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AnalyzeFMRI (version 1.1-24)

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

214

Version

1.1-24

License

GPL (>= 2)

Maintainer

P. de Micheaux

Last Published

October 5th, 2021

Functions in AnalyzeFMRI (1.1-24)

N2G.Density

Calculates the density function for the N2G model
GaussSmoothKernel

Calculates a discrete Gaussian smoothing kernel.
EC.3D

Expected Euler Characteristic for a 3D Random Field
GaussSmoothArray

Spatially smooth an array with Gaussian kernel.
NonLinearSmoothArray

Non-linear spatial smmothing of 3D and 4D arrays.
N2G.Transform

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

Estimates the covariance between neighbouring voxels
cluster.threshold

Cluster threshold an array.
N2G.Inverse

Transform parameters of N2G model back to their real domains
Sim.3D.GammaRF

Simulate Gamma distributed Random Field
N2G.Likelihood.Ratio

N2G Likelihood Ratio's
Sim.3D.GRF

Simulate a GRF
ICAtemp

ICAtemp
N2G.Class.Probability

Posterior Probabilities for N2G model
Threshold.FDR

False Discovery Rate (FDR) Threshold
N2G.Likelihood

Calculates the (negative) Likelihood of the N2G model
N2G

Fits the N2G model
R2Q

Rotation to quaternion
Threshold.Bonferroni

Calculates Bonferroni Threshold
Q2R

Quaternion to rotation
SmoothEst

Estimate the variance-covariance matrix of a Gaussian random field
f.analyzeFMRI.gui

starts AnalyzeFMRI GUI
N2G.Region

N2G Normal component interval
f.analyze.file.summary

prints summary of .img file contents
f.plot.volume.gui

tcltk GUI to display FMRI or MRI images
diminfo2fps

diminfo2fps
N2G.Spatial.Mixture

fMRI Spatial Mixture Modelling
eigenvalues

eigenvalues
analyze2nifti

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

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

Read in a volume at one time point
Threshold.RF

Random Field Theory Thersholds.
f.nifti.file.summary

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

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

centering
f.complete.hdr.nifti.list.create

creates complete .hdr list in NIFTI format
f.basic.hdr.nifti.list.create

creates basic .hdr list in NIFTI format
f.basic.hdr.list.create

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

read Analyze header file
f.read.nifti.ts

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

read in one voxel time series
f.plot.ica.fmri

Plots a specified component from the output of f.ica.fmri
f.read.nifti.volume

read whole image file
f.spectral.summary.nifti

plots graphical summary of spectral properties of an fMRI dataset
f.plot.ica.fmri.jpg

Plot the components of the ouput of f.ica.fmri to a series of jpeg files
f.write.array.to.img.float

write array of 4 byte floats
f.write.analyze

writes an array to a .img/.hdr pair in ANALYZE format
f.read.analyze.volume

read whole .img file
f.read.nifti.header

read Nifti header file
f.ica.fmri.gui

tcltk GUI to apply ICA to fMRI datasets
f.read.header

read ANALYZE or NIFTI header file
f.write.array.to.img.8bit

write array of 1 byte integers
f.write.array.to.img.2bytes

write array of 2 byte integers
st2xyzt

st2xyzt
f.write.list.to.hdr

writes a .hdr file in ANALYZE format
f.read.nifti.tpt

Read in a volume at one time point
model.2.est.gamma

Estimate gamma for Model 2 of Hartvig and Jensen (2000)
f.read.nifti.slice.at.all.timepoints

reads a slice at all time points from a NIFTI .img or .nii file
fps2diminfo

fps2diminfo
ijk2xyz

ijk2xyz
f.read.analyze.slice

read one slice from a .img file
f.icast.fmri

Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasets
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
nifti.quatern.to.mat44

Quaternion (etc..) to affine 4x4 matrix
threeDto4D

threeDto4D
reduction

reduction
f.read.nifti.slice

read one slice from a .img or .nii file in NIFTI format
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.nii.array.to.img.8bit

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

Orientation storage
f.read.analyze.slice.at.all.timepoints

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

read whole image file
xyzt2st

xyzt2st
mat34.to.TZSR

Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and Rotation
model.2.cov.func

Calculates covariance from Hartvig Model 2
f.write.nifti

writes an array to a .img/.hdr pair in NIFTI format or to a .nii file
f.spectral.summary

plots graphical summary of spectral properties of an fMRI dataset
magicfield

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

writes a .hdr file in NITI format
mat34.to.TRSZ

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

twoDto4D
xyz2ijk

xyz2ijk
N2G.Fit

Optimzation function for N2G model
ICAspat

ICAspat