Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format.

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Documentation for package ‘AnalyzeFMRI’ version 1.1-10

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cluster.threshold Cluster threshold an array.
cov.est Estimates the covariance between neighbouring voxels
EC.3D Expected Euler Characteristic for a 3D Random Field
f.analyze.file.summary prints summary of .img file contents
f.analyzeFMRI.gui starts AnalyzeFMRI GUI
f.basic.hdr.list.create creates basic .hdr list in ANALYZE format
f.basic.hdr.nifti.list.create creates basic .hdr list in NIFTI format
f.ica.fmri Applies Spatial ICA (Independent Component Analysis) to fMRI datasets
f.ica.fmri.gui tcltk GUI to apply ICA to fMRI datasets
f.nifti.file.summary prints summary of .img file contents
f.plot.ica.fmri Plots a specified component from the output of f.ica.fmri
f.plot.ica.fmri.jpg Plot the components of the ouput of f.ica.fmri to a series of jpeg files
f.read.analyze.header read Analyze header file
f.read.analyze.slice read one slice from a .img file
f.read.analyze.slice.at.all.timepoints reads a slice at all time points from a .img file
f.read.analyze.tpt Read in a volume at one time point
f.read.analyze.ts read in one voxel time series
f.read.analyze.volume read whole .img file
f.read.header read ANALYZE or NIFTI header file
f.read.nifti.header read Nifti header file
f.read.nifti.slice read one slice from a .img file in NIFTI format
f.read.nifti.slice.at.all.timepoints reads a slice at all time points from a NIFTI .img file
f.read.nifti.tpt Read in a volume at one time point
f.read.nifti.ts read in one voxel time series
f.read.nifti.volume read whole .img file
f.spectral.summary plots graphical summary of spectral properties of an fMRI dataset
f.spectral.summary.nifti plots graphical summary of spectral properties of an fMRI dataset
f.write.analyze writes an array to a .img/.hdr pair in ANALYZE format
f.write.array.to.img.2bytes write array of 2 byte integers
f.write.array.to.img.8bit write array of 1 byte integers
f.write.array.to.img.float write array of 4 byte floats
f.write.list.to.hdr writes a .hdr file in ANALYZE format
f.write.list.to.hdr.nifti writes a .hdr file in NITI format
f.write.nifti writes an array to a .img/.hdr pair in NIFTI format or to a .nii 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.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.write.nii.array.to.img.float write array of 4 byte floats and add at the begining of the file the NIFTI header part
GaussSmoothArray Spatially smooth an array with Gaussian kernel.
GaussSmoothKernel Calculates a discrete Gaussian smoothing kernel.
model.2.cov.func Calculates covariance from Hartvig Model 2
model.2.est.gamma Estimate gamma for Model 2 of Hartvig and Jensen (2000)
N2G Fits the N2G model
N2G.Class.Probability Posterior Probabilities for N2G model
N2G.Density Calculates the density function for the N2G model
N2G.Fit Optimzation function for N2G model
N2G.Inverse Transform parameters of N2G model back to their real domains
N2G.Likelihood Calculates the (negative) Likelihood of the N2G model
N2G.Likelihood.Ratio N2G Likelihood Ratio's
N2G.Region N2G Normal component interval
N2G.Spatial.Mixture fMRI Spatial Mixture Modelling
N2G.Transform Transform parameters of N2G model so as to lie on the real line.
NonLinearSmoothArray Non-linear spatial smmothing of 3D and 4D arrays.
Sim.3D.GammaRF Simulate Gamma distributed Random Field
Sim.3D.GRF Simulate a GRF
SmoothEst Estimate the variance-covariance matrix of a Gaussian random field
Threshold.Bonferroni Calculates Bonferroni Threshold
Threshold.FDR False Discovery Rate (FDR) Threshold
Threshold.RF Random Field Theory Thersholds.