VrlWiki - User contributions [en]

Plans and Goals

2010-05-18T18:19:13Z

Eni Halilaj: /* Current Plans and Goals (Summer/Fall '10) */

Plans and Goals

2010-05-18T18:17:53Z

Eni Halilaj: /* Current Plans and Goals (Summer/Fall '10) */

Plans and Goals

2010-02-01T03:44:09Z

Eni Halilaj:

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

----
=== [[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
# 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

== 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]]

Cartilage building

2009-09-29T15:50:48Z

Eni Halilaj:

Follow these steps to build cartilage:
#cp .iv files into subject directory
#cp collected_results directory into sucject directory
#cp <bone_tag>_coord.dat files from bioeng
#run matlab -nojvm -nosplash -r "addpath('/map/gfx0/users/USER/project/wrist/pipeline'); genGlobalRt('/map/gfx0/"datapath"/collected_results/','outRT_*L.txt','/map/gfx0/"datapath"/','%s15L_anim.RT','log-genGlobalRt.txt',1); exit;"
#edit joints_linux and joints_one_linux as in “trail_contact_areas.txt”
#run cleanup_sepPoses.m & cleanup.m
#run run_cart_script & run_cart_script_app

Cartilage building

2009-09-29T15:49:21Z

Eni Halilaj:

Follow these steps to build cartilage:
#cp .iv files into subject directory
#cp collected_results directory into sucject directory
#cp <bone_tag>_coord.dat files from bioeng
#run matlab -nojvm -nosplash -r "addpath('/map/gfx0/users/USER/project/wrist/pipeline'); genGlobalRt('/map/gfx0/users/ehalilaj/backup_project/wrist/cart_data/E06001/collected_results/','outRT_*L.txt','/map/gfx0/users/ehalilaj/backup_project/wrist/cart_data/E06001/','%s15L_anim.RT','log-genGlobalRt.txt',1); exit;"
#edit joints_linux and joints_one_linux as in “trail_contact_areas.txt”
#run cleanup_sepPoses.m & cleanup.m
#run run_cart_script & run_cart_script_app

Plans and Goals

2009-09-14T15:40:17Z

Eni Halilaj:

Cartilage building

2009-08-31T15:26:34Z

Eni Halilaj: New page: Follow these steps to build cartilage: #cp .iv files into subject directory #cp collected_results directory into sucject directory #cp <bone_tag>_coord.dat files from bioeng #run matlab -...

Follow these steps to build cartilage:
#cp .iv files into subject directory
#cp collected_results directory into sucject directory
#cp <bone_tag>_coord.dat files from bioeng
#run matlab -nojvm -nosplash -r "addpath('/map/gfx0/tools/linux/bin/jspBin'); genGlobalRt('/map/gfx0/users/ehalilaj/backup_project/wrist/cart_data/E06001/collected_results/','outRT_*L.txt','/map/gfx0/users/ehalilaj/backup_project/wrist/cart_data/E06001/','%s15L_anim.RT','log-genGlobalRt.txt',1); exit;"
#edit joints_linux and joints_one_linux as in “trail_contact_areas.txt”
#run cleanup_sepPoses.m & cleanup.m
#run run_cart_script & run_cart_script_app

Inter-bone Joint Space Area Calculations

2009-08-31T15:01:54Z

Eni Halilaj: Replacing page with 'This stage of the pipeline computes the shortest distance between surface points on the bones.'

This stage of the pipeline computes the shortest distance between surface points on the bones.

Joint space area calculations

2009-08-31T15:01:11Z

Eni Halilaj:

(Liz Marai and Leor's notes for this process are at [[$G/src/jspBin/README.txt]] and [[$G/src/jspBin/trail_contact_areas.txt]])

Follow these steps to compute the distance maps:

# Get required data files into the data root directory
## get the bone Geomagic meshes in OpenInventor format (e.g., <bone_tag>.iv)
## get the "animation file" for each bone, (e.g., <bone_tag>_anim.RT)
## get anatomical coordinate system for each bone (e.g., <bone_tag>_coord.dat)
# Prepare scripts
## copy the "joints_one_linux" and "joints_linux" from $G/bin/jspBin/ to your data's top-level directory
## replace "set data_directory" lines in both with the path to your directory
## replace bone tags with the ones of interest (e.g., bone_tag_1=sca15L and bone_tag_2=lun15L)
## see further options at [[$G/src/jspBin/trail_contact_areas.txt]]
# Run scripts
## ./joints_one_linux
## ./joints_linux

For more details, see [[$G/src/jspBin/README.txt]] and [[$G/src/jspBin/trail_contact_areas.txt]].

Joint space area calculations

2009-08-31T14:59:32Z

Eni Halilaj: New page: (Liz Marai and Leor's notes for this process are at $G/src/jspBin/README.txt and $G/src/jspBin/trail_contact_areas.txt) Follow these steps to compute the distance maps: 1. Get required...

(Liz Marai and Leor's notes for this process are at $G/src/jspBin/README.txt and $G/src/jspBin/trail_contact_areas.txt)

Follow these steps to compute the distance maps:

1. Get required data files into the data root directory
1. get the bone Geomagic meshes in OpenInventor format (e.g., <bone_tag>.iv)
2. get the "animation file" for each bone, (e.g., <bone_tag>_anim.RT)
3. get anatomical coordinate system for each bone (e.g., <bone_tag>_coord.dat)
2. Prepare scripts
1. copy the "joints_one_linux" and "joints_linux" from $G/bin/jspBin/ to your data's top-level directory
2. replace "set data_directory" lines in both with the path to your directory
3. replace bone tags with the ones of interest (e.g., bone_tag_1=sca15L and bone_tag_2=lun15L)
4. see further options at $G/src/jspBin/trail_contact_areas.txt
3. Run scripts
1. ./joints_one_linux
2. ./joints_linux

For more details, see $G/src/jspBin/README.txt and $G/src/jspBin/trail_contact_areas.txt.

Wrists

2009-08-31T14:57:08Z

Eni Halilaj:

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#[[Data]]
#[[Bone Surface Extraction]]
#[[Registration of Bones Across Positions]]
#[[Retrieval of Kinematics]]
#[[Inter-bone Joint Space Area Calculations]]
#[[Ligament Path Calculations]]
#[[Cartilage Maps (location & thickness)]]
#[[Cartilage Surface Deformations]]
#[[Joint Simulation]]

==Tools==

#[[registration]]
#[[joint space area calculations]]
#[[cartilage building]]
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Plans and Goals

2009-06-03T18:32:26Z

Eni Halilaj: /* Eni */

Registration of Bones Across Positions

2009-05-20T19:45:35Z

Eni Halilaj:

The registration process uses bone surfaces extracted from the neutral position and CT volumes to calculate bone kinematics, i.e rotations and translations of the center of mass of each each bone, across each position. This method has 2 steps.

==Tissue Classification and Localized Distance Fields==

Bone, soft tissue, and air are represented by different intensities in CT images. Our tissue classification algorithm goes thought the non-neutral CT volumes and calculates a distance from the center of each voxel to the closest material boundary. The output of classification is a distance field for each material. We are interested only in the distance field of the bone material.

==Object Tracking==

The geometrical model obtained from the neutral CT scans and the classification results are used to retrieve bone kinematics across positions. The model is registered in a given non-neutral position by searching until distance field similarity is maximized.

Registration of Bones Across Positions

2009-05-20T19:45:01Z

Eni Halilaj: New page: The registration process uses bone surfaces extracted from the neutral position and CT volumes to calculate bone kinematics, i.e rotations and translations of the center of mass of each ea...

The registration process uses bone surfaces extracted from the neutral position and CT volumes to calculate bone kinematics, i.e rotations and translations of the center of mass of each each bone, across each position. This method has 2 steps.

==Tissue classification and Localized Distance fields==

Bone, soft tissue, and air are represented by different intensities in CT images. Our tissue classification algorithm goes thought the non-neutral CT volumes and calculates a distance from the center of each voxel to the closest material boundary. The output of classification is a distance field for each material. We are interested only in the distance field of the bone material.

==Object tracking==

The geometrical model obtained from the neutral CT scans and the classification results are used to retrieve bone kinematics across positions. The model is registered in a given non-neutral position by searching until distance field similarity is maximized.

Wrists

2009-05-07T20:21:01Z

Eni Halilaj: /* Tools */

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#[[Data]]
#[[Bone Surface Extraction]]
#[[Registration of Bones Across Positions]]
#[[Retrieval of Kinematics]]
#[[Inter-bone Joint Space Area Calculations]]
#[[Ligament Path Calculations]]
#[[Cartilage Maps (location & thickness)]]
#[[Cartilage Surface Deformations]]
#[[Joint Simulation]]

==Tools==

#[[registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Bone Surface Extraction

2009-05-07T20:20:45Z

Eni Halilaj: New page: One of the CT volumes is referenced as the neutral position. This volume is manually segmented via the Analyze software package in order to extract the bone surfaces. These bone surfaces a...

One of the CT volumes is referenced as the neutral position. This volume is manually segmented via the Analyze software package in order to extract the bone surfaces. These bone surfaces are represented by discrete points and are used for the automated registration of the remaining positions.

Wrists

2009-05-07T20:20:09Z

Eni Halilaj: /* Overall Pipeline */

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#[[Data]]
#[[Bone Surface Extraction]]
#[[Registration of Bones Across Positions]]
#[[Retrieval of Kinematics]]
#[[Inter-bone Joint Space Area Calculations]]
#[[Ligament Path Calculations]]
#[[Cartilage Maps (location & thickness)]]
#[[Cartilage Surface Deformations]]
#[[Joint Simulation]]

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Wrists

2009-05-07T20:17:50Z

Eni Halilaj: /* Overall Pipeline */

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#[[Data]]
#[[Bone Surface Extraction]]
#[[Registration]]
#[[Retrieval of Kinematics]]
#[[Inter-bone Joint Space Area Calculations]]
#[[Ligament Path Calculations]]
#[[Cartilage Maps (location & thickness)]]
#[[Cartilage Surface Deformations]]
#[[Joint Simulation]]

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Segmentation of Neutral Wrist

2009-05-07T20:12:38Z

Data

2009-05-07T19:58:08Z

Eni Halilaj: New page: CT volume images of several wrist positions are usually collected for our studies. The acquisition parameters vary form one dataset to the other. The data are usually converted to MRI form...

CT volume images of several wrist positions are usually collected for our studies. The acquisition parameters vary form one dataset to the other. The data are usually converted to MRI format at the Bioengineering lab for consistency purposes and to ensure compatibility with our tools.

Wrists

2009-05-07T19:57:30Z

Eni Halilaj: /* Overall Pipeline */

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#[[Data]]
#[[Segmentation of Neutral Wrist]]
#[[Registration of Non-neutral Positions]]
#[[Retrieval of Kinematics]]
#[[Inter-bone Joint Space Area Calculations]]
#[[Ligament Path Calculations]]
#[[Cartilage Maps (location & thickness)]]
#[[Cartilage Surface Deformations]]
#[[Joint Simulation]]

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Data acquisition

2009-05-07T19:55:29Z

Eni Halilaj:

Data acquisition

2009-05-07T19:48:15Z

Eni Halilaj: New page: CT volume images of several wrist positions are usually collected for our studies. The acquisition parameters vary form one dataset to the other.

CT volume images of several wrist positions are usually collected for our studies. The acquisition parameters vary form one dataset to the other.

Wrists

2009-05-07T19:43:36Z

Eni Halilaj: /* Overall Pipeline */

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#[[Data acquisition]]
#[[Segmentation of neutral wrist]]
#[[Registration of non-neutral positions]]
#[[Retrieval of kinematics]]
#[[Inter-bone joint space area calculations]]
#[[Ligament path calculations]]
#[[Cartilage maps (location & thickness)]]
#[[Cartilage surface deformations]]
#[[Joint simulation]]

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Registration

2009-05-07T17:52:03Z

Eni Halilaj:

[https://wiki.brown.edu/confluence/display/orthobio/Compiling+the+CS+Carpal+Pipeline|Compiling the CS Carpal Pipeline]

#Create the subject directory [EXXXXX_scan] & import files/folders from Bioengineering:
##CT_Scans [scans of all wrist positions]
##original_stacks [segmented neutral position of wrist]
##crop_values.txt
#Run batchGen.pl to create the master batch files
##should always be run from the top level of the subject directory
##the first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.
##batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three
##/map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl --crop
#Run unixbatch from the top level of the subject directory.
##This should go through and run all the major steps
##./unixbatch
#After unixbatch finishes, you need to validate the output of the registration steps
##Use WristVis to check the registration
##If there are errors, re-run batchGen.pl, without the --crop option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.
#Folders collected_results & auto_registr_resuls contain the same registration results in different formats, whereas classified_scans contains the tissue classification results

Wrists

2009-05-04T17:41:11Z

Eni Halilaj:

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="250px">
Image:Wrist.jpg.jpeg| X-ray of the wrist with bone names
Image:Ligaments.jpg| Ligaments: posterior view of left wrist
</gallery>

==Overall Pipeline==

#Data acquisition
#Segmentation of neutral wrist
#Registration of non-neutral positions
#Retrieval of kinematics
#Inter-bone joint space area calculations
#Ligament path calculations
#Cartilage maps (location & thickness)
#Cartilage surface deformations
#Joint simulation

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Wrists

2009-05-04T17:37:47Z

Eni Halilaj:

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

<gallery widths="250px" heights="200px">
Image:Wrist.jpg.jpeg| ''X-ray of the wrist with bone names''
Image:Ligaments.jpg| ''Ligaments: posterior view of left wrist''
</gallery>

==Overall Pipeline==

#Data acquisition
#Segmentation of neutral wrist
#Registration of non-neutral positions
#Retrieval of kinematics
#Inter-bone joint space area calculations
#Ligament path calculations
#Cartilage maps (location & thickness)
#Cartilage surface deformations
#Joint simulation

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

File:Ligaments.jpg

2009-05-04T17:25:06Z

Eni Halilaj:

File:Wrist.jpg.jpeg

2009-05-04T16:52:27Z

Eni Halilaj:

Wrists

2009-05-04T01:28:59Z

Eni Halilaj:

The wrist is a diarthrodial anatomical joint consisting of 8 small bones (scaphoid, capitate, hamate, lunate, trapezium, trapezoid, triquetrum, pisiform) and 7 long bones (radius, ulna, and 5 metacarpals). When subject to injury and disease the wrist undergoes changes in kinematics, inter-bone joint space areas, cartilage thickness, length of ligament paths, etc. Developing computational tools for the analysis of anatomical joint characteristics, is important in understanding the cause of injury, tracing the progress of disease, and taking preventative measures.

==Overall Pipeline==

#Data acquisition
#Segmentation of neutral wrist
#Registration of non-neutral positions
#Retrieval of kinematics
#Inter-bone joint space area calculations
#Ligament path calculations
#Cartilage maps (location & thickness)
#Cartilage surface deformations
#Joint simulation

==Tools==

#[[Registration]]
#cartilage building
#"wiggling" bones around
#ligament length measures
#<fill in with more tools..>

Propose your PhD

2009-03-21T22:11:21Z

Eni Halilaj: /* PhD Proposal Examples */

{{stub}}

== PhD Proposal Examples ==

While we're waiting to cook up some specific advice on proposing your PhD thesis, check out these example proposals from previous years:

* [[: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]]

== Grant Proposals ==

The older examples above are "proposals" in the sense used by the CS department; they come rather late in the PhD process and are 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. Check the following links for grant proposal guidelines and examples:

=== 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]

[[Category:HOWTO]]

File:Pepe's proposal.pdf

2009-03-21T22:08:38Z

Eni Halilaj:

Defend your PhD

2009-03-18T14:50:11Z

Eni Halilaj: New page: == Dissertation Examples == * Liz Marai's visualization dissertation from 2007 * [[:Image:Evan Leventhal dissertation.pdf|Evan Leventhal's biomedical...

== Dissertation Examples ==

* [[:Image:Liz Marai dissertation.pdf|Liz Marai's visualization dissertation]] from 2007
* [[:Image:Evan Leventhal dissertation.pdf|Evan Leventhal's biomedical engineering dissertation]] from 2009

Propose your PhD

2009-03-18T14:49:35Z

Eni Halilaj:

{{stub}}

== PhD Proposal Examples ==

While we're waiting to cook up some specific advice on proposing your PhD thesis, check out these example proposals from previous years:

* [[: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

== Grant Proposals ==

The older examples above are "proposals" in the sense used by the CS department; they come rather late in the PhD process and are 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. Check the following links for grant proposal guidelines and examples:

=== 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]

[[Category:HOWTO]]

Propose your PhD

2009-03-18T14:46:13Z

Eni Halilaj:

{{stub}}

== PhD Proposal Examples ==

While we're waiting to cook up some specific advice on proposing your PhD thesis, check out these example proposals from previous years:

* [[: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

== Dissertation Examples ==

* [[:Image:Liz Marai dissertation.pdf|Liz Marai's visualization dissertation]] from 2007
* [[:Image:Evan Leventhal dissertation.pdf|Evan Leventhal's biomedical engineering dissertation]] from 2009

== Grant Proposals ==

The older examples above are "proposals" in the sense used by the CS department; they come rather late in the PhD process and are 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. Check the following links for grant proposal guidelines and examples:

=== 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]

[[Category:HOWTO]]

File:Liz Marai dissertation.pdf

2009-03-18T14:45:45Z

Eni Halilaj:

Propose your PhD

2009-03-18T14:38:48Z

Eni Halilaj: /* Example PhD Proposals */

{{stub}}

== Example PhD Proposals ==

While we're waiting to cook up some specific advice on proposing your PhD thesis, check out these example proposals from previous years:

* [[: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

== Grant Proposals ==

The older examples above are "proposals" in the sense used by the CS department; they come rather late in the PhD process and are 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. Check the following links for grant proposal guidelines and examples:

=== 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]

[[Category:HOWTO]]

File:Evan Leventhal PhD proposal.pdf

2009-03-18T14:38:06Z

Eni Halilaj:

File:Evan Leventhal dissertation.pdf

2009-03-18T14:26:56Z

Eni Halilaj:

File:Evan Leventhatl proposal.pdf

2009-03-18T14:26:00Z

Eni Halilaj:

Diffusion MRI

2009-02-04T21:35:18Z

Eni Halilaj: /* Collaboration Table */

''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 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.

== 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" column, "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" | 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 $G/data/diffusion?">F</abbr>
! {{Hl2}} | <abbr title="DWIs converted to MriImage?">M</abbr>
! {{Hl2}} | <abbr title="Tensors fit?">F</abbr>
! {{Hl2}} | <abbr title="Tubes generated?">T</abbr>
! {{Hl2}} | <abbr title="Works in Brainapp?">B</abbr>
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
|-
| {{Hl2}} | Cognitive Aging
| St. Louis
| Rob Paul ([[Wikipedia:UMSL|UMSL]]), Tom Conturo ([[Wikipedia:WUSTL|WUSTL]])
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-20
| content = <code>$G/data/diffusion/st_louis/cognitive_aging.2008.07.20</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[Interfile]]
| 1
| 83x110x64
| 36
| 2.0x2.0x2.0
| colspan="6" {{?}}
|-
| {{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" {{?}}
|-
| 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" {{?}}
|-
| {{Hl2}} rowspan="4" | HIV
| Memorial Hospital
| rowspan="4" | Steve Correia, Ron Cohen
| {{?}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| {{?}}
| [[DICOM]]
| {{?}}
| 256x256x90
| {{?}}
| 0.8477x0.8477x1.667
| 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>$G/data/diffusion/brown3t/302CK.2007.11.30</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| rowspan="3" | 3T
| rowspan="3" {{?}}
| [[DICOM]]
| 1
| 256x256x180
| 74
| .8828x.8828x.7
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-21
| content = <code>$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" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-10-09
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study_registered.2007.02.07</code>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| [[NIfTI]]
| 8
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| R || L || A || P || I || S
|-
| {{Hl2}} | Macaques
| Caltech
| Jason Kaufman
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-21
| content = <code>$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" {{?}}
|-
| {{Hl2}} rowspan="3" | SA HIV
| rowspan="3" | Cape Town
| rowspan="3" | Bruce Spottiswoode
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-10-22
| content = <code>$G/data/diffusion/south_africa/normal.2007.10.22</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| 1
| 127x128x70
| 40
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-09
| content = <code>$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}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| 3
| 127x127x75
| 66
| 1.71875x1.71875x1.7
| 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>$G/data/diffusion/south_africa/hiv_positive_apathy_negative_15patients.2008.07.24</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| 4-D [[NIfTI]]
| 15
| 128x128x75
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 9ex; | contentcss = font-size: 90%; width: 25ex;
| header = 65
| content = For each patient, there are 5 acquisitions in 13 directions each, all registered to each other. Each acquisition is a separate 4-D [[NIfTI]] file.
}}
| 1.875x1.875x1.9
| L || R || A || P || I || S
|-
| {{Hl2}} rowspan="2" | Tumors
| rowspan="2" | Edinburgh
| rowspan="2" | Mark Bastin
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-11-06
| content = <code>$G/data/diffusion/edinburgh/tumor.2007.11.06</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM]]
| 1
| {{?}}
| 9
| {{?}}
| 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> 2 scans uploaded 2008-08-06 need to be filed in with this group.
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM]]
| 5
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|}

== 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>
|-
| [[DICOM#Mosaic|DICOM Mosaic]]
| <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 ==
* [[Diagnose tensor orientation problems]]

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

Diffusion MRI

2009-02-04T20:25:20Z

Eni Halilaj: /* Collaboration Table */

''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 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.

== 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" column, "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" | 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 $G/data/diffusion?">F</abbr>
! {{Hl2}} | <abbr title="DWIs converted to MriImage?">M</abbr>
! {{Hl2}} | <abbr title="Tensors fit?">F</abbr>
! {{Hl2}} | <abbr title="Tubes generated?">T</abbr>
! {{Hl2}} | <abbr title="Works in Brainapp?">B</abbr>
! {{Hl2}} | <abbr title="Field strength">F</abbr>
! {{Hl2}} | <abbr title="Brand/Manufacturer">B</abbr>
! {{Hl2}} | -X
! {{Hl2}} | +X
! {{Hl2}} | -Y
! {{Hl2}} | +Y
! {{Hl2}} | -Z
! {{Hl2}} | +Z
|-
| {{Hl2}} | Cognitive Aging
| St. Louis
| Rob Paul ([[Wikipedia:UMSL|UMSL]]), Tom Conturo ([[Wikipedia:WUSTL|WUSTL]])
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-20
| content = <code>$G/data/diffusion/st_louis/cognitive_aging.2008.07.20</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[Interfile]]
| 1
| 83x110x64
| 36
| 2.0x2.0x2.0
| colspan="6" {{?}}
|-
| {{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" {{?}}
|-
| 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" {{?}}
|-
| {{Hl2}} rowspan="4" | HIV
| Memorial Hospital
| rowspan="4" | Steve Correia, Ron Cohen
| {{?}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| 1.5T
| {{?}}
| [[DICOM]]
| {{?}}
| 256x256x90
| {{?}}
| 0.8477x0.8477x1.667
| 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>$G/data/diffusion/brown3t/302CK.2007.11.30</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| rowspan="3" | 3T
| rowspan="3" {{?}}
| [[DICOM]]
| 1
| 256x256x180
| 74
| .8828x.8828x.7
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-07-21
| content = <code>$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" {{?}}
|-
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-10-09
| content = <code>$G/data/diffusion/brown3t/cohen_hiv_study_registered.2007.02.07</code>
}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| {{y}}
| [[NIfTI]]
| 8
| 128x128x70
| 74
| 1.76562x1.76562x1.8
| R || L || A || P || I || S
|-
| {{Hl2}} | Macaques
| Caltech
| Jason Kaufman
| {{hidden | fw1 = normal |ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-21
| content = <code>$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" {{?}}
|-
| {{Hl2}} rowspan="3" | SA HIV
| rowspan="3" | Cape Town
| rowspan="3" | Bruce Spottiswoode
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-10-22
| content = <code>$G/data/diffusion/south_africa/normal.2007.10.22</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| 1
| 127x128x70
| 40
| 1.71875x1.71875x1.7
| colspan="6" {{?}}
|-
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2008-05-09
| content = <code>$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}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM#Mosaic|DICOM Mosaic]]
| 3
| 127x127x75
| 66
| 1.71875x1.71875x1.7
| 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>$G/data/diffusion/south_africa/hiv_positive_apathy_negative_15patients.2008.07.24</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{?}}
| {{?}}
| 4-D [[NIfTI]]
| 15
| 128x128x75
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 9ex; | contentcss = font-size: 90%; width: 25ex;
| header = 65
| content = For each patient, there are 5 acquisitions in 13 directions each, all registered to each other. Each acquisition is a separate 4-D [[NIfTI]] file.
}}
| 1.875x1.875x1.9
| L || R || A || P || I || S
|-
| {{Hl2}} rowspan="2" | Tumors
| rowspan="2" | Edinburgh
| rowspan="2" | Mark Bastin
| {{hidden | fw1 = normal | ta1 = left | headercss = font-size: 100%; width: 18ex; | contentcss = font-size: 90%; width: 60ex;
| header = 2007-11-06
| content = <code>$G/data/diffusion/edinburgh/tumor.2007.11.06</code>
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM]]
| 1
| {{?}}
| 9
| {{?}}
| 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> 2 scans uploaded 2008-08-06 need to be filed in with this group.
}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{yes}}
| {{no}}
| {{no}}
| {{no}}
| {{no}}
| {{?}}
| {{?}}
| [[DICOM]]
| 5
| {{?}}
| {{?}}
| {{?}}
| colspan="6" {{?}}
|}

== 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>
|-
| [[DICOM#Mosaic|DICOM Mosaic]]
| <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 ==
* [[Diagnose tensor orientation problems]]

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

Diffusion MRI

2009-02-04T20:07:24Z

Eni Halilaj: /* Collaboration Table */

Nascent Papers

2009-02-04T15:29:21Z

Eni Halilaj: /* Eni */

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

1. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

i.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

ii.Comparing motor control test results with the same metrics, in the SLF

2. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''

1.

i. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

ii. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

2. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

'''Tentative Abstract'''

In this study we examine the interdependence of cognitive test results and white matter integrity, as assessed by quantitative tractography metrics. Different fiber tracts in the brain are related to different congnitive functions, e.g. the SLF is related to working memory. Therefore atrophy in a certain tract leads to impaired performance in functions controlled by that tract. Knowing that CADASIL causes severe injury in the SLF, but not the fornix, we chose to compare the structural integrity of these tracts, as measured by several quatitative tractography metrics, against working memory test results and motor control test results. The n-back test was used to test working memory and the X-test was used to test motor control. The results of the n-back correlated well with the metrics, in the SLF. They did not correlate with the metrics, in the fornix. Among the metrics NTWLad expressed the highest correlation with the n-back test results, suggesting that there is more axonal loss than demyelination in the tract. The results of the X-test did not correlate significantly with any of the metrics, in the SLF. These results confirm that there is a strong relationship among performance in cognitive tests and white matter health, measured by quantitative tractography. Furthermore, they draw some light on the nature of axonal damage caused by CADASIL.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----

Nascent Papers

2009-02-04T15:25:27Z

Eni Halilaj:

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

1. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

i.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

ii.Comparing motor control test results with the same metrics, in the SLF

2. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''

1.

i. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

ii. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

2. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

'''Tentative Abstract'''

In this study we investigate on the interdependence of cognitive test results and white matter integrity, as assessed by quantitative tractography metrics. Different fiber tracts in the brain are related to different congnitive functions, e.g. the SLF is related to working memory. Therefore atrophy in a certain tract leads to impaired performance in functions controlled by that tract. Knowing that CADASIL causes severe injury in the SLF, but not the fornix, we chose to compare the structural integrity of these tracts, as measured by several quatitative tractography metrics, against working memory test results and motor control test results. The n-back test was used to test working memory and the X-test was used to test motor control. The results of the n-back correlated well with the metrics, in the SLF. They did not correlate with the metrics, in the fornix. Among the metrics NTWLad expressed the highest correlation with the cognitive test results, sugesting that there is more axonal loss than demyelination in the tract. The results of the X-test did not correlate significantly with any of the metrics, in the SLF. These results confirm that there is a strong relationship among performance in cognitive tests and white matter health, measured by quantitative tractography. Furthermore, they draw some light on the nature of axonal damage caused by CADASIL.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----

Nascent Papers

2009-02-04T15:24:52Z

Eni Halilaj: /* Eni */

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

1. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

i.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

ii.Comparing motor control test results with the same metrics, in the SLF

2. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''

1.

i. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

ii. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

2. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

'''Tentative Abstract'''
In this study we investigate on the interdependence of cognitive test results and white matter integrity, as assessed by quantitative tractography metrics. Different fiber tracts in the brain are related to different congnitive functions, e.g. the SLF is related to working memory. Therefore atrophy in a certain tract leads to impaired performance in functions controlled by that tract. Knowing that CADASIL causes severe injury in the SLF, but not the fornix, we chose to compare the structural integrity of these tracts, as measured by several quatitative tractography metrics, against working memory test results and motor control test results. The n-back test was used to test working memory and the X-test was used to test motor control. The results of the n-back correlated well with the metrics, in the SLF. They did not correlate with the metrics, in the fornix. Among the metrics NTWLad expressed the highest correlation with the cognitive test results, sugesting that there is more axonal loss than demyelination in the tract. The results of the X-test did not correlate significantly with any of the metrics, in the SLF. These results confirm that there is a strong relationship among performance in cognitive tests and white matter health, measured by quantitative tractography. Furthermore, they draw some light on the nature of axonal damage caused by CADASIL.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----

Nascent Papers

2009-02-02T22:16:57Z

Eni Halilaj: /* Eni */

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

1. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

i.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

ii.Comparing motor control test results with the same metrics, in the SLF

2. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''

1.

i. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

ii. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

2. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----

Nascent Papers

2009-02-02T22:16:32Z

Eni Halilaj: /* Eni */

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

1. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

i.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

ii.Comparing motor control test results with the same metrics, in the SLF

2. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''

1.
i. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

ii. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

2. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----

Nascent Papers

2009-02-02T22:15:56Z

Eni Halilaj: /* Eni */

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

1. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

i.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

ii.Comparing motor control test results with the same metrics, in the SLF

2. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''

1.
i. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

ii. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

2. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----

Nascent Papers

2009-02-02T22:14:14Z

Eni Halilaj: /* Eni */

== Eni ==

'''A Comparative Study of Cognitive Functioning and Fiber Tract Integrity'''

'''Contributions'''

I. The paper presents a twofold comparison of cognitive test results and white matter integrity, in specific fiber tracts of CADASIL patients, by:

a.Comparing working memory test results with several quantitative tractography metrics of structural integrity in the SLF and the fornix

b.Comparing motor control test results with the same metrics, in the SLF

II. The paper draws on the relationship between axial or radial diffusivity and the nature of axonal damage, to infer the prevalent type of damage in tracts affected by CADASIL

'''Results'''
I.
a. Working memory test results should correlate with most metrics, in the SLF. They should not however correlate as much with the metrics, in the fornix, since CADASIL affects SLF more drastically than it affects the fornix.

b. In the SLF, motor control test results should not correlate with the metrics as highly as the working memory test results do.

II. Among the metrics, there should be a few that correlate more significantly than others with the cognitive test result. These correlations should provide clues abut the type of damage that CADASIL causes. Also, they will potentially bring out the most effective metrics for the assessment of white matter integrity in CADASIL patients.

== Trevor ==

Tentative Title(s):
:'''Extracting Semantic Content from Interaction Histories in 3D, Time-varying Visualizations'''
:'''Interaction Histories for Collaboration, Search, and Prediction in 3D, Time-Varying Visualizations'''

Contributions:

#Introduces a generalizable framework for automatically generating sharable, editable, searchable interaction histories in time-varying 3D applications.
#Demonstrates utility of Relational Markov Models (RMMs) in extracting semantic information from interaction histories, useful for prediction and automation in scientific exploration.
#Contributes the technical implementation details (software itself? open source project?) for applying said methods in pre-existing applications.

Results:

#Techniques were applied in 3 existing applications: Animal kinematics from CT & X-ray, bat flight kinematics from light capture, and (__?? brain stuff, wrist stuff??, maybe infovis stuff like proteomics??___)
#User evaluation of history generation matched user-defined histories in X% of cases. (Fully-automated, semi-automated, manual)
#Collect data on collaboration? Anecdotal evidence on how tools were used for collaboration? (Need to get on this quickly, with new data sets that are actively being explored. Talk to Beth, Sharon.)
#User study on task completion times with tools versus without tools.
#Relational models evaluated against survey data. i.e. User was trying to uncover ''this'' in series of interactions, system interpreted interactions as ''this'' or ''that''.
''(Need to think more about how to objectify the previous two bullets.)''

Abstract: ''TBD.''

References:

:[http://delivery.acm.org/10.1145/260000/253801/p80-wegner.pdf?key1=253801&key2=7045063321&coll=GUIDE&dl=GUIDE&CFID=20148663&CFTOKEN=29763343 Why interaction is more powerful than algorithms]

:[http://www.cs.washington.edu/homes/pedrod/papers/kdd02a.pdf Relational Markov Models and their Application to Adaptive Web Navigation]

:[http://delivery.acm.org/10.1145/340000/336374/p220-dieberger.pdf?key1=336374&key2=4394063321&coll=GUIDE&dl=GUIDE&CFID=20718099&CFTOKEN=73103245 Visualizing Interaction History on a Collaborative Web Server]

:[http://delivery.acm.org/10.1145/360000/353487/p174-hollan.pdf?key1=353487&key2=1205063321&coll=GUIDE&dl=GUIDE,ACM&CFID=20147967&CFTOKEN=42850857 Distributed Cognition: Toward a New Foundation for Human-Computer Interaction Research]

----

== Çağatay ==

====Coloring 3d line fields using Boy’s real projective plane immersion====

''Abstract'':

It’s often useful to visualize a line field, a function that sends each
point P of the plane or of space to a line through P; such fields
arise in the study of tensor fields, where the principal eigendirection
at each point determines a line (but not a vector, since if v is an
eigenvector, so is −v). To visualize such a field, we often assign
a color to each line; thus we consider the coloring of line fields as
a mapping from the real projective plane (RP2) to color space.
Ideally, such a coloring scheme should be smooth and one-to-one,
so that the color uniquely identifies the line; unfortunately, there
is not such mapping. We introduce Boy’s surface, an immersion
of the projective plane in 3D, as a model for coloring line fields,
and show results from its application in visualizing orientation in
diffusion tensor fields. This coloring method is smooth and one to
one except on a set of measure zero (the double curve of Boy’s
surface).
----