Package: AnalyzeFMRI 1.1-25

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. Note that the latest version of 'XQuartz' seems to be necessary under MacOS.

Authors:Pierre Lafaye De Micheaux [aut, cre], Jonathan L Marchini [aut], Cleve Moler [cph], Jack Dongarra [cph], Richard Hanson [cph], Sven Hammarling [cph], Jeremy Du Croz [cph]

AnalyzeFMRI_1.1-25.tar.gz
AnalyzeFMRI_1.1-25.zip(r-4.7)AnalyzeFMRI_1.1-25.zip(r-4.6)AnalyzeFMRI_1.1-25.zip(r-4.5)
AnalyzeFMRI_1.1-25.tgz(r-4.6-x86_64)AnalyzeFMRI_1.1-25.tgz(r-4.6-arm64)AnalyzeFMRI_1.1-25.tgz(r-4.5-x86_64)AnalyzeFMRI_1.1-25.tgz(r-4.5-arm64)
AnalyzeFMRI_1.1-25.tar.gz(r-4.7-arm64)AnalyzeFMRI_1.1-25.tar.gz(r-4.7-x86_64)AnalyzeFMRI_1.1-25.tar.gz(r-4.6-arm64)AnalyzeFMRI_1.1-25.tar.gz(r-4.6-x86_64)
AnalyzeFMRI_1.1-25.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
AnalyzeFMRI/json (API)

# Install 'AnalyzeFMRI' in R:
install.packages('AnalyzeFMRI', repos = c('https://lafaye.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openblas– Optimized BLAS

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblas

3.04 score 217 scripts 419 downloads 5 mentions 112 exports 5 dependencies

Last updated from:4ac2a95772. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK130
linux-devel-x86_64OK129
source / vignettesOK165
linux-release-arm64OK119
linux-release-x86_64OK118
macos-release-arm64OK125
macos-release-x86_64OK228
macos-oldrel-arm64OK96
macos-oldrel-x86_64OK235
windows-develOK104
windows-releaseOK129
windows-oldrelOK109
wasm-releaseOK106

Exports:analyze2nifticenteringcluster_masscluster.thresholdcov.estcovariance_estdiminfo2fpsEC.3Deigenvaluesf.analyze.file.summaryf.analyzeFMRI.guif.basic.hdr.list.createf.basic.hdr.nifti.list.createf.complete.hdr.nifti.list.createf.ica.fmrif.ica.fmri.guif.icast.fmrif.icast.fmri.guif.nifti.file.summaryf.plot.ica.fmrif.plot.ica.fmri.jpgf.plot.volume.guif.read.analyze.headerf.read.analyze.slicef.read.analyze.slice.at.all.timepointsf.read.analyze.tptf.read.analyze.tsf.read.analyze.volumef.read.headerf.read.nifti.headerf.read.nifti.slicef.read.nifti.slice.at.all.timepointsf.read.nifti.tptf.read.nifti.tsf.read.nifti.volumef.read.volumef.spectral.summaryf.spectral.summary.niftif.write.analyzef.write.array.to.img.2bytesf.write.array.to.img.8bitf.write.array.to.img.floatf.write.list.to.hdrf.write.list.to.hdr.niftif.write.niftif.write.nii.array.to.img.2bytesf.write.nii.array.to.img.8bitf.write.nii.array.to.img.floatfourDto2Dfps2diminfogaussfilter1gaussfilter2GaussSmoothArrayGaussSmoothKernelica_fmri_JMICAspatICAtempijk2xyzmagicfieldmat34.to.TRSZmat34.to.TZSRmodel.2.cov.funcmodel.2.est.gammaN2GN2G.Class.ProbabilityN2G.DensityN2G.FitN2G.InverseN2G.LikelihoodN2G.Likelihood.RatioN2G.RegionN2G.Spatial.MixtureN2G.Transformnifti.quatern.to.mat44non_lin_gauss_smoothNonLinearSmoothArrayorientationQ2RR2Qread_analyze_header_wrap_JMread_nifti_header_wrap_JMread_nifti_magic_wrapread2byte_v1_JMread4byte_v1_JMreadchar_v1_JMreaddouble_v1_JMreadfloat_v1_JMreductionsim_grfSim.3D.GammaRFSim.3D.GRFSmoothEstspatial_mixturest2xyztswaptest_wrap_JMtemporal_non_lin_gauss_smooththreeDto4DThreshold.BonferroniThreshold.FDRThreshold.RFtwoDto4Dwith_dirwrite_analyze_header_wrap_JMwrite_nifti_header_wrap_JMwrite2byte_JMwrite2byteappend_JMwrite8bit_JMwrite8bitappend_JMwritefloat_JMwritefloatappend_JMxyz2ijkxyzt2st

Dependencies:fastICAR.matlabR.methodsS3R.ooR.utils

Readme and manuals

Help Manual

Help pageTopics
Create a NIFTI file from an Analyze fileanalyze2nifti
centeringcentering
Cluster threshold an array.cluster.threshold cluster_mass
Estimates the covariance between neighbouring voxelscov.est covariance_est
diminfo2fpsdiminfo2fps
Expected Euler Characteristic for a 3D Random FieldEC.3D
eigenvalueseigenvalues
prints summary of .img file contentsf.analyze.file.summary
starts AnalyzeFMRI GUIf.analyzeFMRI.gui
creates basic .hdr list in ANALYZE formatf.basic.hdr.list.create
creates basic .hdr list in NIFTI formatf.basic.hdr.nifti.list.create
creates complete .hdr list in NIFTI formatf.complete.hdr.nifti.list.create
Applies Spatial ICA (Independent Component Analysis) to fMRI datasetsf.ica.fmri
tcltk GUI to apply ICA to fMRI datasetsf.ica.fmri.gui
Applies Spatial or Temporal ICA (Independent Component Analysis) to fMRI NIFTI datasetsf.icast.fmri
tcltk GUI to apply Spatial or Temporal ICA to fMRI NIFTI datasetsf.icast.fmri.gui
prints summary of .img file contentsf.nifti.file.summary
Plots a specified component from the output of f.ica.fmrif.plot.ica.fmri
Plot the components of the ouput of f.ica.fmri to a series of jpeg filesf.plot.ica.fmri.jpg
tcltk GUI to display FMRI or MRI imagesf.plot.volume.gui
read Analyze header filef.read.analyze.header
read one slice from a .img filef.read.analyze.slice
reads a slice at all time points from a .img filef.read.analyze.slice.at.all.timepoints
Read in a volume at one time pointf.read.analyze.tpt
read in one voxel time seriesf.read.analyze.ts
read whole .img filef.read.analyze.volume read2byte_v1_JM read4byte_v1_JM readchar_v1_JM readdouble_v1_JM readfloat_v1_JM read_analyze_header_wrap_JM swaptest_wrap_JM write2byte_JM
read ANALYZE or NIFTI header filef.read.header
read Nifti header filef.read.nifti.header read_nifti_header_wrap_JM read_nifti_magic_wrap
read one slice from a .img or .nii file in NIFTI formatf.read.nifti.slice
reads a slice at all time points from a NIFTI .img or .nii filef.read.nifti.slice.at.all.timepoints
Read in a volume at one time pointf.read.nifti.tpt
read in one voxel time seriesf.read.nifti.ts
read whole image filef.read.nifti.volume
read whole image filef.read.volume
plots graphical summary of spectral properties of an fMRI datasetf.spectral.summary
plots graphical summary of spectral properties of an fMRI datasetf.spectral.summary.nifti
writes an array to a .img/.hdr pair in ANALYZE formatf.write.analyze write2byteappend_JM write8bitappend_JM write8bit_JM writefloatappend_JM writefloat_JM write_analyze_header_wrap_JM write_nifti_header_wrap_JM
write array of 2 byte integersf.write.array.to.img.2bytes
write array of 1 byte integersf.write.array.to.img.8bit
write array of 4 byte floatsf.write.array.to.img.float
writes a .hdr file in ANALYZE formatf.write.list.to.hdr
writes a .hdr file in NITI formatf.write.list.to.hdr.nifti
writes an array to a .img/.hdr pair in NIFTI format or to a .nii filef.write.nifti
write array of 2 byte integers and add at the begining of the file the NIFTI header partf.write.nii.array.to.img.2bytes
write array of 1 byte integers and add at the begining of the file the NIFTI header partf.write.nii.array.to.img.8bit
write array of 4 byte floats and add at the begining of the file the NIFTI header partf.write.nii.array.to.img.float
fourDto2DfourDto2D
fps2diminfofps2diminfo
Spatially smooth an array with Gaussian kernel.GaussSmoothArray
Calculates a discrete Gaussian smoothing kernel.gaussfilter1 gaussfilter2 GaussSmoothKernel
ICAspatICAspat ica_fmri_JM
ICAtempICAtemp
ijk2xyzijk2xyz
Get magicfield from the header of an image filemagicfield
Affine 4x4 (or 3x4) matrix to Translation, Rotation, Shear and Scalemat34.to.TRSZ
Affine 4x4 (or 3x4) matrix to Translation, Scale, Shear and Rotationmat34.to.TZSR
Calculates covariance from Hartvig Model 2model.2.cov.func
Estimate gamma for Model 2 of Hartvig and Jensen (2000)model.2.est.gamma
Fits the N2G modelN2G
Posterior Probabilities for N2G modelN2G.Class.Probability
Calculates the density function for the N2G modelN2G.Density
Optimzation function for N2G modelN2G.Fit
Transform parameters of N2G model back to their real domainsN2G.Inverse
Calculates the (negative) Likelihood of the N2G modelN2G.Likelihood
N2G Likelihood Ratio'sN2G.Likelihood.Ratio
N2G Normal component intervalN2G.Region
fMRI Spatial Mixture ModellingN2G.Spatial.Mixture spatial_mixture
Transform parameters of N2G model so as to lie on the real line.N2G.Transform
Quaternion (etc..) to affine 4x4 matrixnifti.quatern.to.mat44
Non-linear spatial smmothing of 3D and 4D arrays.NonLinearSmoothArray non_lin_gauss_smooth temporal_non_lin_gauss_smooth
Orientation storageorientation
Quaternion to rotationQ2R
Rotation to quaternionR2Q
reductionreduction
Simulate Gamma distributed Random FieldSim.3D.GammaRF
Simulate a GRFSim.3D.GRF sim_grf
Estimate the variance-covariance matrix of a Gaussian random fieldSmoothEst
st2xyztst2xyzt
threeDto4DthreeDto4D
Calculates Bonferroni ThresholdThreshold.Bonferroni
False Discovery Rate (FDR) ThresholdThreshold.FDR
Random Field Theory Thersholds.Threshold.RF
twoDto4DtwoDto4D
Working directorywith_dir
xyz2ijkxyz2ijk
xyzt2stxyzt2st