- PostScript preprint of a paper [Magn Reson Med, 42:Â 1014-1018,Â 1999] on how 3D registration works in 3dvolreg and in realtimeAFNI. [Here is the PDF version.]
- Another interesting paper (not available here, unfortunately) is S Gold, B Christian, S Arndt, G Zeien, T Cizadlo, DL Johnson, M Flaum, and NC Andreasen. Functional MRI statistical software packages: a comparative analysis. Human Brain Mapping, 6:73-84, 1998.
- The first (660 KB) and second (1.0 MB) papers on AFNI. These are PostScript preprints of RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29:162-173, 1996. RW Cox and JS Hyde. Software tools for analysis and visualization of FMRI Data. NMR in Biomedicine, 10:171-178, 1997.
- If you use AFNI and find it valuable, I'd appreciate it if you could cite one of these papers in your publications. The list of papers (that I know of) that cite AFNI are here --Bob Cox.
RW Cox papers
(Some) Papers by RW Cox -- PDF Reprints
RW Cox, A Jesmanowicz, JS Hyde. Real-Time Functional Magnetic Resonance Imaging. Magnetic Resonance in Medicine 33:230-236 (1995).
A DeYoe, GJ Carman, PA Bandettini, S Glickman, J Wieser, RW Cox, D Miller, and J Neitz. Mapping striate and extrastriate visual areas in human cerebral cortex. Proceedings of the National Academy of Sciences of the USA, 93: 2382-2386, 1996.
RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29: 162-173, 1996.
MS Beauchamp, RW Cox, and EA DeYoe. Graded effects of spatial and featural attention on human area MT and associated motion processing areas. Journal of Neurophysiology, 78: 516-520, 1997.
S Hyde, HS Mchaourab, TG Camenisch, JJ Ratke, RW Cox, and W Froncisz. Electron paramagnetic resonance detection by time-locked subsampling. Review of Scientific Instruments, 69: 2622-2628, 1998.
Realtime Registration - MRM 1999
RW Cox and A Jesmanowicz. Real-time 3D image registration for functional MRI. Magnetic Resonance in Medicine, 42: 1014-1018, 1999.
R Tong and RW Cox. Rotation of NMR images using the 2D chirp-z transform. Magnetic Resonance in Medicine, 41: 253-256, 1999.
JA Frost, JR Binder, JA Springer, TA Hammeke, PSF Bellgowan, SM Rao, and RW Cox. Language processing is strongly left lateralized in both sexes - evidence from functional MRI. Brain, 122 (part 2): 199-208, 1999.
JR Binder, JA Frost, TA Hammeke, PSF Bellgowan, SM Rao, and RW Cox. Conceptual processing during the conscious resting state: a functional MRI study. Journal of Cognitive Neuroscience, 11: 80-95, 1999.
MM Klosek and RW Cox. Steady-state currents in sharp stochastic ratchets. Physical Review E, 60: 3727-3735, 1999.
PA Bandettini and RW Cox. Event-related fMRI contrast when using constant interstimulus interval: theory and experiment. Magnetic Resonance in Medicine, 43: 540-548, 2000.
K Space Partition Diagrams 2000
RW Cox. k-space partition diagrams: a graphical tool for analysis of MRI pulse sequences. Magnetic Resonance in Medicine, 43: 160-162, 2000.
ZS Saad, KM Ropella, RW Cox, and EA DeYoe. Analysis and use of FMRI response delays. Human Brain Mapping, 13: 74-93, 2001.
GE Sarty, R Bennett, and RW Cox. Direct reconstruction of non-Cartesian k-space data using a non-uniform fast Fourier transform. Magnetic Resonance in Medicine, 45: 908-915, 2001.
MK Kern, RM Birn, S Jaradeh, A Jesmanowicz, RW Cox, JS Hyde, and R Shaker. Swallow-related cerebral cortical activity maps are not specific to deglutition. American Journal of Physiology-Gastrointestinal and Liver Physiology, 280: G531-G538, 2001.
RM Birn, RW Cox, and PA Bandettini. Detection versus estimation in event-related fMRI: choosing the optimal stimulus timing. NeuroImage, 15: 252-264, 2002.
V Roopchansingh, RW Cox, A Jesmanowicz, BD Ward, and JS Hyde. Single-shot magnetic field mapping and applications. Magnetic Resonance in Medicine, 50: 839-843, 2003.
RM Birn, RW Cox, and PA Bandettini. Experimental designs and processing strategies for fMRI studies involving overt verbal responses. NeuroImage, 23: 1046-1058, 2004.
ZS Saad, G Chen, RC Reynolds, PP Christidis, KR Hammett, PSF Bellgowan, and RW Cox. FIAC Analysis According to AFNI and SUMA. Human Brain Mapping, 27: 417-424, 2006.
ZS Saad, RC Reynolds, B Argall, S Japee, RW Cox. SUMA: An Interface For Surface-Based Intra- And Inter-Subject Analysis With AFNI. 2004 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. IEEE, Arlington, VA, pp. 1510-1513 (2004).
2006 - Standard Surfaces in SUMA
BD Argall, ZS Saad, MS Beauchamp. Simplified intersubject averaging on the cortical surface using SUMA. Human Brain Mapping 27, 14-27, 2006.
ZS Saad, DR Glen, G Chen, MS Beauchamp, R Desai, and RW Cox. A new method for improving functional-to-structural MRI alignment using local Pearson correlation. NeuroImage, 44: 839-848, 2009
AFNI: What a long strange trip it's been, NeuroImage in press
Paper on why NOT to use the global signal (or anything like it) in resting state FMRI data analyses.