# Functions for Analysis of fMRI Datasets Stored in the ANALYZE or NIFTI Format

## Documentation for package ‘AnalyzeFMRI’ version 1.1-21

- DESCRIPTION file.

## Help Pages

A C D E F G I M N O Q R S T W X

## -- A --

analyze2nifti | Create a NIFTI file from an Analyze file

## -- C --

centering | centering
cluster.threshold | Cluster threshold an array.
cluster_mass | Cluster threshold an array.
cov.est | Estimates the covariance between neighbouring voxels
covariance_est | Estimates the covariance between neighbouring voxels

## -- D --

diminfo2fps | diminfo2fps

## -- E --

EC.3D | Expected Euler Characteristic for a 3D Random Field
eigenvalues | eigenvalues

## -- F --

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.complete.hdr.nifti.list.create | creates complete .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.icast.fmri | Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasets
f.icast.fmri.gui | tcltk GUI to apply Spatial or Temporal ICA to fMRI NIFTI 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.plot.volume.gui | tcltk GUI to display FMRI or MRI images
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 or .nii file in NIFTI format
f.read.nifti.slice.at.all.timepoints | reads a slice at all time points from a NIFTI .img or .nii 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 image file
f.read.volume | read whole image 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
fourDto2D | fourDto2D
fps2diminfo | fps2diminfo

## -- G --

gaussfilter1 | Calculates a discrete Gaussian smoothing kernel.
gaussfilter2 | Calculates a discrete Gaussian smoothing kernel.
GaussSmoothArray | Spatially smooth an array with Gaussian kernel.
GaussSmoothKernel | Calculates a discrete Gaussian smoothing kernel.

## -- I --

ICAspat | ICAspat
ICAtemp | ICAtemp
ica_fmri_JM | ICAspat
ijk2xyz | ijk2xyz

## -- M --

magicfield | Get magicfield 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)

## -- N --

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

## -- O --

orientation | Orientation storage

## -- Q --

Q2R | Quaternion to rotation

## -- R --

R2Q | Rotation to quaternion
read2byte_v1_JM | read whole .img file
read4byte_v1_JM | read whole .img file
readchar_v1_JM | read whole .img file
readdouble_v1_JM | read whole .img file
readfloat_v1_JM | read whole .img file
read_analyze_header_wrap_JM | read whole .img file
read_nifti_header_wrap_JM | read Nifti header file
read_nifti_magic_wrap | read Nifti header file
reduction | reduction

## -- S --

Sim.3D.GammaRF | Simulate Gamma distributed Random Field
Sim.3D.GRF | Simulate a GRF
sim_grf | Simulate a GRF
SmoothEst | Estimate the variance-covariance matrix of a Gaussian random field
spatial_mixture | fMRI Spatial Mixture Modelling
st2xyzt | st2xyzt
swaptest_wrap_JM | read whole .img file

## -- T --

temporal_non_lin_gauss_smooth | Non-linear spatial smmothing of 3D and 4D arrays.
threeDto4D | threeDto4D
Threshold.Bonferroni | Calculates Bonferroni Threshold
Threshold.FDR | False Discovery Rate (FDR) Threshold
Threshold.RF | Random Field Theory Thersholds.
twoDto4D | twoDto4D

## -- W --

write2byteappend_JM | writes an array to a .img/.hdr pair in ANALYZE format
write2byte_JM | read whole .img file
write8bitappend_JM | writes an array to a .img/.hdr pair in ANALYZE format
write8bit_JM | writes an array to a .img/.hdr pair in ANALYZE format
writefloatappend_JM | writes an array to a .img/.hdr pair in ANALYZE format
writefloat_JM | writes an array to a .img/.hdr pair in ANALYZE format
write_analyze_header_wrap_JM | writes an array to a .img/.hdr pair in ANALYZE format
write_nifti_header_wrap_JM | writes an array to a .img/.hdr pair in ANALYZE format

## -- X --

xyz2ijk | xyz2ijk
xyzt2st | xyzt2st