AnalyzeFMRI: Functions for analysis of fMRI datasets stored in the ANALYZE or NIFTI format.
Version 1.1-16

Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format.

AuthorP Lafaye de Micheaux <lafaye@dms.umontreal.ca>, J L Marchini <marchini@stats.ox.ac.uk>
Date of publication2013-03-19 15:38:10
MaintainerP Lafaye de Micheaux <lafaye@dms.umontreal.ca>
LicenseGPL (>= 2)
Version1.1-16
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("AnalyzeFMRI")

Popular man pages

EC.3D: Expected Euler Characteristic for a 3D Random Field
f.plot.ica.fmri: Plots a specified component from the output of f.ica.fmri
f.read.analyze.slice: read one slice from a .img file
f.read.analyze.volume: read whole .img file
f.read.header: read ANALYZE or NIFTI header file
f.read.nifti.slice: read one slice from a .img or .nii file in NIFTI format
GaussSmoothArray: Spatially smooth an array with Gaussian kernel.
See all...

All man pages Function index File listing

Man pages

analyze2nifti: Create a NIFTI file from an Analyze file
centering: centering
cluster.threshold: Cluster threshold an array.
cov.est: Estimates the covariance between neighbouring voxels
diminfo2fps: diminfo2fps
EC.3D: Expected Euler Characteristic for a 3D Random Field
eigenvalues: eigenvalues
f.analyze.file.summary: prints summary of .img file contents
f.analyzeIO.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...
f.ica.fmri.gui: tcltk GUI to apply ICA to fMRI datasets
f.icast.fmri: Applies Spatial or Temporal ICA (Independent Component...
f.icast.fmri.gui: tcltk GUI to apply Spatial or Temporal ICA to fMRI NIFTI...
f.nifti.file.summary: prints summary of .img file contents
fourDto2D: fourDto2D
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...
f.plot.volume.gui: tcltk GUI to display FMRI or MRI images
fps2diminfo: fps2diminfo
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...
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...
f.spectral.summary.nifti: plots graphical summary of spectral properties of an fMRI...
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...
f.write.nii.array.to.img.2bytes: write array of 2 byte integers and add at the begining of the...
f.write.nii.array.to.img.8bit: write array of 1 byte integers and add at the begining of the...
f.write.nii.array.to.img.float: write array of 4 byte floats and add at the begining of the...
GaussSmoothArray: Spatially smooth an array with Gaussian kernel.
GaussSmoothKernel: Calculates a discrete Gaussian smoothing kernel.
ICAspat: ICAspat
ICAtemp: ICAtemp
ijk2xyz: ijk2xyz
magicfield: Get magicfield from the header of an image file
mat34.to.TRSZ: Affine 4x4 (or 3x4) matrix to Translation, Rotation, Shear...
mat34.to.TZSR: Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and...
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...
nifti.quatern.to.mat44: Quaternion (etc..) to affine 4x4 matrix
NonLinearSmoothArray: Non-linear spatial smmothing of 3D and 4D arrays.
Q2R: Quaternion to rotation
R2Q: Rotation to quaternion
reduction: reduction
Sim.3D.GammaRF: Simulate Gamma distributed Random Field
Sim.3D.GRF: Simulate a GRF
SmoothEst: Estimate the variance-covariance matrix of a Gaussian random...
st2xyzt: st2xyzt
threeDto4D: threeDto4D
Threshold.Bonferroni: Calculates Bonferroni Threshold
Threshold.FDR: False Discovery Rate (FDR) Threshold
Threshold.RF: Random Field Theory Thersholds.
twoDto4D: twoDto4D
xyz2ijk: xyz2ijk
xyzt2st: xyzt2st

Functions

EC.3D Man page Source code
GaussSmoothArray Man page Source code
GaussSmoothKernel Man page Source code
ICAspat Man page Source code
ICAtemp Man page Source code
N2G Man page Source code
N2G.Class.Probability Man page Source code
N2G.Density Man page Source code
N2G.Fit Man page Source code
N2G.Inverse Man page Source code
N2G.Likelihood Man page Source code
N2G.Likelihood.Ratio Man page Source code
N2G.Region Man page Source code
N2G.Spatial.Mixture Man page Source code
N2G.Transform Man page Source code
NonLinearSmoothArray Man page Source code
Q2R Man page Source code
R2Q Man page Source code
Sim.3D.GRF Man page Source code
Sim.3D.GammaRF Man page Source code
SmoothEst Man page Source code
Threshold.Bonferroni Man page Source code
Threshold.FDR Man page Source code
Threshold.RF Man page Source code
analyze2nifti Man page Source code
centering Man page Source code
cluster.threshold Man page Source code
cov.est Man page Source code
diminfo2fps Man page Source code
eigenvalues Man page Source code
f.analyze.file.summary Man page Source code
f.analyzeFMRI.gui Man page Source code
f.basic.hdr.list.create Man page Source code
f.basic.hdr.nifti.list.create Man page Source code
f.complete.hdr.nifti.list.create Man page Source code
f.ica.fmri Man page Source code
f.ica.fmri.gui Man page Source code
f.icast.fmri Man page Source code
f.icast.fmri.gui Man page Source code
f.nifti.file.summary Man page Source code
f.plot.ica.fmri Man page Source code
f.plot.ica.fmri.jpg Man page Source code
f.plot.volume.gui Man page Source code
f.read.analyze.header Man page Source code
f.read.analyze.slice Man page Source code
f.read.analyze.slice.at.all.timepoints Man page Source code
f.read.analyze.tpt Man page Source code
f.read.analyze.ts Man page Source code
f.read.analyze.volume Man page Source code
f.read.header Man page Source code
f.read.nifti.header Man page Source code
f.read.nifti.slice Man page Source code
f.read.nifti.slice.at.all.timepoints Man page Source code
f.read.nifti.tpt Man page Source code
f.read.nifti.ts Man page Source code
f.read.nifti.volume Man page Source code
f.read.volume Man page Source code
f.spectral.summary Man page Source code
f.spectral.summary.nifti Man page Source code
f.write.analyze Man page Source code
f.write.array.to.img.2bytes Man page Source code
f.write.array.to.img.8bit Man page Source code
f.write.array.to.img.float Man page Source code
f.write.list.to.hdr Man page Source code
f.write.list.to.hdr.nifti Man page Source code
f.write.nifti Man page Source code
f.write.nii.array.to.img.2bytes Man page Source code
f.write.nii.array.to.img.8bit Man page Source code
f.write.nii.array.to.img.float Man page Source code
fourDto2D Man page Source code
fps2diminfo Man page Source code
ijk2xyz Man page Source code
magicfield Man page Source code
mat34.to.TRSZ Man page Source code
mat34.to.TZSR Man page Source code
model.2.cov.func Man page Source code
model.2.est.gamma Man page Source code
nifti.quatern.to.mat44 Man page Source code
reduction Man page Source code
st2xyzt Man page Source code
threeDto4D Man page Source code
twoDto4D Man page Source code
xyz2ijk Man page Source code
xyzt2st Man page Source code

Files

MD5
TODO
R
R/analyzeFMRI.R
R/niftiFMRI.R
R/threshold.R
R/spatial.mixture.R
R/f.non.lin.gaussian.spatial.smoothing.functions.R
R/f.gaussian.spatial.smoothing.functions.R
configure.ac
tests
tests/test.array.hdr
tests/test.array.img
tests/test.R
tests/test.Rout.save
configure.win
tst.hdr
cleanup
src
src/lsame.unused
src/slamc.unused
src/sblas.unused
src/spatial.mixture.c
src/lsame.f
src/spatial.est.c
src/slamc.f
src/sim.3d.GRF.c
src/spatial.filters.linear.f
src/spatial.c
src/analyzeFMRI.c
src/spatial.filters.non.linear.c
src/Makevars.in
src/niftiFMRI.c
src/verR.h
src/slapack.unused
inst
inst/README
inst/plot.volume.gui.R
inst/README.win
inst/GRF.examples.R
inst/ICA.gui.R
inst/ICAst.gui.R
inst/example.img
inst/HISTORY
inst/example-nifti.img
inst/smoothing.examples.R
inst/example-nifti.hdr
inst/AnalyzeFMRI.gui.R
inst/example.hdr
inst/CITATION
inst/example.mat
INDEX
tst.img
NAMESPACE
man
man/analyze2nifti.Rd
man/model.2.cov.func.Rd
man/eigenvalues.Rd
man/diminfo2fps.Rd
man/f.read.analyze.volume.Rd
man/f.nifti.file.summary.Rd
man/f.read.header.Rd
man/R2Q.Rd
man/N2G.Region.Rd
man/f.write.analyze.Rd
man/cov.est.Rd
man/model.2.est.gamma.Rd
man/Threshold.RF.Rd
man/f.write.nii.array.to.img.8bit.Rd
man/N2G.Inverse.Rd
man/ijk2xyz.Rd
man/f.ica.fmri.Rd
man/f.read.nifti.volume.Rd
man/fourDto2D.Rd
man/f.read.nifti.ts.Rd
man/f.write.list.to.hdr.nifti.Rd
man/f.read.nifti.slice.at.all.timepoints.Rd
man/Threshold.Bonferroni.Rd
man/f.analyzeIO.gui.Rd
man/Sim.3D.GammaRF.Rd
man/Q2R.Rd
man/GaussSmoothArray.Rd
man/centering.Rd
man/GaussSmoothKernel.Rd
man/nifti.quatern.to.mat44.Rd
man/f.read.analyze.tpt.Rd
man/f.read.nifti.tpt.Rd
man/f.ica.fmri.gui.Rd
man/N2G.Fit.Rd
man/st2xyzt.Rd
man/f.read.volume.Rd
man/mat34.to.TZSR.Rd
man/twoDto4D.Rd
man/f.icast.fmri.Rd
man/cluster.threshold.Rd
man/threeDto4D.Rd
man/reduction.Rd
man/f.basic.hdr.nifti.list.create.Rd
man/f.read.analyze.ts.Rd
man/ICAspat.Rd
man/f.read.analyze.slice.at.all.timepoints.Rd
man/f.plot.volume.gui.Rd
man/N2G.Density.Rd
man/N2G.Rd
man/N2G.Likelihood.Rd
man/f.basic.hdr.list.create.Rd
man/N2G.Likelihood.Ratio.Rd
man/f.complete.hdr.nifti.list.create.Rd
man/f.spectral.summary.Rd
man/f.read.analyze.header.Rd
man/f.write.array.to.img.2bytes.Rd
man/NonLinearSmoothArray.Rd
man/f.write.nifti.Rd
man/magicfield.Rd
man/xyz2ijk.Rd
man/f.plot.ica.fmri.Rd
man/N2G.Class.Probability.Rd
man/mat34.to.TRSZ.Rd
man/N2G.Transform.Rd
man/f.icast.fmri.gui.Rd
man/f.write.array.to.img.float.Rd
man/EC.3D.Rd
man/f.read.nifti.header.Rd
man/Sim.3D.GRF.Rd
man/f.write.array.to.img.8bit.Rd
man/f.write.nii.array.to.img.2bytes.Rd
man/xyzt2st.Rd
man/f.spectral.summary.nifti.Rd
man/ICAtemp.Rd
man/f.read.nifti.slice.Rd
man/f.plot.ica.fmri.jpg.Rd
man/SmoothEst.Rd
man/Threshold.FDR.Rd
man/f.write.list.to.hdr.Rd
man/f.read.analyze.slice.Rd
man/N2G.Spatial.Mixture.Rd
man/f.write.nii.array.to.img.float.Rd
man/f.analyze.file.summary.Rd
man/fps2diminfo.Rd
DESCRIPTION
configure
niftidoc
niftidoc/intent-code.txt
niftidoc/xyzt-units.txt
AnalyzeFMRI documentation built on May 19, 2017, 6:14 p.m.

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