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AnalyzeFMRI (version 1.1-25)

Functions for Analysis of fMRI Datasets Stored in the ANALYZE or 'NIFTI' Format

Description

Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or 'NIFTI' format. Note that the latest version of 'XQuartz' seems to be necessary under MacOS.

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Version

Install

install.packages('AnalyzeFMRI')

Monthly Downloads

508

Version

1.1-25

License

GPL (>= 2)

Maintainer

P. de Micheaux

Last Published

July 24th, 2025

Functions in AnalyzeFMRI (1.1-25)

NonLinearSmoothArray

Non-linear spatial smmothing of 3D and 4D arrays.
Threshold.Bonferroni

Calculates Bonferroni Threshold
N2G

Fits the N2G model
N2G.Likelihood

Calculates the (negative) Likelihood of the N2G model
R2Q

Rotation to quaternion
SmoothEst

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

Random Field Theory Thersholds.
centering

centering
Threshold.FDR

False Discovery Rate (FDR) Threshold
analyze2nifti

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

tcltk GUI to apply ICA to fMRI datasets
cluster.threshold

Cluster threshold an array.
f.analyzeFMRI.gui

starts AnalyzeFMRI GUI
f.basic.hdr.list.create

creates basic .hdr list in ANALYZE format
eigenvalues

eigenvalues
f.analyze.file.summary

prints summary of .img file contents
f.icast.fmri.gui

tcltk GUI to apply Spatial or Temporal ICA to fMRI NIFTI datasets
N2G.Spatial.Mixture

fMRI Spatial Mixture Modelling
diminfo2fps

diminfo2fps
f.read.analyze.ts

read in one voxel time series
cov.est

Estimates the covariance between neighbouring voxels
f.basic.hdr.nifti.list.create

creates basic .hdr list in NIFTI format
N2G.Region

N2G Normal component interval
f.nifti.file.summary

prints summary of .img file contents
f.icast.fmri

Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasets
f.read.analyze.tpt

Read in a volume at one time point
f.plot.volume.gui

tcltk GUI to display FMRI or MRI images
f.read.analyze.header

read Analyze header file
f.complete.hdr.nifti.list.create

creates complete .hdr list in NIFTI format
f.ica.fmri

Applies Spatial ICA (Independent Component Analysis) to fMRI datasets
f.read.analyze.slice

read one slice from a .img file
f.plot.ica.fmri

Plots a specified component from the output of f.ica.fmri
f.read.analyze.slice.at.all.timepoints

reads a slice at all time points from a .img file
f.read.analyze.volume

read whole .img file
f.plot.ica.fmri.jpg

Plot the components of the ouput of f.ica.fmri to a series of jpeg files
f.read.nifti.ts

read in one voxel time series
f.read.header

read ANALYZE or NIFTI header file
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
f.read.nifti.slice

read one slice from a .img or .nii file in NIFTI format
fourDto2D

fourDto2D
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.header

read Nifti header file
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.spectral.summary

plots graphical summary of spectral properties of an fMRI dataset
f.write.nifti

writes an array to a .img/.hdr pair in NIFTI format or to a .nii file
f.read.nifti.tpt

Read in a volume at one time point
f.write.analyze

writes an array to a .img/.hdr pair in ANALYZE format
f.write.array.to.img.8bit

write array of 1 byte integers
orientation

Orientation storage
f.write.array.to.img.2bytes

write array of 2 byte integers
f.spectral.summary.nifti

plots graphical summary of spectral properties of an fMRI dataset
f.read.nifti.slice.at.all.timepoints

reads a slice at all time points from a NIFTI .img or .nii file
st2xyzt

st2xyzt
magicfield

Get magicfield from the header of an image file
f.write.list.to.hdr.nifti

writes a .hdr file in NITI format
model.2.est.gamma

Estimate gamma for Model 2 of Hartvig and Jensen (2000)
reduction

reduction
f.read.nifti.volume

read whole image file
ijk2xyz

ijk2xyz
fps2diminfo

fps2diminfo
mat34.to.TZSR

Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and Rotation
f.write.array.to.img.float

write array of 4 byte floats
xyzt2st

xyzt2st
with_dir

Working directory
f.write.list.to.hdr

writes a .hdr file in ANALYZE format
nifti.quatern.to.mat44

Quaternion (etc..) to affine 4x4 matrix
model.2.cov.func

Calculates covariance from Hartvig Model 2
threeDto4D

threeDto4D
xyz2ijk

xyz2ijk
mat34.to.TRSZ

Affine 4x4 (or 3x4) matrix to Translation, Rotation, Shear and Scale
twoDto4D

twoDto4D
N2G.Class.Probability

Posterior Probabilities for N2G model
GaussSmoothArray

Spatially smooth an array with Gaussian kernel.
N2G.Likelihood.Ratio

N2G Likelihood Ratio's
ICAspat

ICAspat
EC.3D

Expected Euler Characteristic for a 3D Random Field
ICAtemp

ICAtemp
N2G.Transform

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

Calculates a discrete Gaussian smoothing kernel.
N2G.Density

Calculates the density function for the N2G model
N2G.Inverse

Transform parameters of N2G model back to their real domains
Q2R

Quaternion to rotation
N2G.Fit

Optimzation function for N2G model
Sim.3D.GammaRF

Simulate Gamma distributed Random Field
Sim.3D.GRF

Simulate a GRF