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


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Documentation for package ‘AnalyzeFMRI’ version 1.1-24

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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