Notes regarding AFNI and its operation...
A tremendous presentation by Doug Ward about proper thresholding for your functional results, based on a function space method that allows you to infer causality, is linked to here: http://gablab.stanford.edu/docs/supporting/FncSpace.ppt
- "noise" in the scanner operation from shot to shot (e.g., a wire in the shim coils moving slightly)
That's all I can think of offhand, but I'm sure there are other sources. bob cox
Home Site: http://afni.nimh.nih.gov/afni/
AFNI Educational Material http://afni.nimh.nih.gov/afni/edu/
AFNI seminar notes http://www.bol.ucla.edu/glahn/AFNI_Handouts.pdf
Hillary Schaefer has created a good introduction: http://tezpur.keck.waisman.wisc.edu/oakes/afni/afni_intro.pdf
Analysis of fMRI data with AFNI http://tezpur.keck.waisman.wisc.edu/tjohnstone/AFNI_I.htm#_1._Reconstruction_of
AFNI documentation on how to get started http://prana.usask.ca/fMRI/afni.html
Math explanations http://mathworld.wolfram.com
Comput Biomed Res. 1996 Jun;29(3):162-73. AFNI: software for analysis and visualization of functional magnetic resonance neuroimages.
Biophysics Research Institute, Medical College of Wisconsin, Milwaukee 53226-0509, USA.
A package of computer programs for analysis and visualization of three-dimensional human brain functional magnetic resonance imaging (FMRI) results is described. The software can color overlay neural activation maps onto higher resolution anatomical scans. Slices in each cardinal plane can be viewed simultaneously. Manual placement of markers on anatomical landmarks allows transformation of anatomical and functional scans into stereotaxic (Talairach-Tournoux) coordinates. The techniques for automatically generating transformed functional data sets from manually labeled anatomical data sets are described. Facilities are provided for several types of statistical analyses of multiple 3D functional data sets. The programs are written in ANSI C and Motif 1.2 to run on Unix workstations.
http://afni.nimh.nih.gov/afni/docpdf/3dFDR.pdf How to use FDR manual