Blohm Lab Wiki

Welcome to CoSMo 2012!

To upload, you must first log in using the id/password combination of the name of the summer school (id) and the year (pw). Here are some upload instructions or you can go straight to the upload file page. Anything uploaded will be viewable by the internet at large, so sensitive files should be uploaded in encrypted .zip files.

Email ben-walker@northwestern.edu if you need assistance.

Sensory-motor transformations

Aug 6-7

Lecturers: Gunnar Blohm, Philip Sabes

Blohm lecture 1
Blohm lecture 2

Sabes Lecture 1
Sabes Lecture 2

Afternoon Tutorial Session 1
GradientDescent: View as .txt file or download the .m file
NNet_toolboxR2010: View as .txt file or download the .m file
RFanalysis: View as .txt file or download the .m file

Afternoon Tutorial Session 2
LQR and Kalman Filtering
Download the solution .m file: LQG_Solution.m

Introduction to the data and model sharing initiative

Aug 7 (evening)

Lecturer: Konrad Körding

The DREAM project should be on the USB drives of a few different students. If you haven't yet, find someone who has the data and get it from them. DREAM can also be downloaded piece-wise (data sets, models, tools, and documentation) from CRCNS: http://crcns.org/data-sets/movements/dream/downloading-dream. You will need to create an account on CRCNS to be able to download the project files.

If you're familiar with svn and would like info/credentials for code in the repository, contact Ben Walker

Update: Here's the fixed version of LoadDreamPaths.m. (The originally distributed version had Windows directory formatting using '/' and would not work for *nix. This script should work for all OSes.)

Description of data sets:

• Burns -- reaching with head tilt and left/right visual perturbations
• Fernandes -- reaching with uncertain and rotated midpoint feedback
• Kording -- reaching with uncertain midpoint feedback
• Mattar 07 -- generalizing from one, two or multi targets to another direction
• Mattar 10 -- reaching to a distance (short/long), generalizing to the other one (long/short)
• Ostry -- move in force field, get an estimation of where the hand is
• Scott -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back
• Stevenson -- center out, monkey with neural time stamps
• Vahdat -- movement in force field with FMRI scans pre/post learning
• Wei 08 -- visual perturbations, cursor shown only at target
• Wei 10 -- movement in differing force fields
• Young -- movement time stayed the same, but distance changed; fast, medium, slow reaches.

Cue combination

Aug 8-9

Lecturers: Mike Landy, Paul Schrater

Reading: introductory chapter on cue integration from Sensory Cue Integration
Entire syllabus and exercises
Landy Lecture 1a
Landy Lecture 1b
Landy Lecture 2
Schrater Lecture 1
Schrater Lecture 2

Afternoon Tutorial Session 1
Basic Bayes with Koerding and Wolpert Tutorial Matlabfile 1
based on Tutorial paper reference
and needs the following data DataSet

Landy/Kojima experiment: Matlab code and other interesting stuff, Stimuli, part 1 Stimuli, part 2. Note that the stimuli need to be in subdirectory "stimuli" (relative to the directory with the experimental code), and you will need the MGL toolbox for running psychophysical experiments: http://gru.brain.riken.jp/doku.php/mgl/download
You'll need to set the screen variable "scr" to 0 (to run in a window) or 1 (to run full-screen on your primary screen).

Motion Integration Tutorial Matlab files to implement Weiss et al, 2002

Afternoon Problem Session 2
Try to do 2 out of 3 problems.
Problem 1: Download this file and simulate Size/Distance Explaining away from Battaglia et al, 2010

Problem 2: Simulate the Kalman filter model in Haith et. al, 2008 The kalman filter has been implemented for you the matlab filter code , and the simulation model is described in this paper the paper . You will need this as well more matlab functions

Y Problem 3: This problem explores the discovery of possible cues to facial attractiveness.
Download the following files: the data needed , the instructions , and a gui to view the faces and dimensions

Learning, adaptation and generalization

Aug 10-11

Lecturers: John Krakauer, David Ostry, Konrad Körding

Ostry Lecture 1
Ostry Lecture 2

Krakauer Part 1
Krakauer Part 2

Tutorial: Simple introduction to Bayesian approaches
TutorialFiles

Advanced neural data analysis:
AnalysisFiles

A guide to Paper_Writing_101

Neuromechanics & spinal cord

Aug 13-14

Lecturers: Sandro Mussa-Ivaldi, Jason Kutch

Tutorial: Motor Primitives
by: Alejandro Melendez-Calderon, Ali Farshchian

Presentation
Simulink files

Sandro's presentation

Jason's Presentation

Tutorial: Day 2
Databaser and redundancy analysis code
Databaser and redundancy analysis code part 2

Robotics & brain-machine interfaces

Aug 15-16

Lecturers: Brenna Argall, Byron Yu, Lee Miller

Yu Lecture 1
Yu Lecture 2

Tutorial

Brain-machine interface exercises
Robotics exercises

and here is the time chapter from a Book Konrad is co-writing with Weiji Ma and Dan Goldreich. TimeChapter password is lowercase and describes the statistics that Konrad likes to do.

Computational neuroimaging

Aug 17-18

Lecturers: Rhodri Cusack, Alex Wade, Scott Grafton

Lecture One
Lecture Two: part 1, part 2

Tutorial:

Workshop‎

The secret of becoming a successful scientist

Aug 17 (evening)

Lecturer: Luís Amaral

Powerpoint presentation

Group Presentations

Aug 16 - 17

Students: Upload .ppt files and any other (.m, .mat, .zip, etc.) files you'd like to share. (Upload instructions at the top of the page.) Let others know about your work! Please include group member names on this wiki with the link.

Example:
Comparison of Decoding and Encoding Methods for Motor Cortical Spiking Data by Mikael Lindahl, Alexander Rajan, Stefan Habenschuss, John Butcher, Naama Kadmon

Thursday night groups:

Variability in Motor Learning by Farnaz Abdollahi, Katie Bankieris, Keturah Bixby, Moria Fisher, Ryan Morehead

Temporal influence on subject reaching strategies in Kording & Wolpert (2004) (Abstract) by Matt Balcarras, Irene Tamagnone, Leonie Oostwoud Wijdenes, Andrew Brennan, Deborah Barany, Yashar Zeighami.

Predicting Cognitive Function in Older Adults by Niousha Bolandzadeh & Nicole Salowitz

Modeling Skilled Habitual Learning by Maria Bengtson and Joseph DeSouza

Friday night groups:

Kiwii Platform: Using Kinect and Wii Board to Probe Visual and Postural Effects on Balance. by " John Rocamora, Frank Schumann, Yoshiyuki Sato, Scott Yang, Kahori Kita"

Using the Wii Remote to investigate model-based and model-free learning of visuo-motor rotations with the wrist by " Alvin Chin, Kasey Hemington, Luca Lonini and Angelina Paolozza"

Deciding when to cut your losses (Abstract) by "Matt Cieslak, Tobias Kluth, Maren Stiels, Daniel Wood"

The relationship between activity of neurons recorded simultaneously in primary motor cortex. by " Maxym Myroshnychenko, Joan Deffeyes, Azadeh Yazdan, Diana Mitchell" (Abstract)

Advanced fMRI analyses and Kalman filter application by Sara Fabbri, Heather McGregor, Simona Monaco, and Na Jin Seo