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.

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

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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.