Function reference • oro.nifti

All functions
`show(<afni>)`	Class "afni"
`show(<anlz>)`	Class "anlz"
`Ops(<anlz>,<anlz>)` `Ops(<anlz>,<numeric>)` `Ops(<numeric>,<anlz>)` `Ops(<nifti>,<anlz>)` `Ops(<anlz>,<nifti>)`	Operations for Objects in the ANALYZE and NIfTI classes
`anlz()`	Constructor for Analyze
`as.anlz()`	as.anlz
`as.nifti()`	as.nifti
`audit.trail()` `audit.trail<-`()	Extract or Replace NIfTI Audit Trail
`oro.nifti.info()` `enableAuditTrail()` `getLastCallWithName()` `newAuditTrail()` `niftiExtensionToAuditTrail()` `niftiAuditTrailSystemNode()` `niftiAuditTrailSystemNodeEvent()` `niftiAuditTrailCreated()` `niftiAuditTrailEvent()`	Facilitate the Creation and Modification of Audit Trails
`aux_file()` `aux_file<-`() `aux.file()` `aux.file<-`()	Extract Image Attribute `aux_file`
`bitpix()` `bitpix<-`()	Extract Image Attribute `bitpix`
`xyzt2space()` `xyzt2time()` `space.time2xyzt()` `dim2freq()` `dim2phase()` `dim2slice()`	Bitwise Conversion Subroutines
`blendVolumes()` `blend(<nifti>,<nifti>)` `blend(<anlz>,<anlz>)` `blend(<anlz>,<nifti>)` `blend(<nifti>,<anlz>)`	Merge Two NIfTI or ANALYZE Volumes
`calibrateImage()` `cal_img()`	Set Minimum/Maximum Values for NIfTI data
`cal_max()` `cal_max<-`() `cal.max()` `cal.max<-`()	Extract Image Attribute `cal_max`
`cal_min()` `cal_min<-`() `cal.min()` `cal.min<-`()	Extract Image Attribute `cal_min`
`cal_units()` `cal_units<-`() `cal.units()` `cal.units<-`()	Extract Image Attribute `cal_units`
`coerce-methods`	Force an Object to Belong to the ANALYZE or NIfTI Class
`compressed()` `compressed<-`()	Extract Image Attribute `compressed`
`convert.scene()`	Convert AFNI data codes
`convert.bitpix.anlz()` `convert.datatype.anlz()` `convert.orient.anlz()`	Convert ANALYZE Codes
`convert.bitpix()` `convert.datatype()` `convert.intent()` `convert.form()` `convert.units()` `convert.slice()`	Convert NIfTI Codes
`data_type()` `data_type<-`() `data.type()` `data.type<-`() `datatype(<niftiImage>)`	Extract Image Attribute `data_type`
`datatype()` `datatype<-`()	Extract Image Attribute `datatype`
`db_name()` `db_name<-`() `db.name()` `db.name<-`()	Extract Image Attribute `db_name`
`descrip()` `descrip<-`()	Extract Image Attribute `descrip`
`dim_()` `dim_<-`()	Extract Image Attribute `dim_`
`dim_info()` `dim_info<-`()	Extract Image Attribute `dim_info`
`dim_un0()` `dim_un0<-`()	Extract Image Attribute `dim_un0`
`dropImageDimension()` `drop_img_dim()`	Drop Image Dimension
`exp_date()` `exp_date<-`()	Extract Image Attribute `exp_date`
`exp_time()` `exp_time<-`()	Extract Image Attribute `exp_time`
`extender()` `extender<-`()	Extract Image Attribute `extender`
`extents()` `extents<-`()	Extract Image Attribute `extents`
`field_skip()` `field_skip<-`() `field.skip()` `field.skip<-`()	Extract Image Attribute `field_skip`
`funused1()` `funused1<-`()	Extract Image Attribute `funused1`
`funused2()` `funused2<-`()	Extract Image Attribute `funused2`
`funused3()` `funused3<-`()	Extract Image Attribute `funused3`
`generated()` `generated<-`()	Extract Image Attribute `generated`
`glmax()` `glmax<-`()	Extract Image Attribute `glmax`
`glmin()` `glmin<-`()	Extract Image Attribute `glmin`
`hist_un0()` `hist_un0<-`()	Extract Image Attribute `hist_un0`
`hkey_un0()` `hkey_un0<-`() `hkey.un0()` `hkey.un0<-`()	Extract Image Attribute `hkey_un0`
`hotmetal()`	Hot Metal Color Table
`image(<nifti>)` `image(<anlz>)` `image(<afni>)`	Methods for Function `image'
`img_data()` `img_data<-`()	Extract Image Attribute `.Data`
`img_length()`	Gets Image Length in Each Dimension
`integerTranslation()` `invertIntegerTranslation()`	integerTranslation
`intent_code()` `intent_code<-`() `intent.code()` `intent.code<-`()	Extract Image Attribute `intent_code`
`intent_name()` `intent_name<-`() `intent.name()` `intent.name<-`()	Extract Image Attribute `intent_name`
`intent_p1()` `intent_p1<-`() `intent.p1()` `intent.p1<-`()	Extract Image Attribute `intent_p1`
`intent_p2()` `intent_p2<-`() `intent.p2()` `intent.p2<-`()	Extract Image Attribute `intent_p2`
`intent_p3()` `intent_p3<-`() `intent.p3()` `intent.p3<-`()	Extract Image Attribute `intent_p3`
`internalImage-class`	"internalImage" class
`is.afni()`	check object
`is.anlz()`	check object
`is.nifti()` `is.niftiExtension()`	check object
`magic()` `magic<-`()	Extract Image Attribute `magic`
`nsli()` `NSLI()` `ntim()` `NTIM()`	Dimension Accessor Functions
`show(<nifti>)`	Class "nifti"
`nifti()`	Constructor for NIfTI
`niftiAuditTrail-class`	Class "niftiAuditTrail"
`niftiExtension-class`	Class "niftiExtension"
`niftiExtensionSection-class`	Class "niftiExtensionSection"
`niftiImage-class`	"niftiImage" class
`nifti_assign-methods`	Methods for Function [<- in Package 'base'
`Ops(<nifti>,<nifti>)` `Ops(<nifti>,<numeric>)` `Ops(<numeric>,<nifti>)`	Operations for NIfTI Objects
`nii2oro()`	Convert RNifti niftiImage to oro.nifti nifti object
`omax()` `omax<-`()	Extract Image Attribute `omax`
`omin()` `omin<-`()	Extract Image Attribute `omin`
`onefile()`	Creates the `onefile` Specification for NIfTI
`orient()` `orient<-`()	Extract Image Attribute `orient`
`sform()` `qform()`	Extract NIfTI 3D Image Orientation
`origin()` `origin<-`()	Extract Image Attribute `origin`
`oro2nii()`	Convert oro.nifti nifti to RNifti niftiImage object
`orthographic.nifti()` `orthographic()`	Methods for Function `orthographic' in Package `dcemriS4'
`overlay.nifti()` `overlay()`	Methods for Function overlay
`patient_id()` `patient_id<-`() `patient.id()` `patient.id<-`()	Extract Image Attribute `patient_id`
`performPermutation()`	Transform array with orthogonal permutation matrix
`pixdim()` `pixdim<-`()	Extract Image Attribute `pixdim`
`qform_code()` `qform_code<-`() `qform.code()` `qform.code<-`()	Extract Image Attribute `qform_code`
`qoffset_x()` `qoffset_x<-`() `qoffset.x()` `qoffset.x<-`()	Extract Image Attribute `qoffset_x`
`qoffset_y()` `qoffset_y<-`() `qoffset.y()` `qoffset.y<-`()	Extract Image Attribute `qoffset_y`
`qoffset_z()` `qoffset_z<-`() `qoffset.z()` `qoffset.z<-`()	Extract Image Attribute `qoffset_z`
`quatern_b()` `quatern_b<-`() `quatern.b()` `quatern.b<-`()	Extract Image Attribute `quatern_b`
`quatern_c()` `quatern_c<-`() `quatern.c()` `quatern.c<-`()	Extract Image Attribute `quatern_c`
`quatern_d()` `quatern_d<-`() `quatern.d()` `quatern.d<-`()	Extract Image Attribute `quatern_d`
`quaternion2rotation()` `quaternion2mat44()`	Convert Quaternion into a Rotation Matrix
`readAFNI()`	readAFNI
`readANALYZE()`	readANALYZE
`readNIfTI()` `nifti_header()`	readNIfTI
`regular()` `regular<-`()	Extract Image Attribute `regular`
`rmniigz()` `rmnii()` `rmgz()` `rmhdrgz()` `rmhdr()` `rmimggz()` `rmimg()`	Remove File Extensions Around the NIfTI/ANALYZE Formats
`reorient()` `inverseReorient()`	Reorient Image using NIfTI header
`scannum()` `scannum<-`()	Extract Image Attribute `scannum`
`scl_inter()` `scl_inter<-`() `scl.inter()` `scl.inter<-`()	Extract Image Attribute `scl_inter`
`scl_slope()` `scl_slope<-`() `scl.slope()` `scl.slope<-`()	Extract Image Attribute `scl_slope`
`session_error()` `session_error<-`() `session.error()` `session.error<-`()	Extract Image Attribute `session_error`
`sform_code()` `sform_code<-`() `sform.code()` `sform.code<-`()	Extract Image Attribute `sform_code`
`sizeof_hdr()` `sizeof.hdr()` `sizeof_hdr<-`()	Extract Image Attribute `sizeof_hdr`
`slice()`	Methods for Function `slice'
`slice_code()` `slice_code<-`() `slice.code()` `slice.code<-`()	Extract Image Attribute `slice_code`
`slice_duration()` `slice_duration<-`() `slice.duration()` `slice.duration<-`()	Extract Image Attribute `slice_duration`
`slice_end()` `slice_end<-`() `slice.end()` `slice.end<-`()	Extract Image Attribute `slice_end`
`slice_overlay.nifti()` `slice_overlay()`	Methods for Function slice_overlay
`slice_start()` `slice_start<-`() `slice.start()` `slice.start<-`()	Extract Image Attribute `slice_start`
`smax()` `smax<-`()	Extract Image Attribute `smax`
`smin()` `smin<-`()	Extract Image Attribute `smin`
`srow_x()` `srow_x<-`() `srow.x()` `srow.x<-`()	Extract Image Attribute `srow_x`
`srow_y()` `srow_y<-`() `srow.y()` `srow.y<-`()	Extract Image Attribute `srow_y`
`srow_z()` `srow_z<-`() `srow.z()` `srow.z<-`()	Extract Image Attribute `srow_z`
`start_field()` `start_field<-`()	Extract Image Attribute `start_field`
`tim.colors()`	Tim's Useful Color Table
`toffset()` `toffset<-`()	Extract Image Attribute `toffset`
`translateCoordinate()`	Translate Voxel Coordinates
`unused1()` `unused1<-`()	Extract Image Attribute `unused1`
`verified()` `verified<-`()	Extract Image Attribute `verified`
`views()` `views<-`()	Extract Image Attribute `views`
`vols_added()` `vols_added<-`() `vols.added()` `vols.added<-`()	Extract Image Attribute `vols_added`
`vox_offset()` `vox_offset<-`() `vox.offset()` `vox.offset<-`()	Extract Image Attribute `vox_offset`
`vox_units()` `vox_units<-`() `vox.units()` `vox.units<-`()	Extract Image Attribute `vox_units`
`voxdim()`	Gets Voxel Dimensions
`voxres()`	Gets Voxel Resolution
`writeAFNI()`	writeAFNI
`writeANALYZE(<anlz>)`	writeANALYZE
`writeNIfTI(<nifti>)` `writeNIfTI(<niftiExtension>)` `writeNIfTI(<anlz>)` `writeNIfTI(<array>)`	writeNIfTI
`xyzt_units()` `xyzt_units<-`() `xyzt.units()` `xyzt.units<-`()	Extract Image Attribute `xyzt_units`
`resetSlopeIntercept()` `zero_trans()`	Change Intercept to 0 and Slope to 1 in NIfTI Object

Reference

All functions