== Acquisition and Analysis of Neuronal Data ==

'''Integrated lecture and tutorials'''

=== Dates, Lecturers, and Location ===

||<(|2> '''Dates and Rooms:''' || Lecture: Fridays from 09:15 to 10:45 in the lecture hall 102 (Haus 6) ||
|| Tutorials: Fridays from 11:00 (st!) to 12:30 in the computer pool of Haus 2 ||
||<(|2> '''Lecturers:''' || ''Part 1:'' [[http://itb.biologie.hu-berlin.de/~kempter/|Richard Kempter]] ||
|| ''Part 2:'' [[http://user.cs.tu-berlin.de/~blanker/|Benjamin Blankertz]], Carmen Vidaurre  ||
|| '''Location:''' || Bernstein Center for Computational Neurosciences Berlin, [[http://maps.google.de/maps?f=q&hl=de&geocode=&q=Philippstr.+13,+Berlin&jsv=107&sll=50.889174,10.546875&sspn=11.859882,34.453125&ie=UTF8&ll=52.525034,13.38757&spn=0.011162,0.033646&z=16|Haus 6 (lecture) and Haus 2 (tutorials), Philippstr. 13]] ||

Further Information on the web page of the [[http://www.bccn-berlin.de/Graduate+Programs/Courses+and+Modules/Acquisition_and_Analysis_of_Neural_Data/?contentId=2050|BCCN-B]].


=== Topics ===

This part of the module "Acquisition and Analysis of Neural Data" of the [[http://www.bccn-berlin.de/Graduate+Programs/Master_Program/|Master Program in Computational Neuroscience]] provides knowledge on statistical analyses of neural data: 
   * ''Part 1:'' Analysis of Spike Trains (spike statistics, neural coding, theory of point processes, linear systems theory, correlation analysis, spike-triggered average, reverse correlation, STRF, neural decoding, signal detection theory, infomation theory, signal-to-noise ratio analysis) - see [[http://itb.biologie.hu-berlin.de/~kempter/Teaching/2011-SS-AAND/index.html|here]] for details on the first part.
   * ''Part 2:'' Statistical analysis of electroencephalogram (EEG) data, e.g., investigation of event-related potentials (ERPs) and event-related desynchronization (ERD); spatial filters; classification, adaptive classifiers. 

Required background knowledge: Basic knowledge in Neurobiology and Mathematics at the level of the first year of the Masters Program in Computational Neuroscience. 

=== Course Certificates ===

To obtain course certificates, at least 75% of the points in the exercises (5 ECTS) must be obtained. 

To obtain the full 5 ECTS for the tutorial, every student has to complete an additional small project (2 ECTS). Topics will be distributed in May 2011. More information can be obtained [[http://itb.biologie.hu-berlin.de/~bergmann/learningandmemory2011.html|here]].

The final oral exam on the module "Acquisition and Analysis of Neuronal Data" will take place on September 20th, 2011. 

=== Material ===

   * Lecture #07: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_lecture07.pdf|Script]] | Exercises: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet07.pdf|Sheet]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet07_appendix.pdf|Appendix]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet07_material.zip|Material]] | Solution: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/solution_sheet07.m|Script]]
   * Lecture #08: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_lecture08.pdf|Script]] | Exercises: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet08.pdf|Sheet]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet08_appendix.pdf|Appendix]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/RSVP_Monochrome133msVPmg.mat|Data]]; [[http://ml.cs.tu-berlin.de/publications/AcqTreSchBla10.pdf|Paper]] | Solution: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/solution_sheet08.m|Script]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/xval.m|XVal]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/trainLDA.m|LDA]]
   * Lecture #09: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_lecture09.pdf|Script]] | Exercises: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet09.pdf|Sheet]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/erp_hexVPsag.mat|Data]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/trainLDAshrink.m|Matlab function]] | Solution: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/solution_sheet09.m|Script]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/signed_r_square.m|BiserialCC]]
   * Lecture #10: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_lecture10.pdf|Script]] | Exercises: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/AAND2011_sheet10.pdf|Sheet]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/imagVPaw.mat|Data]] | Solution: [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/solution_sheet10.m|Script]]; [[http://ml.cs.tu-berlin.de/~blanker/AAND2011/trainCSP.m|CSP]]
   * Lecture #12: [[http://www.user.tu-berlin.de/j.hoehne/tmp/AAND2011_lecture12_part1.pdf|Script part 1]] [[http://www.martijnschreuder.nl/AAND2011_lecture12_part2.pdf|Script part 2]] 

=== Background material ===

==== Part 2 (EEG) ====
   * Blankertz B, Lemm S, Treder MS, Haufe S, Müller KR. ''Single-trial analysis and classification of ERP components - a tutorial''. !NeuroImage, 56:814-825, 2011. [[http://ml.cs.tu-berlin.de/publications/BlaLemTreHauMue10.pdf|pdf]] [[http://dx.doi.org/10.1016/j.neuroimage.2010.06.048|url]]
   * Blankertz B, Tomioka R, Lemm S, Kawanabe M, Müller KR. ''Optimizing spatial filters for robust EEG single-trial analysis''. IEEE Signal Proc Magazine, 25(1):41-56, 2008. [[http://ml.cs.tu-berlin.de/publications/BlaTomLemKawMue08.pdf|pdf]] [[http://dx.doi.org/10.1109/MSP.2008.4408441|url]]
   * Treder MS, Blankertz B, ''(C)overt attention and visual speller design in an ERP-based brain-computer interface''. Behav Brain Funct, 6:28, 2010. [[http://www.behavioralandbrainfunctions.com/content/6/1/28|url]]
   * Parra LC, Spence CD, Gerson AD, Sajda P. ''Recipes for the linear analysis of EEG''. !NeuroImage, 28(2):326-341, 2005. [[http://ml.cs.tu-berlin.de/bbci/papers/ParSpeGerSaj05.pdf|pdf]]
   * Parra LC, Christoforou C, Gerson AD, Dyrholm M, Luo A, Wagner M, Philastides M, Sajda P. ''Spatiotemporal Linear Decoding of Brain State''. IEEE Signal Proc Magazine, 25(1): 107-115, 2008. [[http://ml.cs.tu-berlin.de/bbci/papers/ParChrGerDyrLuoWagPhiSaj08.pdf|pdf]]
   * Key AP, Dove GO, Maguire MJ. ''Linking brainwaves to the brain: an ERP primer''. Dev Neuropsychol. 2005;27(2):183-215. [[http://ml.cs.tu-berlin.de/bbci/papers/KeyDovMag05.pdf|pdf]]
   * Pfurtscheller G, Lopes da Silva FH. ''Event-related EEG/MEG synchronization and desynchronization: basic principles''. Clin Neurophysiol, 110(11):1842-1857, Nov 1999. [[http://ml.cs.tu-berlin.de/bbci/papers/PfuSil99.pdf|pdf]]
   * Wolpaw JR, Birbaumer N, !McFarland DJ, Pfurtscheller G, Vaughan TM. ''Brain-computer interfaces for communication and control''. Clin. Neurophysiol., 113:767-791, 2002. [[http://ml.cs.tu-berlin.de/bbci/papers/WolBirFarPfuVau02.pdf|pdf]]
   * Dornhege G, Millán J del R, Hinterberger T, !McFarland DJ, Müller KR, editors. ''Toward Brain-Computer Interfacing''. MIT Press, Cambridge, MA, 2007.