Difference between revisions of "CoSMo 2012"
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Welcome to CoSMo 2012!
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This page contains course materials for the [http://www.compneurosci.com/CoSMo2012/program.html CoSMo 2012] summer school. 
  
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Please use this page to upload information that will be used during the summer school.  If you need to add documents, you can use the account cosmo/cosmo.  Follow these [[upload instructions]] if you need to upload files.  Email ben-walker@northwestern.edu if you need assistance.
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To upload files, you must log in with an account that has upload access.  Here are some [[upload instructions]] or you can go straight to the [[Special:Upload | upload file page]].   
  
 +
Contact [[Ben Walker]] if you need assistance.
 +
----
  
 
== Sensory-motor transformations ==
 
== Sensory-motor transformations ==
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Lecturers: Gunnar Blohm, Philip Sabes
 
Lecturers: Gunnar Blohm, Philip Sabes
  
 +
[[Media:Sensory-motor-Blohm-1.pdf | Blohm lecture 1]] <br>
 +
[[Media:Sensory-motor-Blohm-2.pdf | Blohm lecture 2]]
 +
 +
[[Media:2012-08-CoSoMo-1-NeuralCircuits-and-Behavior.pdf | Sabes Lecture 1]] <br>
 +
[[Media:2012-08-CoSoMo-2-SensoryIntegration-and-Learning.pdf | Sabes Lecture 2]]
 +
 +
'''Afternoon Tutorial Session 1''' <br>
 +
GradientDescent:  View as [[Media:GradientDescent.txt | .txt file]]  or download the [[Media:GradientDescent.m | .m file]] <br>
 +
NNet_toolboxR2010:  View as [[Media:NNet_toolboxR2010.txt | .txt file]] or download the [[Media:NNet_toolbox.m | .m file]] <br>
 +
RFanalysis:  View as [[Media:RFanalysis.txt | .txt file]] or download the [[Media:RFanalysis.m | .m file]]
 +
 +
'''Afternoon Tutorial Session 2''' <br>
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[[Media:LQR and Kalman Filtering Tutorial.pdf | LQR and Kalman Filtering]] <br>
 +
Download the solution .m file: [[Media:LQG_Solution.m | LQG_Solution.m]]
 +
 +
----
  
 
==Introduction to the data and model sharing initiative==
 
==Introduction to the data and model sharing initiative==
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Lecturer: Konrad Körding
 
Lecturer: Konrad Körding
  
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The DREAM project can be download from CRCNS.org/hosted-projects/dream
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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 [https://crcns.org/join_form?came_from=http%3A//crcns.org/data-sets/movements/dream/downloading-dream create] an account on CRCNS to be able to download the project files.
 +
 
 +
<!--[[File:AllDream.zip]]
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 +
If you want "all" of DREAM (models, tools, and documentation), click here: [http://klab.smpp.northwestern.edu/wiki/images/d/d2/AllDream.zip AllDream.zip] <br>
 +
-->
 +
: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 [[Media:LoadDreamPaths.m | LoadDreamPaths.m]].  (The originally distributed version had Windows directory formatting using '/' and would not work for *nix.  This script should work for all OSes.)
 +
 
 +
 
 +
Here is a [[Media:DataSetDescriptions.txt| description of data sets]] currently in Dream.  Dream is growing, but this list is accurate as of the time of the summer school.
 +
<!--*Burns -- reaching with head tilt and left/right visual perturbations
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*Fernandes -- reaching with uncertain and rotated midpoint feedback
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*Kording -- reaching with uncertain midpoint feedback
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*Mattar 07 -- generalizing from one, two or multi targets to another direction
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*Mattar 10 -- reaching to a distance (short/long), generalizing to the other one (long/short)
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*Ostry -- move in force field, get an estimation of where the hand is
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*Scott -- monkey (no spike), center out: even and not evenly distributed targets, also a forward/back
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*Stevenson -- center out, monkey with neural time stamps
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*Vahdat -- movement in force field with FMRI scans pre/post learning
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*Wei 08 -- visual perturbations, cursor shown only at target
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*Wei 10 -- movement in differing force fields
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*Young -- movement time stayed the same, but distance changed; fast, medium, slow reaches.
 +
-->
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 +
----
  
 
==Cue combination ==
 
==Cue combination ==
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Lecturers: Mike Landy, Paul Schrater
 
Lecturers: Mike Landy, Paul Schrater
  
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[[Media:Cueint.pdf | Reading: introductory chapter on cue integration from Sensory Cue Integration]] <br>
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[[Media:COSMOsyllabus.pdf | Entire syllabus and exercises]] <br>
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[[Media:Cosmolecturesmsl-I-IV_1_22.pdf |  Landy Lecture 1a]] <br>
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[[Media:Cosmolecturesmsl-I-IV_23_38.pdf |  Landy Lecture 1b]] <br>
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[[Media:COSMOlecturesmsl-VIII.pdf | Landy Lecture 2]] <br>
 +
[[Media:COSMOlecturesprs-motint.pdf |Schrater Lecture 1]] <br>
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[[Media:Cosmo2schrater.pdf |Schrater Lecture 2]]
 +
 +
 +
'''Afternoon Tutorial Session 1''' <br><br>
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''Basic Bayes with Koerding and Wolpert''
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[[Media:CueIntegrationTutorialKW.m‎ | Tutorial Matlabfile 1]] <br>
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based on [[Media:Kording_Bayes_integrate_sensorimotor_learn_2004.pdf | Tutorial paper reference]] <br>
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and needs the following data  [[Media:KordingRed_2004.mat | DataSet ]] <br>
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<br>
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''Landy/Kojima experiment'':
 +
[[Media:Exptcode.zip | Matlab code and other interesting stuff]],
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[[Media: Stimuli1.zip | Stimuli, part 1]]
 +
[[Media: Stimuli2.zip | 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.stanford.edu/doku.php/mgl/beta
 +
<br>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).
 +
<br>
 +
<br>
 +
''Motion Integration Tutorial''
 +
[[Media: MotionIntegrationTutorial2.zip | Matlab files to implement Weiss et al, 2002 ]]
 +
 +
 +
'''Afternoon Problem Session 2''' <br>
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Try to do 2 out of 3 problems. <br> <br>
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'''Problem 1: '''
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[[Media:ExplainingAway.m | Download this file and simulate Size/Distance Explaining away from Battaglia et al, 2010]] <br> <br>
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'''Problem 2: '''
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[[Media:KalmanSimulation.m | Simulate the Kalman filter model in Haith et. al, 2008]]  The kalman filter has been implemented for you [[Media:Kalman_filter.m |the matlab filter code ]], and the simulation model is described in this paper  [[Media:haith-NIPS2008.pdf |the paper ]]. You will need this as well [[Media:gaussian_prob.m |more matlab functions]]<br><br>
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'''Problem 3:'''  This problem explores the discovery of possible cues to facial attractiveness. <br>  Download the following files: [[Media:Faceimananalysis.mat| the data needed ]], [[Media:AttractProjectGoals.m | the instructions ]], and [[Media:faceimgui.m | a gui to view the faces and dimensions ]]
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 +
----
  
 
== Learning, adaptation and generalization ==
 
== Learning, adaptation and generalization ==
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Lecturers:  John Krakauer, David Ostry, Konrad Körding
 
Lecturers:  John Krakauer, David Ostry, Konrad Körding
  
 +
[[Media:Ostry Lecture 1.pdf | Ostry Lecture 1]] <br>
 +
[[Media:Ostry Lecture 2.pdf | Ostry Lecture 2]]
 +
 +
[[Media:NorthwesternKRAKAUER.pdf| Krakauer Part 1]] <br>
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[[Media:NortwesternKRAKAUER_Part_2.pdf| Krakauer Part 2]]
 +
 +
'''Tutorial: Simple introduction to Bayesian approaches''' <br>
 +
[http://compneurosci.com/wiki/images/School_Tutorial.zip TutorialFiles]
 +
 +
Advanced neural data analysis:<br>
 +
[http://compneurosci.com/wiki/images/DREAM_exercise.docx AnalysisFiles]
 +
 +
A guide to [[Paper_Writing_101]]
 +
 +
----
  
 
==Neuromechanics & spinal cord==
 
==Neuromechanics & spinal cord==
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Lecturers: Sandro Mussa-Ivaldi, Jason Kutch
 
Lecturers: Sandro Mussa-Ivaldi, Jason Kutch
  
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'''Tutorial: Motor Primitives''' <br>
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by: Alejandro Melendez-Calderon, Ali Farshchian
 +
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[[Media:Motor primitives - presentation2.zip| Presentation]] <br>
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[[Media:Motor_primitives_-_simulink.zip | Simulink files]]
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[http://compneurosci.com/wiki/images/CoSMo2012.MussaIvaldi.pdf Sandro's presentation]
 +
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[[Media:NeuromechanicsCosmo2012_Kutch.pdf‎ | Jason's Presentation]]
 +
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'''Tutorial: Day 2''' <br>
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[[Media:DatabaserProjectCoSMo2012.zip | Databaser and redundancy analysis code]] <br>
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[[Media:DatabaserProjectCoSMo2012 p2.zip  | Databaser and redundancy analysis code part 2]]
 +
 +
----
  
 
==Robotics & brain-machine interfaces==
 
==Robotics & brain-machine interfaces==
 
''Aug 15-16''
 
''Aug 15-16''
  
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Lecturers: Brenna Argall, Byron Yu
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Lecturers: Brenna Argall, Byron Yu, Lee Miller
  
 +
[[Media:20120815_cosmo.pdf | Yu Lecture 1]] <br>
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[[Media:kf_notes.pdf | Yu Lecture 2]]
 +
 +
[[Media:12cosmo_argall.pdf| Argall Lecture]]
 +
 +
'''Tutorial''' <br>
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 +
[[Media:bmi_exercises.pdf | Brain-machine interface exercises]] <br>
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[[Media:cosmo_robotics.zip | Robotics exercises]] <br>
 +
 +
and here is the time chapter from a Book Konrad is co-writing with Weiji Ma and Dan Goldreich.
 +
[http://compneurosci.com/wiki/images/TimeChapterBook.pdf TimeChapter]
 +
password is lowercase and describes the statistics that Konrad likes to do.
 +
 +
----
  
 
==Computational neuroimaging==
 
==Computational neuroimaging==
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Lecturers: Rhodri Cusack, Alex Wade, Scott Grafton
 
Lecturers: Rhodri Cusack, Alex Wade, Scott Grafton
  
 +
[[Media:Cusack_cosmo_2012_part1.pdf|Cusack Lecture One]]<br>
 +
Cusack Lecture Two: [[Media:Cusack cosmo 2012 part2 firsthalf.pdf|part 1]], [[Media:Cusack cosmo 2012 part2 secondhalf.pdf|part 2]]
 +
 +
[[Media:Grafton MRInetworks.pdf |Grafton MRI networks]]<br>
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[[Media:Grafton MRIglm.pdf| Grafton MRI GLM]]
 +
 +
[[Media:wade_day1.pdf|Wade lecture - day 1]] <br>
 +
[[Media:wade_day2.pdf|Wade lecture - day 2]]
 +
 +
'''Tutorial:'''
 +
 +
[[Media:Workshop.pptx | Workshop‎]]
 +
 +
----
  
 
==The secret of becoming a successful scientist==
 
==The secret of becoming a successful scientist==
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Lecturer: Luís Amaral
 
Lecturer: Luís Amaral
 +
 +
[[Media:Amaral_2012-Aug_17-NU_School.pptx |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.
 +
 +
'''Thursday night groups:'''
 +
 +
[[Media:Variability in Motor Learning.pdf|Variability in Motor Learning]] ([[Media:Effect of Baseline Variability in Motor Learning.pdf |Abstract]]) by ''Farnaz Abdollahi, Katie Bankieris, Keturah Bixby, Moria Fisher, Ryan Morehead'' *winner student presentation competition*
 +
 +
[[Media:MILADYfinal.pptx|Temporal influence on subject reaching strategies in Kording & Wolpert (2004)]] ([[Media:MILADYabstract.pdf‎|Abstract]]) by ''Matt Balcarras, Irene Tamagnone, Leonie Oostwoud Wijdenes, Andrew Brennan, Deborah Barany, Yashar Zeighami.''
 +
 +
[[Media:PredictingCognitiveFunction.zip‎|Predicting Cognitive Function in Older Adults]] by ''Niousha Bolandzadeh & Nicole Salowitz''
 +
 +
[[Media:ModelingSkilledHabitualLearning.rtf|Modeling Skilled Habitual Learning]] by ''Maria Bengtson and Joseph DeSouza''
 +
 +
 +
'''Friday night groups:'''
 +
 +
[[Media:Kiwii_Slides_Compressed.pptx|Kiwii Platform: Using Kinect and Wii Board to Probe Visual and Postural Effects on Balance.]] ([[Media:Abstract_KiWiiPlatform.pdf|Abstract]]) by ''Kahori Kita, John Rocamora, Yoshiyuki Sato, Frank Schumann, Scott Yang''
 +
 +
[[Media:WiiGroup.zip|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''
 +
 +
[[Media:Decoding Encoding in M1.docx|Comparison of Decoding and Encoding Methods for Motor Cortical Spiking Data]] by ''Mikael Lindahl, Alexander Rajan, Stefan Habenschuss, John Butcher, Naama Kadmon''
 +
 +
[[Media:Cieslak_Kluth_Stiels_Wood-deciding2012.pdf‎|Deciding when to cut your losses]] ([[Media:Cieslak_Kluth_Stiels_Wood-decision2012_abstract.pdf‎|Abstract]]) by ''Matt Cieslak, Tobias Kluth, Maren Stiels, Daniel Wood''
 +
 +
[[Media:M1 neurons.pdf | The relationship between activity of neurons recorded simultaneously in primary motor cortex.]] by ''Maxym Myroshnychenko, Joan Deffeyes, Azadeh Yazdan, Diana Mitchell''
 +
([[Media:M1 neurons abstract.pdf|Abstract]])
 +
 +
[[Media:Fabbri_CoSMo_Project_Abstract.docx|Advanced fMRI analyses and Kalman filter application]] by ''Sara Fabbri, Heather McGregor, Simona Monaco, and Na Jin Seo''

Latest revision as of 18:09, 1 August 2019

This page contains course materials for the CoSMo 2012 summer school.

To upload files, you must log in with an account that has upload access. Here are some upload instructions or you can go straight to the upload file page.

Contact Ben Walker 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.)


Here is a description of data sets currently in Dream. Dream is growing, but this list is accurate as of the time of the summer school.

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.stanford.edu/doku.php/mgl/beta
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

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

Argall Lecture

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

Cusack Lecture One
Cusack Lecture Two: part 1, part 2

Grafton MRI networks
Grafton MRI GLM

Wade lecture - day 1
Wade lecture - day 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.

Thursday night groups:

Variability in Motor Learning (Abstract) by Farnaz Abdollahi, Katie Bankieris, Keturah Bixby, Moria Fisher, Ryan Morehead *winner student presentation competition*

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. (Abstract) by Kahori Kita, John Rocamora, Yoshiyuki Sato, Frank Schumann, Scott Yang

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

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

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

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