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AnalyzeFMRI (version 1.1-1)

Functions for analysis of fMRI datasets stored in the ANALYZE format.

Description

Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE format.

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Version

Install

install.packages('AnalyzeFMRI')

Monthly Downloads

418

Version

1.1-1

License

GPL (version 2 or later)

Maintainer

J Marchini

Last Published

July 24th, 2025

Functions in AnalyzeFMRI (1.1-1)

N2G.Class.Probability

Posterior Probabilities for N2G model
N2G.Transform

Transform parameters of N2G model so as to lie on the real line.
N2G.Likelihood

Calculates the (negative) Likelihood of the N2G model
f.analyze.file.summary

prints summary of .img file contents
N2G.Fit

Optimzation function for N2G model
f.read.analyze.slice

read one slice from a .img file
f.read.analyze.tpt

Read in a volume at one time point
N2G.Spatial.Mixture

fMRI Spatial Mixture Modelling
N2G

Fits the N2G model
N2G.Region

N2G Normal component interval
cluster.threshold

Cluster threshold an array.
f.basic.hdr.nifti.list.create

creates basic .hdr list in NIFTI format
f.read.analyze.ts

read in one voxel time series
f.spectral.summary

plots graphical summary of spectral properties of an fMRI dataset
model.2.est.gamma

Estimate gamma for Model 2 of Hartvig and Jensen (2000)
Sim.3D.GammaRF

Simulate Gamma distributed Random Field
Threshold.RF

Random Field Theory Thersholds.
NonLinearSmoothArray

Non-linear spatial smmothing of 3D and 4D arrays.
f.write.list.to.hdr

writes a .hdr file
f.read.analyze.volume

read whole .img file
N2G.Likelihood.Ratio

N2G Likelihood Ratio's
N2G.Density

Calculates the density function for the N2G model
f.read.analyze.slice.at.all.timepoints

reads a slice at all time points from a .img file
f.read.nifti.ts

read in one voxel time series
f.read.analyze.header

read Analyze header file
SmoothEst

Estimate the variance-covariance matrix of a Gaussian random field
Threshold.FDR

False Discovery Rate (FDR) Threshold
f.write.array.to.img.float

write array of 4 byte floats
f.write.analyze

writes an array to a .img/.hdr pair
f.analyzeFMRI.gui

starts AnalyzeFMRI GUI
N2G.Inverse

Transform parameters of N2G model back to their real domains
f.read.nifti.slice

read one slice from a .img file in NIFTI format
f.read.nifti.volume

read whole .img file
f.write.array.to.img.2bytes

write array of 2 byte integers
Q2R

Quaternion to rotation
GaussSmoothArray

Spatially smooth an array with Gaussian kernel.
cov.est

Estimates the covariance between neighbouring voxels
Sim.3D.GRF

Simulate a GRF
f.ica.fmri.gui

tcltk GUI to apply ICA to fMRI datasets
f.plot.ica.fmri

Plots a specified component from the output of f.ica.fmri
EC.3D

Expected Euler Characteristic for a 3D Random Field
f.plot.ica.fmri.jpg

Plot the components of the ouput of f.ica.fmri to a series of jpeg files
model.2.cov.func

Calculates covariance from Hartvig Model 2
f.basic.hdr.list.create

creates basic .hdr list in ANALYZE format
f.read.header

read ANALYZE or NIFTI header file
GaussSmoothKernel

Calculates a discrete Gaussian smoothing kernel.
f.write.array.to.img.8bit

write array of 1 byte integers
f.write.nii.array.to.img.8bit

write array of 1 byte integers and add at the begining of the file the NIFTI header part
R2Q

Rotation to quaternion
eigenvalues

eigenvalues
Threshold.Bonferroni

Calculates Bonferroni Threshold
analyze2nifti

Create a NIFTI file from an Analyze file
f.ica.fmri

Applies Spatial ICA (Independent Component Analysis) to fMRI datasets
f.read.nifti.slice.at.all.timepoints

reads a slice at all time points from a NIFTI .img file
ICAspat

ICAspat
centering

centering
f.nifti.file.summary

prints summary of .img file contents
f.read.nifti.header

read Nifti header file
fourDto2D

fourDto2D
nifti.quatern.to.mat44

Quaternion (etc..) to affine 4x4 matrix
diminfo2fps

diminfo2fps
fps2diminfo

fps2diminfo
f.write.nifti

writes an array to a .img/.hdr pair in NIFTI format or to a .nii file
mat34.to.TZSR

Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and Rotation
f.complete.hdr.nifti.list.create

creates complete .hdr list in NIFTI format
reduction

reduction
st2xyzt

st2xyzt
mat34.to.TRSZ

Affine 4x4 (or 3x4) matrix to Translation, Rotation, Shear and Scale
f.read.volume

read whole image file
f.write.nii.array.to.img.2bytes

write array of 2 byte integers and add at the begining of the file the NIFTI header part
f.write.list.to.hdr.nifti

writes a .hdr file in NITI format
f.spectral.summary.nifti

plots graphical summary of spectral properties of an fMRI dataset
xyz2ijk

xyz2ijk
f.icast.fmri.gui

tcltk GUI to apply Spatial or Temporal ICA to fMRI NIFTI datasets
magicfield

Get magicfield from the header of an image file
twoDto4D

twoDto4D
f.write.nii.array.to.img.float

write array of 4 byte floats and add at the begining of the file the NIFTI header part
f.read.nifti.tpt

Read in a volume at one time point
f.icast.fmri

Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasets
ijk2xyz

ijk2xyz
xyzt2st

xyzt2st
ICAtemp

ICAtemp
threeDto4D

threeDto4D
f.plot.volume.gui

tcltk GUI to display FMRI or MRI images