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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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Install
install.packages('AnalyzeFMRI')
Monthly Downloads
406
Version
1.1-16
License
GPL (>= 2)
Maintainer
P de Micheaux
Last Published
March 19th, 2013
Functions in AnalyzeFMRI (1.1-16)
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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