tomer Moscovich PhD proposal.pdf|Tomer Moscovich's graphics PhD proposal]] from 2006
* [[:Image:Daf phd proposal.pdf|Daniel Acevedo's visualization PhD proposal]] from 2006 ([[:Image:Daf phd proposal presentation.ppt|presentation PPT]])
* [[:Image:Dana Tenneson phd proposal.pdf|Dana Tenneson's graphics PhD proposal]] from 2007 ([[:Image:Dana Tenneson phd proposal talk.ppt|presentation PPT]])
* [[:Image:Example biomed-eng PhD proposal by awald.pdf|Andy Wald's biomedical engineering PhD proposal]] from 2007
* [[:Image:Evan Leventhal PhD proposal.pdf|Evan Leventhal's biomedical engineering PhD proposal]] from 2008
* [[:Image:Pepe's proposal.pdf|Pepe's ecology & evolutionary biology PhD proposal]]

[[Category:HOWTO]][[Category:The PhD Process]]

Propose your PhD

2009-10-14T18:22:37Z

Wenjin Zhou: /* Examples */

{{stub}}

In the past, PhD proposals in our department have come rather late in the PhD process; often they were balanced more toward reporting extensive thesis work so far than toward actually proposing work to be done. It may be useful to model PhD proposals that truly ''propose'' work after grant proposals. This page collects references, guidelines, and examples for crafting a PhD proposal document early on in the thesis work. David's vision for the proposal process is for the student's committee to be involved in three evaluations of the research:
# Review the proposal document before most of the work it proposes has begun; due by the end of third academic year
# Review the student's progress at a formal CS department-style "proposal" presentation; due by the end of fourth academic year
# Sign off on the student's research at the public thesis defense presentation; due by the end of fifth academic year

The goal for timing of these events would be one year between each pair.

== NIH-Style PhD Proposals ==
There are five sections in the NIH grant proposal format relevant to PhD propsals:
# Vision / Introduction / Summary
#* A (strictly) one-page summary of the context of your work, the "hole in the web of knowledge" that you perceive in this area, and what you plan to do to fill it. The page limit seems short but you only need enough background to give a general picture; arguments to establish novelty and significance go in the ''Significance'' section, accompanied with any more specific background required to make those arguments.
# Contributions
#* An approximately one-page summary of the specific contributions you intend to make; in other words, deliverables. Each one needs only a short blurb to describe it, but it should include a sketch of how you intend to "prove" your contribution.
# Significance
#* A longer section explaining the significance and novelty of your proposed work, along with any further background you need to provide in order to argue these points. You need not refer to individual contributions, though that might be useful. This section should be chock-full of references to back up your arguments. The level of detail in the descriptions of your proposed work in this section should be between the ''Contributions'' section (where everything's high-level and you only have a page to fit it all in) and the ''Research Design'' section (where you get into the specifics of each proposed experiment); the emphasis is on impact and context rather than mechanics.
# Preliminary Work
#* For a PhD proposal, this may include published work, informal feasibility studies for your various contributions, established relationships with collaborators, or unpublished (and perhaps even unpublishable) work demonstrating your familiarity with the field. You should try to cover everything that's relevant at all to your ability to complete the proposed research.
# Research Design
#* Talk about the specific experiments you will perform and arrange them into a timeline. This will likely be a quite long section.
# References

The ''Contributions'' section should be about one page long, and in total the ''Contributions'', ''Significance'', ''Preliminary Work'', and ''Research Plan'' sections should total no more than ten pages---the NIH is strict about this, and David intends to be, too. You may take as much space as you need for references.

== NIH-Style Revised PhD Proposals ==

Unless you get your proposal perfect the first time around, feedback from your committee is likely to require changes at a number of levels. You are expected to produce a revised proposal based on this feedback. It should differ from your initial proposal as follows:

# It will have an additional one-page introduction outlining the major criticisms together with how and where you addressed them in the revised proposal. Typically, this introduction should not argue against a critique, but rather state how it is addressed in the revision. Sometimes that may mean that a description in the revision is clarified. Sometimes it means that a piece of the proposal is removed. Sometimes it means that significant new work must be added to the proposal. Some interaction with your committee is likely to help in crafting this introduction.
# The other proposal sections will be revised as outlined in the introduction.
# Some mechanism for distinguishing changes (text color, change bars, etc.) must be used to show where any substantive changes were made.

Note that the revised proposal is still subject to the 10-page limit (plus the single introduction page).

NIH has a very similar revision process. Their guides to writing proposals describe this, if you would like further reading. This revision process is also very similar to the revision process at many journals. Example of journal-paper response letters from your colleagues may be enlightening.

=== Evaluation Rubric ===
David's rubric for this proposal format follows:
# Vision
#* concise
#* convincing
# Contributions
#* contributions clear
#* evaluations of contributions clear
# Significance
#* well established
#* assertions cited
#* related well to the literature
# Research Plan
#* clear
#* concise
#* appropriate scale
#* no wasted effort
#* risks identified and sized
#* contingencies

=== LaTeX Templates ===
You can copy the files <tt>nih.cls</tt> and <tt>prop.tex</tt> in <tt>/pro/graphics/proposals/nih/bisti</tt> to serve as templates for your proposal, but please don't modify the originals.

=== Examples ===
* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Jadrian Miles's initial diffusion MRI proposal]], submitted to his committee summer 2009
* [Wenjin Zhou's initial diffusion MRI proposal]], submitted to his committee summer 2009

== Grant Proposals ==

Since this brave new world of authentic PhD research proposals is supposed to be modeled after the grant proposal and review process, here are guidelines and examples for two major granting agencies to which the VRL has applied in the past.

=== NIH ===

* [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2001-PHS.pdf NIH guide to proposals]
* Example proposal: ''DTI+MRI-based Tools for Analyzing White Matter Variation'' by Laidlaw, Ahrens, Allman, and Bastin
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DTI.pdf First submission]
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DTI.pdf NIH Reviews]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DA1.pdf Revision A1], in response to the first round of reviews
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DRV.PDF NIH Reviews of the revised proposal]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2005-DA2.pdf Revision A2], in response to the second round of reviews

=== NSF ===
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPG.pdf NSF grant proposal guide]
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPW.pdf NSF guide to proposal writing]

== Older PhD Proposal Examples ==

Most of these example PhD "proposals" from previous years are proposals in the CS department sense: they report on a large body of completed work and propose the completion of the dissertation research. Some are from biomed, where the format is more similar to David's.

* [[:Image:Dan Keefe PhD proposal.pdf|Dan Keefe's visualization PhD proposal]] from 2006
* [[:Image:Tomer Moscovich PhD proposal.pdf|Tomer Moscovich's graphics PhD proposal]] from 2006
* [[:Image:Daf phd proposal.pdf|Daniel Acevedo's visualization PhD proposal]] from 2006 ([[:Image:Daf phd proposal presentation.ppt|presentation PPT]])
* [[:Image:Dana Tenneson phd proposal.pdf|Dana Tenneson's graphics PhD proposal]] from 2007 ([[:Image:Dana Tenneson phd proposal talk.ppt|presentation PPT]])
* [[:Image:Example biomed-eng PhD proposal by awald.pdf|Andy Wald's biomedical engineering PhD proposal]] from 2007
* [[:Image:Evan Leventhal PhD proposal.pdf|Evan Leventhal's biomedical engineering PhD proposal]] from 2008
* [[:Image:Pepe's proposal.pdf|Pepe's ecology & evolutionary biology PhD proposal]]

[[Category:HOWTO]][[Category:The PhD Process]]

File:Proposal wzhou smaller.pdf

2009-10-14T18:21:06Z

Wenjin Zhou:

Propose your PhD

2009-10-14T18:19:38Z

Wenjin Zhou: /* Examples */

{{stub}}

In the past, PhD proposals in our department have come rather late in the PhD process; often they were balanced more toward reporting extensive thesis work so far than toward actually proposing work to be done. It may be useful to model PhD proposals that truly ''propose'' work after grant proposals. This page collects references, guidelines, and examples for crafting a PhD proposal document early on in the thesis work. David's vision for the proposal process is for the student's committee to be involved in three evaluations of the research:
# Review the proposal document before most of the work it proposes has begun; due by the end of third academic year
# Review the student's progress at a formal CS department-style "proposal" presentation; due by the end of fourth academic year
# Sign off on the student's research at the public thesis defense presentation; due by the end of fifth academic year

The goal for timing of these events would be one year between each pair.

== NIH-Style PhD Proposals ==
There are five sections in the NIH grant proposal format relevant to PhD propsals:
# Vision / Introduction / Summary
#* A (strictly) one-page summary of the context of your work, the "hole in the web of knowledge" that you perceive in this area, and what you plan to do to fill it. The page limit seems short but you only need enough background to give a general picture; arguments to establish novelty and significance go in the ''Significance'' section, accompanied with any more specific background required to make those arguments.
# Contributions
#* An approximately one-page summary of the specific contributions you intend to make; in other words, deliverables. Each one needs only a short blurb to describe it, but it should include a sketch of how you intend to "prove" your contribution.
# Significance
#* A longer section explaining the significance and novelty of your proposed work, along with any further background you need to provide in order to argue these points. You need not refer to individual contributions, though that might be useful. This section should be chock-full of references to back up your arguments. The level of detail in the descriptions of your proposed work in this section should be between the ''Contributions'' section (where everything's high-level and you only have a page to fit it all in) and the ''Research Design'' section (where you get into the specifics of each proposed experiment); the emphasis is on impact and context rather than mechanics.
# Preliminary Work
#* For a PhD proposal, this may include published work, informal feasibility studies for your various contributions, established relationships with collaborators, or unpublished (and perhaps even unpublishable) work demonstrating your familiarity with the field. You should try to cover everything that's relevant at all to your ability to complete the proposed research.
# Research Design
#* Talk about the specific experiments you will perform and arrange them into a timeline. This will likely be a quite long section.
# References

The ''Contributions'' section should be about one page long, and in total the ''Contributions'', ''Significance'', ''Preliminary Work'', and ''Research Plan'' sections should total no more than ten pages---the NIH is strict about this, and David intends to be, too. You may take as much space as you need for references.

== NIH-Style Revised PhD Proposals ==

Unless you get your proposal perfect the first time around, feedback from your committee is likely to require changes at a number of levels. You are expected to produce a revised proposal based on this feedback. It should differ from your initial proposal as follows:

# It will have an additional one-page introduction outlining the major criticisms together with how and where you addressed them in the revised proposal. Typically, this introduction should not argue against a critique, but rather state how it is addressed in the revision. Sometimes that may mean that a description in the revision is clarified. Sometimes it means that a piece of the proposal is removed. Sometimes it means that significant new work must be added to the proposal. Some interaction with your committee is likely to help in crafting this introduction.
# The other proposal sections will be revised as outlined in the introduction.
# Some mechanism for distinguishing changes (text color, change bars, etc.) must be used to show where any substantive changes were made.

Note that the revised proposal is still subject to the 10-page limit (plus the single introduction page).

NIH has a very similar revision process. Their guides to writing proposals describe this, if you would like further reading. This revision process is also very similar to the revision process at many journals. Example of journal-paper response letters from your colleagues may be enlightening.

=== Evaluation Rubric ===
David's rubric for this proposal format follows:
# Vision
#* concise
#* convincing
# Contributions
#* contributions clear
#* evaluations of contributions clear
# Significance
#* well established
#* assertions cited
#* related well to the literature
# Research Plan
#* clear
#* concise
#* appropriate scale
#* no wasted effort
#* risks identified and sized
#* contingencies

=== LaTeX Templates ===
You can copy the files <tt>nih.cls</tt> and <tt>prop.tex</tt> in <tt>/pro/graphics/proposals/nih/bisti</tt> to serve as templates for your proposal, but please don't modify the originals.

=== Examples ===
* [[:Image:Jadrian Miles PhD Proposal original 2009-06-22.pdf‎|Jadrian Miles's initial diffusion MRI proposal]], submitted to his committee summer 2009
* [[:Image:Wenjin Zhou PhD Proposal original 2009-06-22.pdf‎|Wenjin Zhou's initial diffusion MRI proposal]], submitted to his committee summer 2009

== Grant Proposals ==

Since this brave new world of authentic PhD research proposals is supposed to be modeled after the grant proposal and review process, here are guidelines and examples for two major granting agencies to which the VRL has applied in the past.

=== NIH ===

* [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2001-PHS.pdf NIH guide to proposals]
* Example proposal: ''DTI+MRI-based Tools for Analyzing White Matter Variation'' by Laidlaw, Ahrens, Allman, and Bastin
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DTI.pdf First submission]
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DTI.pdf NIH Reviews]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2004-DA1.pdf Revision A1], in response to the first round of reviews
*# [http://vis.cs.brown.edu/docs/pdf/bib/NIH-2004-DRV.PDF NIH Reviews of the revised proposal]
*# [http://vis.cs.brown.edu/docs/pdf/bib/Laidlaw-2005-DA2.pdf Revision A2], in response to the second round of reviews

=== NSF ===
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPG.pdf NSF grant proposal guide]
* [http://vis.cs.brown.edu/docs/pdf/NSF-2004-GPW.pdf NSF guide to proposal writing]

== Older PhD Proposal Examples ==

Most of these example PhD "proposals" from previous years are proposals in the CS department sense: they report on a large body of completed work and propose the completion of the dissertation research. Some are from biomed, where the format is more similar to David's.

* [[:Image:Dan Keefe PhD proposal.pdf|Dan Keefe's visualization PhD proposal]] from 2006
* [[:Image:Tomer Moscovich PhD proposal.pdf|Tomer Moscovich's graphics PhD proposal]] from 2006
* [[:Image:Daf phd proposal.pdf|Daniel Acevedo's visualization PhD proposal]] from 2006 ([[:Image:Daf phd proposal presentation.ppt|presentation PPT]])
* [[:Image:Dana Tenneson phd proposal.pdf|Dana Tenneson's graphics PhD proposal]] from 2007 ([[:Image:Dana Tenneson phd proposal talk.ppt|presentation PPT]])
* [[:Image:Example biomed-eng PhD proposal by awald.pdf|Andy Wald's biomedical engineering PhD proposal]] from 2007
* [[:Image:Evan Leventhal PhD proposal.pdf|Evan Leventhal's biomedical engineering PhD proposal]] from 2008
* [[:Image:Pepe's proposal.pdf|Pepe's ecology & evolutionary biology PhD proposal]]

[[Category:HOWTO]][[Category:The PhD Process]]

Plans and Goals

2009-09-24T19:43:11Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-09-16T19:25:27Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-09-16T18:10:46Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-09-14T14:50:37Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-09-14T14:49:57Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-09-14T14:47:26Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-06-22T18:51:22Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-06-22T18:50:09Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-03-07T21:50:35Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T19:24:45Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:54:30Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:48:02Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:47:24Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:46:58Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:42:40Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:42:03Z

Wenjin Zhou: /* Wenjin */

Plans and Goals

2009-02-09T17:39:15Z

Wenjin Zhou: /* Wenjin */

NSF Nuggets

2008-11-17T15:45:39Z

Wenjin Zhou:

The 2008 request for NSF nuggets, aka Highlights, came in the following e-mail from the visualization program officer at NSF

:NSF Graphics/Visualization Program Grantee:

:It’s that time again … the annual HIGHLIGHT call.

:One way you can contribute to maintaining funding for the field is by helping to assure that the graphics/visualization program maintains strong visibility. HIGHLIGHTS are used by NSF to show congress and others what NSF is accomplishing, so they are important tools in gaining acceptance for the importance of NSF-funded research. One of our recent HIGHLIGHTS was one of a very small number inserted into last years briefing book that NSF sends to congress in support of its funding request. We have produced more highlights than other programs in the past and should strive to maintain this visibility.

:Use the attached template for submission. I am requesting that all graphics/visualization program PIs provide me with a HIGHLIGHT not later than December 1. The best of these will be forwarded to the CCF Division Director for Division approval.

:Typically, write two paragraphs. The first should describe the general research problem and the approach to a solution as well as the science advance. The second should discuss the scientific/commercial/educational/societal impact of the advance. Remember to describe your achievement in terms understandable by the intelligent layman (not a subject matter expert). Define words and simplify ideas that would not typically be familiar to someone outside the field.

:You can insert text into the textbox in the template by cutting and pasting. Include one or two images with captions, credits, and publication permissions. Images must be in gif or jpeg formats. If you have any questions, let me know by email or phone.

:Please read the instructions and style guides contained at the end of the attached highlight template.

:The HIGHLIGHT template and three sample, successful recent HIGHLIGHTS are attached. In addition to the HIGHLIGHT process at NSF, the images and descriptions you provide will help us fulfill many other needs to show scientific impact. PIs with projects that were awarded in 2008 are excused for this year.

:Cheers,

:Larry

Everyone should fill in at least one potential nugget title by Nov 14, 2008. Candidates thus far are:

Eni: "Quantitative tractography metrics using axial and radial diffusivity can help characterize the type of axonal damage"

Radu: "We describe novel visualization and interaction paradigms that
accelerate the analysis of quantitative proteomic data in the context
of published protein-protein interaction networks and canonical
signaling pathway models."

Wenjin: "We present an Analytical Model of Diffusion and Exchange of Water in White Matter from Diffusion-MRI and its Application in Measuring Axon Radii"