oro.nifti: Rigorous - NIfTI+ANALYZE+AFNI Input / Output
Version 0.4.3

Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. This package is part of the Rigorous Analytics bundle.

Browse man pages Browse package API and functions Browse package files

AuthorBrandon Whitcher, Volker Schmid and Andrew Thornton, with contributions by Karsten Tabelow and Jon Clayden
Date of publication2015-01-17 15:39:57
MaintainerBrandon Whitcher <bwhitcher@gmail.com>
LicenseBSD_3_clause + file LICENSE
Version0.4.3
URL http://rig.oro.us.com http://rigorousanalytics.blogspot.com
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("oro.nifti", repos="http://R-Forge.R-project.org")

Man pages

afni: is.afni
afni-class: Class "afni"
anlz: Constructor for Analyze
anlz-class: Class "anlz"
as_nifti: as.nifti
audit_trail: Facilitate the Creation and Modification of Audit Trails
audit_trail-methods: Extract or Replace NIfTI Audit Trail
aux_file-methods: Extract or Replace NIfTI/Analyze Auxiliary File
bitwise: Bitwise Conversion Subroutines
calmin-methods: Extract or Replace NIfTI/Analyze Min or Max Values
coerce-methods: Force an Object to Belong to the ANALYZE or NIfTI Class
convert_afni: Convert AFNI data codes
convert_anlz: Convert NIfTI Codes
convert_nifti: Convert NIfTI Codes
descrip-methods: Extract or Replace NIfTI/Analyze Description
hotmetal: Hot Metal Color Table
image-methods: Methods for Function 'image'
integerTranslation: integerTranslation
miscellaneous: Dimension Accessor Functions
nifti: Constructor for NIfTI
nifti_assign-methods: ~~ Methods for Function [<- in Package 'base' ~~
niftiAuditTrail-class: Class "niftiAuditTrail"
nifti-class: Class "nifti"
niftiExtension-class: Class "niftiExtension"
niftiExtensionSection-class: Class "niftiExtensionSection"
orthographic-methods: Methods for Function 'orthographic' in Package 'dcemriS4'
overlay-methods: Methods for Function overlay
performPermutation: performPermutation
pixdim-methods: Extract or Replace NIfTI/Analyze Pixel Dimensions
q2R: Convert Quaternion into a Rotation Matrix
qformsform: Extract NIfTI 3D Image Orientation
read_afni: readAFNI
read_anlz: readANALYZE
read_nifti: readNIfTI
remove: Remove File Extensions Around the NIfTI/ANALYZE Formats
reorient: reorient
tim_colors: Tim's Useful Color Table
transformCoordinate: translateCoordinate
write_afni: writeAFNI
write_anlz: writeANALYZE
write_nifti: writeNIfTI

Functions

AFNIheaderpart Source code
NSLI Man page Source code
NTIM Man page Source code
[<-,ANY,ANY,ANY,ANY-method Man page
[<-,nifti,ANY,ANY,ANY-method Man page
[<-,nifti,ANY,missing,ANY-method Man page
[<-,nifti,missing,missing,array-method Man page
[<-,nifti,numeric,missing,ANY-method Man page
[<-,nifti,numeric,numeric,ANY-method Man page
[<--methods Man page
afni-class Man page
anlz Man page Source code
anlz-class Man page
as,array,anlz-method Man page
as,array,nifti-method Man page
as.anlz Man page Source code
as.nifti Man page Source code
as<-,array,anlz-method Man page
as<-,array,nifti-method Man page Man page
audit.trail Man page
audit.trail,nifti-method Man page
audit.trail-methods Man page
audit.trail<- Man page
audit.trail<-,nifti-method Man page
aux.file Man page
aux.file,anlz-method Man page
aux.file,nifti-method Man page
aux.file-methods Man page
aux.file<- Man page
aux.file<-,anlz-method Man page
aux.file<-,nifti-method Man page
cal.max Man page
cal.max,anlz-method Man page
cal.max,nifti-method Man page
cal.max-methods Man page
cal.max<- Man page
cal.max<-,anlz-method Man page
cal.max<-,nifti-method Man page
cal.min Man page
cal.min,anlz-method Man page
cal.min,nifti-method Man page
cal.min-methods Man page
cal.min<- Man page
cal.min<-,anlz-method Man page
cal.min<-,nifti-method Man page
coerce,anlz,nifti-method Man page
coerce,array,anlz-method Man page
coerce,array,nifti-method Man page
coerce,list,anlz-method Man page
coerce,list,nifti-method Man page
coerce-methods Man page
coerce<-,anlz,nifti-method Man page
coerce<-,array,anlz-method Man page
coerce<-,array,nifti-method Man page
coerce<-,list,anlz-method Man page
coerce<-,list,nifti-method Man page
convert.bitpix Man page Source code
convert.bitpix.anlz Man page Source code
convert.datatype Man page Source code
convert.datatype.anlz Man page Source code
convert.form Man page Source code
convert.intent Man page Source code
convert.orient.anlz Man page Source code
convert.scene Man page Source code
convert.slice Man page Source code
convert.units Man page Source code
descrip Man page
descrip,anlz-method Man page
descrip,nifti-method Man page
descrip-methods Man page
descrip<- Man page
descrip<-,anlz-method Man page
descrip<-,nifti-method Man page
dim2freq Man page Source code
dim2phase Man page Source code
dim2slice Man page Source code
enableAuditTrail Man page Source code
getLastCallWithName Man page Source code
hotmetal Man page Source code
image,ANY-method Man page
image,afni-method Man page
image,anlz-method Man page
image,nifti-method Man page
image-methods Man page
image.nifti Man page Source code
integerTranslation Man page Source code
inverseReorient Man page Source code
invertIntegerTranslation Man page Source code
is.afni Man page Source code
is.anlz Man page Source code
is.nifti Man page Source code
listToNodes Source code
newAuditTrail Man page Source code
nifti Man page Source code
nifti-class Man page
niftiAuditTrail-class Man page
niftiAuditTrailCreated Man page Source code
niftiAuditTrailEvent Man page Source code
niftiAuditTrailSystemNode Man page Source code
niftiAuditTrailSystemNodeEvent Man page Source code
niftiAuditTrailToExtension Man page Source code
niftiExtension-class Man page
niftiExtensionSection-class Man page
niftiExtensionToAuditTrail Man page Source code
niftiWrapper Source code
nsli Man page Source code
ntim Man page Source code
onAttach Source code
onLoad Source code
oro.nifti.info Man page Source code
orthographic Man page
orthographic,afni-method Man page
orthographic,anlz-method Man page
orthographic,array-method Man page
orthographic,nifti-method Man page
orthographic-methods Man page
orthographic.nifti Man page Source code
overlay Man page
overlay,afni,afni-method Man page
overlay,afni,array-method Man page
overlay,anlz,anlz-method Man page
overlay,anlz,array-method Man page
overlay,anlz,nifti-method Man page
overlay,array,anlz-method Man page
overlay,array,array-method Man page
overlay,array,nifti-method Man page
overlay,nifti,anlz-method Man page
overlay,nifti,array-method Man page
overlay,nifti,nifti-method Man page
overlay-methods Man page
overlay.nifti Man page Source code
performPermutation Man page Source code
pixdim Man page
pixdim,anlz-method Man page
pixdim,nifti-method Man page
pixdim-methods Man page
pixdim<- Man page
pixdim<-,anlz-method Man page
pixdim<-,nifti-method Man page
qform Man page
qform,nifti-method Man page
qform-methods Man page
quaternion2mat44 Man page Source code
quaternion2rotation Man page Source code
read.afni.content Man page Source code
read.analyze.content Man page Source code
read.nifti.content Man page Source code
readAFNI Man page Source code
readANALYZE Man page Source code
readCharWithEmbeddedNuls Source code
readNIfTI Man page Source code
reorient Man page Source code
rmgz Man page Source code
rmhdr Man page Source code
rmhdrgz Man page Source code
rmimg Man page Source code
rmimggz Man page Source code
rmnii Man page Source code
rmniigz Man page Source code
sform Man page
sform,nifti-method Man page
sform-methods Man page
show,afni-method Man page
show,anlz-method Man page
show,nifti-method Man page
space.time2xyzt Man page Source code
tim.colors Man page Source code
translateCoordinate Man page Source code
wrapper Source code
writeAFNI Man page Source code
writeAFNI,ANY-method Man page
writeAFNI,afni-method Man page
writeAFNI-methods Man page
writeANALYZE Man page Source code
writeANALYZE,anlz-method Man page
writeANALYZE-methods Man page
writeNIfTI Man page Source code
writeNIfTI,anlz-method Man page
writeNIfTI,array-method Man page
writeNIfTI,nifti-method Man page
writeNIfTI-methods Man page
xyzt2space Man page Source code
xyzt2time Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/afniS4.R
R/analyzeS4.R
R/auditTrail.R
R/convert_anlz.R
R/convert_nifti.R
R/hotmetal.R
R/miscellaneous.R
R/niftiS4.R
R/plot.R
R/readS4.R
R/remove.R
R/tim_colors.R
R/transform.R
R/wrappers.R
R/writeS4.R
R/zzz.R
build
build/vignette.rds
demo
demo/00Index
demo/avg152T1.R
demo/avg152T1LR.R
demo/avg152T1RL.R
demo/filtered_func_data.R
inst
inst/CITATION
inst/afni
inst/afni/ARzs_CW_avvr.DEL+orig.BRIK
inst/afni/ARzs_CW_avvr.DEL+orig.HEAD
inst/afni/TT_N27_EZ_LR+tlrc.BRIK.gz
inst/afni/TT_N27_EZ_LR+tlrc.HEAD
inst/anlz
inst/anlz/avg152T1.hdr.gz
inst/anlz/avg152T1.img.gz
inst/doc
inst/doc/ANALYZE75.pdf
inst/doc/nifti.R
inst/doc/nifti.Rnw
inst/doc/nifti.pdf
inst/nifti
inst/nifti/filtered_func_data.nii.gz
inst/nifti/mniLR.nii.gz
inst/nifti/mniRL.nii.gz
inst/nifti/zstat1.nii.gz
man
man/afni-class.Rd
man/afni.Rd
man/anlz-class.Rd
man/anlz.Rd
man/as_nifti.Rd
man/audit_trail-methods.Rd
man/audit_trail.Rd
man/aux_file-methods.Rd
man/bitwise.Rd
man/calmin-methods.Rd
man/coerce-methods.Rd
man/convert_afni.Rd
man/convert_anlz.Rd
man/convert_nifti.Rd
man/descrip-methods.Rd
man/hotmetal.Rd
man/image-methods.Rd
man/integerTranslation.Rd
man/miscellaneous.Rd
man/nifti-class.Rd
man/nifti.Rd
man/niftiAuditTrail-class.Rd
man/niftiExtension-class.Rd
man/niftiExtensionSection-class.Rd
man/nifti_assign-methods.Rd
man/orthographic-methods.Rd
man/overlay-methods.Rd
man/performPermutation.Rd
man/pixdim-methods.Rd
man/q2R.Rd
man/qformsform.Rd
man/read_afni.Rd
man/read_anlz.Rd
man/read_nifti.Rd
man/remove.Rd
man/reorient.Rd
man/tim_colors.Rd
man/transformCoordinate.Rd
man/write_afni.Rd
man/write_anlz.Rd
man/write_nifti.Rd
tests
tests/Examples
tests/Examples/oro.nifti-Ex.Rout.save
vignettes
vignettes/nifti.Rnw
vignettes/nifti.bib
oro.nifti documentation built on May 21, 2017, 1:26 a.m.