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AnalyzeFMRI (version 1.1-11)

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

1.1-11

License

GPL (>= 2)

Maintainer

P de Micheaux

Last Published

October 19th, 2009

Functions in AnalyzeFMRI (1.1-11)

f.read.analyze.tpt

Read in a volume at one time point
EC.3D

Expected Euler Characteristic for a 3D Random Field
diminfo2fps

diminfo2fps
f.read.analyze.slice.at.all.timepoints

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

read in one voxel time series
N2G

Fits the N2G model
N2G.Fit

Optimzation function for N2G model
N2G.Density

Calculates the density function for the N2G model
ICAtemp

ICAtemp
Q2R

Quaternion to rotation
ICAspat

ICAspat
eigenvalues

eigenvalues
f.write.nifti

writes an array to a .img/.hdr pair in NIFTI format or to a .nii file
Sim.3D.GRF

Simulate a GRF
f.ica.fmri.gui

tcltk GUI to apply ICA to fMRI datasets
f.read.nifti.slice

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

read whole image file
Threshold.Bonferroni

Calculates Bonferroni Threshold
f.analyze.file.summary

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

prints summary of .img file contents
N2G.Transform

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

N2G Likelihood Ratio's
f.ica.fmri

Applies Spatial ICA (Independent Component Analysis) to fMRI datasets
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
cov.est

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

Simulate Gamma distributed Random Field
GaussSmoothArray

Spatially smooth an array with Gaussian kernel.
N2G.Inverse

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

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

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

reduction
f.analyzeFMRI.gui

starts AnalyzeFMRI GUI
f.spectral.summary

plots graphical summary of spectral properties of an fMRI dataset
N2G.Likelihood

Calculates the (negative) Likelihood of the N2G model
N2G.Region

N2G Normal component interval
f.read.analyze.volume

read whole .img file
R2Q

Rotation to quaternion
f.basic.hdr.list.create

creates basic .hdr list in ANALYZE format
f.read.nifti.slice.at.all.timepoints

reads a slice at all time points from a NIFTI .img file
analyze2nifti

Create a NIFTI file from an Analyze file
f.write.array.to.img.2bytes

write array of 2 byte integers
f.read.nifti.header

read Nifti header file
nifti.quatern.to.mat44

Quaternion (etc..) to affine 4x4 matrix
f.icast.fmri

Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasets
Threshold.RF

Random Field Theory Thersholds.
SmoothEst

Estimate the variance-covariance matrix of a Gaussian random field
f.write.array.to.img.float

write array of 4 byte floats
Threshold.FDR

False Discovery Rate (FDR) Threshold
f.write.array.to.img.8bit

write array of 1 byte integers
f.icast.fmri.gui

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

Posterior Probabilities for N2G model
ijk2xyz

ijk2xyz
f.basic.hdr.nifti.list.create

creates basic .hdr list in NIFTI format
model.2.est.gamma

Estimate gamma for Model 2 of Hartvig and Jensen (2000)
f.plot.ica.fmri

Plots a specified component from the output of f.ica.fmri
f.spectral.summary.nifti

plots graphical summary of spectral properties of an fMRI dataset
centering

centering
f.read.header

read ANALYZE or NIFTI header file
threeDto4D

threeDto4D
f.read.analyze.header

read Analyze header file
twoDto4D

twoDto4D
magicfield

Get magicfield from the header of an image file
fps2diminfo

fps2diminfo
st2xyzt

st2xyzt
f.read.analyze.slice

read one slice from a .img file
f.read.nifti.volume

read whole image file
xyzt2st

xyzt2st
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.list.to.hdr

writes a .hdr file in ANALYZE format
NonLinearSmoothArray

Non-linear spatial smmothing of 3D and 4D arrays.
xyz2ijk

xyz2ijk
cluster.threshold

Cluster threshold an array.
model.2.cov.func

Calculates covariance from Hartvig Model 2
mat34.to.TRSZ

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

Calculates a discrete Gaussian smoothing kernel.
N2G.Spatial.Mixture

fMRI Spatial Mixture Modelling
f.plot.volume.gui

tcltk GUI to display FMRI or MRI images
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
fourDto2D

fourDto2D