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AFNI specifications


Unique identifier OMICS_14800
Alternative name Analysis of Functional NeuroImages
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format NIfTI-1
Output format NIfTI-1
Operating system Unix/Linux, Mac OS
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes


  • DBSproc
  • ETAC (Equitable Thresholding and Clustering)




No version available


  • person_outline Robert Cox
  • person_outline Kamil Grajski

Publications for Analysis of Functional NeuroImages

AFNI citations


The cholinergic contribution to the resting state functional network in non demented Parkinson’s disease

Sci Rep
PMCID: 5955917
PMID: 29769626
DOI: 10.1038/s41598-018-26075-3

[…] Functional brain MRI analyses were performed following a previously described method. Preprocessing of resting-state fMRI data was conducted using the Analysis of Functional NeuroImages, ( software. For stabilization of the magnetic field, the initial five volumes from each functional image were eliminated. The eliminat […]


Prefrontoparietal dysfunction during emotion regulation in anxiety disorder: a meta analysis of functional magnetic resonance imaging studies

PMCID: 5953307
PMID: 29785110
DOI: 10.2147/NDT.S165677
call_split See protocol

[…] methodological differences between studies, we then performed several subgroup meta-analyses including medicine-naive patients, patients with SAD, patients with GAD and SAD, data processing software (AFNI), and MRI field strengths (3.0 T). Given the variability that exists in treatment status, we defined the sample of medicine-naive patients as participants who had been free of psychotropic medica […]


Altered Amygdala Resting State Functional Connectivity and Hemispheric Asymmetry in Patients With Social Anxiety Disorder

PMCID: 5932339
PMID: 29755374
DOI: 10.3389/fpsyt.2018.00164

[…] Anatomical T1 images were coregistered to the first functional image using a local Pearson correlation cost function (). Preprocessing of imaging data was performed using Analysis of Functional NeuroImages (AFNI; software (). The first three volumes from each functional image were removed. We used Physiologic EStimation by Temporal ICA (P […]


Brief exposure to obesogenic diet disrupts brain dopamine networks

PLoS One
PMCID: 5919534
PMID: 29698491
DOI: 10.1371/journal.pone.0191299

[…] d using a one-way ANOVA followed by a Newman-Keuls post-hoc test. Group mean %ΔCBV maps were generated after affine warping (3dWarpDrive) of functional maps to a common anatomic reference image using AFNI ( []. The %∆CBV response slopes (m) between time points 21 and 40 min were calculated for dorsal and ventral striatum, and the slope values for LF versus HF groups w […]


Converging Evidence From Electrocorticography and BOLD fMRI for a Sharp Functional Boundary in Superior Temporal Gyrus Related to Multisensory Speech Processing

Front Hum Neurosci
PMCID: 5928751
PMID: 29740294
DOI: 10.3389/fnhum.2018.00141

[…] ce (Setsompop et al., ) with TR = 1500 ms, TE = 30 ms, flip angle = 72°, in-plane resolution of 2 × 2 mm, 69 2-mm axial slices, multiband factor: 3, GRAPPA factor: 2. fMRI data was analyzed using the pipeline (Cox, ). Data was time shifted to account for different acquisition times for different slices; aligned to the first functional volume which was in turn aligned with the high-res […]


Study of Resting State Functional Connectivity Networks Using EEG Electrodes Position As Seed

Front Neurosci
PMCID: 5928390
PMID: 29740268
DOI: 10.3389/fnins.2018.00235

[…] Data processing was performed using the Analysis of Functional NeuroImages software (AFNI;; Cox, ; Cox and Hyde, ) and fMRIB Software Library (FSL;; Smith et al., ; Jenkinson et al., ). Image preprocessing involved th […]


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AFNI institution(s)
Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Department of Human Biology, Faculty of Health Sciences, University of Cape Town, MRC/UCT Medical Imaging Research Unit, Cape Town, South Africa; African Institute for Mathematical Sciences, Muizenberg, Western Cape, South Africa; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Statistical and Scientific Computing Core, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
AFNI funding source(s)
Supported by a grant from Medtronic Deep Brain Stimulation Therapy Fellowship Grant 2014–2015.

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