====== fMRI Experimental Design ======

===== Tools =====

=== Chris Rorden fMRI Simulator ===
http://www.mccauslandcenter.sc.edu/crnl/tools/fmristim

=== optseq2 === 
optseq2 is a tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events): http://surfer.nmr.mgh.harvard.edu/optseq/

Good explanation about optseq and event-related designs: http://andysbrainblog.blogspot.de/2012/09/optseq-and-event-related-designs.html

=== AFNI tools === 
  * **RSFgen** is a AFNI tool for paradigm design: http://afni.nimh.nih.gov/pub/dist/doc/program_help/RSFgen.html
  * **make_random_timing.py** is a AFNI tool to define multiple events, their responses and their time series: http://afni.nimh.nih.gov/pub/dist/doc/program_help/make_random_timing.py.html 
  * **3dDeconvolve** is a AFNI tool to evaluate the power of each experimental desgin: 
  * http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDeconvolve.html
  * http://afni.nimh.nih.gov/pub/dist/edu/latest/afni07_advanced/afni07_advanced.pdf
  * http://afni.nimh.nih.gov/pub/dist/doc/manual/Deconvolvem.pdf
  * http://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni17_ht03.pdf




AFNI background experimental design: 

http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht03_stim/html/stim_background.html

http://afni.nimh.nih.gov/pub../pub/dist/edu/2007_02_korea/pdfs/ExptDsgn.pdf

http://afni.nimh.nih.gov/pub/dist/HOWTO//howto/ht03_stim/html/AFNI_howto.html


===  Multiple Trial Type fMRI (mttfmri) MATLAB Toolbox  ===
http://fmri.ucsd.edu/tliu/mttfmri_toolbox.html
===== Theory =====

K. J. Friston, E. Zarahn, O. Josephs, R. N. A. Henson, A. M. Dale (1999) Stochastic Designs in Event-Related fMRI, NeuroImage, 10: 607-619. PMID: 10547338 http://www.ncbi.nlm.nih.gov/pubmed/%2010547338
{{:analysis:fmri:friston1999_stochastic_designs_in_event-related_fmri.pdf|}}

Design efficiency in fMRI: http://imaging.mrc-cbu.cam.ac.uk/imaging/DesignEfficiency


MIT imaging library (with paper PDFs): http://web.mit.edu/swg/imaginglibrary.htm