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--- analysis:fmri:experimentaldesign [2015/01/09 09:45] – [Tools] kristin.kaduk
+++ analysis:fmri:experimentaldesign [2022/12/29 07:15] (current) – external edit 127.0.0.1
@@ Line 3: / Line 3: @@
 ===== Tools =====
-  * Chris Rorden **fMRI Simulator**: http://www.mccauslandcenter.sc.edu/CRNL/tools/fmrisim
+=== 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/
-  * **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
+  * **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
-===== 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
-AFNI background experimental design" http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht03_stim/html/stim_background.html
+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