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INDEX
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analyze2nifti Create a NIFTI file from an Analyze file
centering Center the data in the two dimensions
cluster.threshold Cluster threshold an array.
cov.est Estimates the covariance between neighbouring
voxels
diminfo2fps dim.info field to freq.dim, phase.dim and slice.dim fields
EC.3D Expected Euler Characteristic for a 3D Random
Field
eigenvalues Computes the eigenvalues of a centered and reduced data matrix
fourDto2D Transform a 4D image into a 2D image matrix
fps2diminfo freq.dim, phase.dim and slice.dim fields into dim.info field
f.analyze.file.summary Prints summary of ANALYZE .img file contents
f.nifti.file.summary Prints summary of NIFTI .img file contents
f.analyzeFMRI.gui Starts AnalyzeFMRI GUI
f.basic.hdr.list.create Creates basic ANALYZE .hdr list
f.basic.hdr.nifti.list.create
Creates basic NIFTI .hdr list
f.complete.hdr.nifti.list.create
Creates complete NIFTI .hdr list
f.ica.fmri Applies Spatial ICA (Independent Component
Analysis) to fMRI datasets
f.icast.fmri Applies Spatial or Temporal ICA (Independent Component
Analysis) to fMRI NIFTI datasets
f.ica.fmri.gui tcltk GUI to apply Spatial ICA to fMRI Analyze datasets
f.icast.fmri.gui tcltk GUI to apply Spatial or Temporal ICA to NIFTI fMRI datasets
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 an ANALYZE .img file
f.read.nifti.slice Read one slice from a NIFTI .img file
f.read.analyze.slice.at.all.timepoints
Reads a slice at all time points from an ANALYZE .img file
f.read.nifti.slice.at.all.timepoints
Reads a slice at all time points from a NIFTI .img file
f.read.analyze.tpt Read in a volume at one time point from an ANALYZE file
f.read.nifti.tpt Read in a volume at one time point from a NIFTI file
f.read.analyze.ts Read in one voxel time series from an ANALYZE .img file
f.read.nifti.ts Read in one voxel time series from a NIFTI .img or .nii file
f.read.analyze.volume Read whole ANALYZE .img or .nii file
f.read.nifti.volume Read whole NIFTI image file
f.read.volume Read whole ANALYZE or NIFTI image file (autodetecting the format)
f.read.nifti.header Read Nifti header file
f.read.header Read Analyze and Nifti header files
f.spectral.summary Plots graphical summary of spectral properties
of an ANALYZE fMRI dataset
f.spectral.summary.nifti
Plots graphical summary of spectral properties
of a NIFTI fMRI dataset
f.write.analyze Writes an array to an ANALYZE .img/.hdr pair
f.write.nifti Writes an array to a NIFTI .img/.hdr pair
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.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
f.write.list.to.hdr Writes an ANALYZE .hdr file
f.write.list.to.hdr.nifti
Writes a NIFTI .hdr file
GaussSmoothArray Spatially smooth an array with Gaussian kernel.
GaussSmoothKernel Calculates a discrete Gaussian smoothing
kernel.
ICAspat Performs a spatial ICA
ICAtemp Performs a temporal ICA
ijk2xyz Maps from data coordinates (e.g. column i, row j, slice k), into some real world (x,y,z) positions in space.
magicfield Get magic field from the header of an image file
mat34.to.TRSZ Affine 4x4 (or 3x4) matrix to Translation, Rotation, Shear and Scale
mat34.to.TZSR Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and Rotation
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.
nifti.quatern.to.mat44 Quaternion (etc..) to affine 4x4 matrix
NonLinearSmoothArray Non-linear spatial smmothing of 3D and 4D
arrays.
orientation Returns storage mode (Radiological or Neurological)
Q2R Generate a rotation matrix from a quaternion
R2Q Convert from rotation matrix to quaternion form
reduction Reduces the data in the row or col dimension
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
st2xyzt Encode space and time dimensions fields into the xyzt.units field
threeDto4D Read tm functionnal images and concatenate them to obtain one (hdr/img pair) 4D image file (Analyze or Nifti format) which is written on disk
Threshold.Bonferroni Calculates Bonferroni Threshold
Threshold.FDR False Discovery Rate (FDR) Threshold
Threshold.RF Random Field Theory Thresholds.
twoDto4D Transform a 2D matrix of size tm x vm containing images in each row into a 4D array image
xyzt2st Extract space and time dimensions fields from xyzt.units field