Papers about AFNI



  • PostScript preprint of a paper [Magn Reson Med42: 1014-1018, 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 papers Realtime FMRI Paper 1995

RW Cox, A Jesmanowicz, JS Hyde. Real-Time Functional Magnetic Resonance Imaging. Magnetic Resonance in Medicine 33:230-236 (1995). 

RW Cox papers PNAS 1996

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 papers Original AFNI Paper (1996)

RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29: 162-173, 1996.

RW Cox papers Human MT 1997

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.

RW Cox papers EPR TLSS 1998

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. 

RW Cox papers 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. 

RW Cox papers Chirp-z Rotation 1999

R Tong and RW Cox. Rotation of NMR images using the 2D chirp-z transform. Magnetic Resonance in Medicine, 41: 253-256, 1999. 

RW Cox papers Language and Sex 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.

RW Cox papers Resting State 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.

RW Cox papers Stochastic Ratchets 1999

MM Klosek and RW Cox. Steady-state currents in sharp stochastic ratchets. Physical Review E, 60: 3727-3735, 1999. 

RW Cox papers Constant ISI 2000

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.

RW Cox papers 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. 

RW Cox papers FMRI Delays 2001

ZS Saad, KM Ropella, RW Cox, and EA DeYoe. Analysis and use of FMRI response delays. Human Brain Mapping, 13: 74-93, 2001.

RW Cox papers NonUniform FFT 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. 

RW Cox papers Swallowing 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. 

RW Cox papers Optimal Timing 2002

RM Birn, RW Cox, and PA Bandettini. Detection versus estimation in event-related fMRI: choosing the optimal stimulus timing. NeuroImage, 15: 252-264, 2002. 

RW Cox papers Field Mapping 2003

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. 

RW Cox papers Overt Verbal Responses 2004

RM Birn, RW Cox, and PA Bandettini. Experimental designs and processing strategies for fMRI studies involving overt verbal responses. NeuroImage, 23: 1046-1058, 2004. 

RW Cox papers FIAC analysis via AFNI 2006

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. 

RW Cox papers 2004 - SUMA paper

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). 

RW Cox papers 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. 

RW Cox papers 3dAllineate algorithm 2009

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

RW Cox papers AFNI Paper 2011

AFNI: What a long strange trip it's been, NeuroImage in press 

RW Cox papers Trouble at Rest: 2012

Paper on why NOT to use the global signal (or anything like it) in resting state FMRI data analyses.