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

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

Author
P Lafaye de Micheaux <lafaye@dms.umontreal.ca>, J L Marchini <marchini@stats.ox.ac.uk>
Date of publication
2013-03-19 15:38:10
Maintainer
P Lafaye de Micheaux <lafaye@dms.umontreal.ca>
License
GPL (>= 2)
Version
1.1-16

View on CRAN

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

Files in this package

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