== Integrated lecture and tutorials ''Acquisition and Analysis of Neuronal Data'' ==

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

|| '''Module''' || Part of the [[http://www.bccn-berlin.de/Graduiertenprogramm/Masterprogramm/|Master Program Computation Neuroscience]]; [[https://www.bccn-berlin.de/digitalAssets/0/596_2CNS_Catalogue_20130325.pdf|BCCN Modulkatalog]] ||
||<(|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]], Matthias Schultze-Kraft ||
|| '''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]] ||
|| '''TU University calendar:''' || [[http://lsf.tubit.tu-berlin.de/qisserver/servlet/de.his.servlet.RequestDispatcherServlet?state=verpublish&status=init&vmfile=no&publishid=153651&moduleCall=webInfo&publishConfFile=webInfo&publishSubDir=veranstaltung|LSF entry]] ||

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/2014-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 Master Program in Computational Neuroscience. 

=== Course Certificates ===

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

To obtain the full 5 ECTS for the tutorial, every student has to complete an additional small project (2 ECTS). The tasks of the projects will be distributed at the end of the course. Solutions are to be submitted until two weeks before the oral exam.

The final oral exam of the module "Acquisition and Analysis of Neuronal Data will take place October 2nd 2014.

=== Material ===

Removed. See at more recent courses.


=== Projects ===

To obtain the full 5 ECTS for the tutorial, every individual student has to complete an additional small programming project. Project topics will be distributed at the end of the lecture series, and every student should work on her/his topic in the lecture-free time (July/August/September 2014). 

Students are required to turn in a short written report, that is, a self-contained description of results. The report should comprise a single PDF file (including an Introduction, a short description of the experiment, a Results/Discussion section as well as labeled Figures with captions) and the Matlab code as an attachment. [[https://www.bccn-berlin.de/digitalAssets/1/1623_1GuidelineProjectReport_Compendium.pdf|Guidelines]] for Writing a Scientific Report might be helpful.


An overview of the projects is available [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project_overview.pdf|here]].

   * Project BCI #01: Rapid Serial Visual Presentation - [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project01.pdf|Tasks]] | [[http://doc.ml.tu-berlin.de/bbci/publications/AcqTreSchBla10.pdf|Paper 1]], [[http://doc.ml.tu-berlin.de/bbci/publications/AcqBla11.pdf|Paper 2]] | Data: [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/RSVP_Monochrome133msVPmg.mat|Matlab]], [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/RSVP_Monochrome133msVPmg.npz|Python]]
   * Project BCI #02: Motor Imagery based BCI - [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project02.pdf|Tasks]] | [[http://doc.ml.tu-berlin.de/bbci/publications/BlaDorKraMueCur07.pdf|Paper 1]], [[http://doc.ml.tu-berlin.de/bbci/publications/BlaSanHalHamKueMueCurDic10.pdf|Paper 2]] | Data: [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/imag_arrowVPkg.mat|Matlab]], [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/imag_arrowVPkg.npz|Python]]
   * Project BCI #03: Covert Shifts of Visual Attention - [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project03.pdf|Tasks]] | [[http://doc.ml.tu-berlin.de/bbci/publications/SchBlaTre10.pdf|Paper 1]], [[http://www.jneuroengrehab.com/content/8/1/24/abstract|Paper 2]] | Data: [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/covert_VPiac.mat|Matlab]], [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/covert_VPiac.npz|Python]]
   * Project BCI #04: ERP Speller based on Spatial Auditory Attention - [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project04.pdf|Tasks]] | [[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009813|Paper 1]], [[https://www.frontiersin.org/Journal/Abstract.aspx?s=763&name=neuroprosthetics&ART_DOI=10.3389/fnins.2011.00112|Paper 2]] | Data: [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/OnlineTrainFileVPfaz.mat|Matlab]], [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/OnlineTrainFileVPfaz.npz|Python]]
   * Project BCI #05: ERP-based Speller - [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project05.pdf|Tasks]] | [[http://www.behavioralandbrainfunctions.com/content/pdf/1744-9081-6-28.pdf|Paper]] | Data: [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/visual_p300_hex_targetVPsah.mat|Matlab]], [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/visual_p300_hex_targetVPsah.npz|Python]]
   * Project BCI #06: 2D Auditory Speller - [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/AAND2014_project06.pdf|Tasks]] | [[http://www.frontiersin.org/Journal/Abstract.aspx?s=763&name=neuroprosthetics&ART_DOI=10.3389/fnins.2011.00099|Paper]] | Data: [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/PASS2D_VPja.mat|Matlab]], [[http://doc.ml.tu-berlin.de/bbci/SS14_IL_AAND/PASS2D_VPja.npz|Python]]


=== Background material for Part 1 (BCI) ===

   * 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://doc.ml.tu-berlin.de/bbci/references/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://doc.ml.tu-berlin.de/bbci/references/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://doc.ml.tu-berlin.de/bbci/references/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.
   * Wolpaw JR, Wolpaw EW, editors. ''Brain-Computer Interfaces: Principles and Practice''. Oxford University Press, 2012. ISBN-13: 978-0195388855.