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AnalyzeFMRI (version 1.1-16)

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.

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Version

Install

install.packages('AnalyzeFMRI')

Monthly Downloads

214

Version

1.1-16

License

GPL (>= 2)

Maintainer

P de Micheaux

Last Published

March 19th, 2013

Functions in AnalyzeFMRI (1.1-16)

analyze2nifti

Create a NIFTI file from an Analyze file
N2G.Density

Calculates the density function for the N2G model
ICAtemp

ICAtemp
N2G.Region

N2G Normal component interval
eigenvalues

eigenvalues
N2G.Class.Probability

Posterior Probabilities for N2G model
f.read.nifti.slice.at.all.timepoints

reads a slice at all time points from a NIFTI .img or .nii file
f.write.analyze

writes an array to a .img/.hdr pair in ANALYZE format
f.icast.fmri.gui

tcltk GUI to apply Spatial or Temporal ICA to fMRI NIFTI datasets
cov.est

Estimates the covariance between neighbouring voxels
N2G

Fits the N2G model
ICAspat

ICAspat
f.write.list.to.hdr

writes a .hdr file in ANALYZE format
N2G.Transform

Transform parameters of N2G model so as to lie on the real line.
f.icast.fmri

Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasets
fps2diminfo

fps2diminfo
N2G.Fit

Optimzation function for N2G model
N2G.Likelihood

Calculates the (negative) Likelihood of the N2G model
f.read.analyze.tpt

Read in a volume at one time point
Sim.3D.GammaRF

Simulate Gamma distributed Random Field
f.read.nifti.tpt

Read in a volume at one time point
GaussSmoothArray

Spatially smooth an array with Gaussian kernel.
f.write.array.to.img.2bytes

write array of 2 byte integers
f.basic.hdr.list.create

creates basic .hdr list in ANALYZE format
f.read.nifti.ts

read in one voxel time series
f.write.nifti

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

Applies Spatial ICA (Independent Component Analysis) to fMRI datasets
N2G.Likelihood.Ratio

N2G Likelihood Ratio's
Threshold.FDR

False Discovery Rate (FDR) Threshold
f.spectral.summary.nifti

plots graphical summary of spectral properties of an fMRI dataset
GaussSmoothKernel

Calculates a discrete Gaussian smoothing kernel.
f.read.analyze.slice.at.all.timepoints

reads a slice at all time points from a .img file
model.2.est.gamma

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

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

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

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

tcltk GUI to apply ICA to fMRI datasets
N2G.Spatial.Mixture

fMRI Spatial Mixture Modelling
f.write.list.to.hdr.nifti

writes a .hdr file in NITI format
f.write.array.to.img.8bit

write array of 1 byte integers
f.basic.hdr.nifti.list.create

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

read Analyze header file
Threshold.RF

Random Field Theory Thersholds.
f.read.analyze.volume

read whole .img file
f.read.nifti.slice

read one slice from a .img or .nii file in NIFTI format
f.analyze.file.summary

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

tcltk GUI to display FMRI or MRI images
f.nifti.file.summary

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

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

read Nifti header file
f.plot.ica.fmri

Plots a specified component from the output of f.ica.fmri
f.complete.hdr.nifti.list.create

creates complete .hdr list in NIFTI format
SmoothEst

Estimate the variance-covariance matrix of a Gaussian random field
st2xyzt

st2xyzt
f.read.volume

read whole image file
threeDto4D

threeDto4D
f.read.analyze.slice

read one slice from a .img file
xyzt2st

xyzt2st
model.2.cov.func

Calculates covariance from Hartvig Model 2
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.spectral.summary

plots graphical summary of spectral properties of an fMRI dataset
fourDto2D

fourDto2D
nifti.quatern.to.mat44

Quaternion (etc..) to affine 4x4 matrix
Q2R

Quaternion to rotation
diminfo2fps

diminfo2fps
mat34.to.TRSZ

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

Get magicfield from the header of an image file
Sim.3D.GRF

Simulate a GRF
f.analyzeFMRI.gui

starts AnalyzeFMRI GUI
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.read.analyze.ts

read in one voxel time series
mat34.to.TZSR

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

reduction
f.plot.ica.fmri.jpg

Plot the components of the ouput of f.ica.fmri to a series of jpeg files
twoDto4D

twoDto4D
ijk2xyz

ijk2xyz
Threshold.Bonferroni

Calculates Bonferroni Threshold
cluster.threshold

Cluster threshold an array.
centering

centering
f.write.array.to.img.float

write array of 4 byte floats
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.volume

read whole image file
xyz2ijk

xyz2ijk
R2Q

Rotation to quaternion