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

Documentation for package ‘AnalyzeFMRI’ version 1.1-25

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

-- 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 --

with_dir	Working directory
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