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

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.

AuthorBrandon Whitcher [aut, cre], Volker Schmid [aut], Andrew Thornton [aut], Karsten Tabelow [ctb], Jon Clayden [ctb], John Muschelli [ctb]
Date of publication2016-12-31 16:32:14
MaintainerBrandon Whitcher <bwhitcher@gmail.com>
LicenseBSD_3_clause + file LICENSE
Version0.7.2
http://rig.oro.us.com
http://rigorousanalytics.blogspot.com

View on CRAN

Man pages

afni-class: Class "afni"

anlz: Constructor for Analyze

anlz-class: Class "anlz"

anlz-nifti-ops: Operations for Objects in the ANALYZE and NIfTI classes

as.anlz: as.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 Image Attribute 'aux_file'

bitpix-methods: Extract Image Attribute 'bitpix'

bitwise: Bitwise Conversion Subroutines

blend-methods: Merge Two NIfTI or ANALYZE Volumes

cal_img: Set Minimum/Maximum Values for NIfTI data

cal_max-methods: Extract Image Attribute 'cal_max'

cal_min-methods: Extract Image Attribute 'cal_min'

cal_units-methods: Extract Image Attribute 'cal_units'

coerce-methods: Force an Object to Belong to the ANALYZE or NIfTI Class

compressed-methods: Extract Image Attribute 'compressed'

convert_afni: Convert AFNI data codes

convert_anlz: Convert ANALYZE Codes

convert_nifti: Convert NIfTI Codes

data_type-methods: Extract Image Attribute 'data_type'

datatype-methods: Extract Image Attribute 'datatype'

db_name-methods: Extract Image Attribute 'db_name'

descrip-methods: Extract Image Attribute 'descrip'

dim_info-methods: Extract Image Attribute 'dim_info'

dim_-methods: Extract Image Attribute 'dim_'

dim_un0-methods: Extract Image Attribute 'dim_un0'

drop_img_dim: Drop Image Dimension

exp_date-methods: Extract Image Attribute 'exp_date'

exp_time-methods: Extract Image Attribute 'exp_time'

extender-methods: Extract Image Attribute 'extender'

extents-methods: Extract Image Attribute 'extents'

field_skip-methods: Extract Image Attribute 'field_skip'

funused1-methods: Extract Image Attribute 'funused1'

funused2-methods: Extract Image Attribute 'funused2'

funused3-methods: Extract Image Attribute 'funused3'

generated-methods: Extract Image Attribute 'generated'

glmax-methods: Extract Image Attribute 'glmax'

glmin-methods: Extract Image Attribute 'glmin'

hist_un0-methods: Extract Image Attribute 'hist_un0'

hkey_un0-methods: Extract Image Attribute 'hkey_un0'

hotmetal: Hot Metal Color Table

image-methods: Methods for Function 'image'

img_data-methods: Extract Image Attribute '.Data'

integerTranslation: integerTranslation

intent_code-methods: Extract Image Attribute 'intent_code'

intent_name-methods: Extract Image Attribute 'intent_name'

intent_p1-methods: Extract Image Attribute 'intent_p1'

intent_p2-methods: Extract Image Attribute 'intent_p2'

intent_p3-methods: Extract Image Attribute 'intent_p3'

is_afni: check object

is_anlz: check object

is_nifti: check object

magic-methods: Extract Image Attribute 'magic'

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"

niftiops: Operations for NIfTI Objects

nii2oro: Convert RNifti niftiImage to oro.nifti nifti object

omax-methods: Extract Image Attribute 'omax'

omin-methods: Extract Image Attribute 'omin'

onefile: Creates the 'onefile' Specification for NIfTI

orientation-methods: Extract NIfTI 3D Image Orientation

orient-methods: Extract Image Attribute 'orient'

origin-methods: Extract Image Attribute 'origin'

oro2nii: Convert oro.nifti nifti to RNifti niftiImage object

orthographic-methods: Methods for Function 'orthographic' in Package 'dcemriS4'

overlay-methods: Methods for Function overlay

patient_id-methods: Extract Image Attribute 'patient_id'

performPermutation: Transform array with orthogonal permutation matrix

pixdim-methods: Extract Image Attribute 'pixdim'

qform_code-methods: Extract Image Attribute 'qform_code'

qoffset_x-methods: Extract Image Attribute 'qoffset_x'

qoffset_y-methods: Extract Image Attribute 'qoffset_y'

qoffset_z-methods: Extract Image Attribute 'qoffset_z'

quatern_b-methods: Extract Image Attribute 'quatern_b'

quatern_c-methods: Extract Image Attribute 'quatern_c'

quatern_d-methods: Extract Image Attribute 'quatern_d'

quaternion2rotation: Convert Quaternion into a Rotation Matrix

read_afni: readAFNI

read_anlz: readANALYZE

read_nifti: readNIfTI

regular-methods: Extract Image Attribute 'regular'

remove: Remove File Extensions Around the NIfTI/ANALYZE Formats

reorient: Reorient Image using NIfTI header

scannum-methods: Extract Image Attribute 'scannum'

scl_inter-methods: Extract Image Attribute 'scl_inter'

scl_slope-methods: Extract Image Attribute 'scl_slope'

session_error-methods: Extract Image Attribute 'session_error'

sform_code-methods: Extract Image Attribute 'sform_code'

sizeof_hdr-methods: Extract Image Attribute 'sizeof_hdr'

slice_code-methods: Extract Image Attribute 'slice_code'

slice_duration-methods: Extract Image Attribute 'slice_duration'

slice_end-methods: Extract Image Attribute 'slice_end'

slice_start-methods: Extract Image Attribute 'slice_start'

smax-methods: Extract Image Attribute 'smax'

smin-methods: Extract Image Attribute 'smin'

srow_x-methods: Extract Image Attribute 'srow_x'

srow_y-methods: Extract Image Attribute 'srow_y'

srow_z-methods: Extract Image Attribute 'srow_z'

start_field-methods: Extract Image Attribute 'start_field'

tim_colors: Tim's Useful Color Table

toffset-methods: Extract Image Attribute 'toffset'

transformCoordinate: Translate Voxel Coordinates

unused1-methods: Extract Image Attribute 'unused1'

verified-methods: Extract Image Attribute 'verified'

views-methods: Extract Image Attribute 'views'

vols_added-methods: Extract Image Attribute 'vols_added'

voxdim: Gets Voxel Dimensions

vox_offset-methods: Extract Image Attribute 'vox_offset'

voxres: Gets Voxel Resolution

vox_units-methods: Extract Image Attribute 'vox_units'

write_afni-methods: writeAFNI

write_anlz: writeANALYZE

write_nifti: writeNIfTI

xyzt_units-methods: Extract Image Attribute 'xyzt_units'

zero_trans: Change Intercept to 0 and Slope to 1 in NIfTI Object

Files in this package

oro.nifti
oro.nifti/inst
oro.nifti/inst/afni
oro.nifti/inst/afni/TT_N27_EZ_LR+tlrc.BRIK.gz
oro.nifti/inst/afni/TT_N27_EZ_LR+tlrc.HEAD
oro.nifti/inst/afni/ARzs_CW_avvr.DEL+orig.HEAD
oro.nifti/inst/afni/ARzs_CW_avvr.DEL+orig.BRIK
oro.nifti/inst/CITATION
oro.nifti/inst/anlz
oro.nifti/inst/anlz/avg152T1.hdr.gz
oro.nifti/inst/anlz/avg152T1.img.gz
oro.nifti/inst/nifti
oro.nifti/inst/nifti/filtered_func_data.nii.gz
oro.nifti/inst/nifti/mniLR.nii.gz
oro.nifti/inst/nifti/mniRL.nii.gz
oro.nifti/inst/nifti/zstat1.nii.gz
oro.nifti/inst/doc
oro.nifti/inst/doc/nifti.Rnw
oro.nifti/inst/doc/nifti.R
oro.nifti/inst/doc/nifti.pdf
oro.nifti/inst/doc/ANALYZE75.pdf
oro.nifti/tests
oro.nifti/tests/Examples
oro.nifti/tests/Examples/oro.nifti-Ex.Rout.save
oro.nifti/tests/testthat.R
oro.nifti/tests/testthat
oro.nifti/tests/testthat/test_xyzt_units.R
oro.nifti/tests/testthat/test_sizeof_hdr.R
oro.nifti/NAMESPACE
oro.nifti/demo
oro.nifti/demo/avg152T1RL.R
oro.nifti/demo/avg152T1LR.R
oro.nifti/demo/avg152T1.R
oro.nifti/demo/00Index
oro.nifti/demo/filtered_func_data.R
oro.nifti/R
oro.nifti/R/intent_code.R oro.nifti/R/coerce.R oro.nifti/R/srow_z.R oro.nifti/R/session_error.R oro.nifti/R/extender.R oro.nifti/R/scl_inter.R oro.nifti/R/omin.R oro.nifti/R/generated.R oro.nifti/R/smax.R oro.nifti/R/qoffset_z.R oro.nifti/R/exp_time.R oro.nifti/R/regular.R oro.nifti/R/extents.R oro.nifti/R/voxres.R oro.nifti/R/plot.R oro.nifti/R/srow_y.R oro.nifti/R/vols_added.R oro.nifti/R/views.R oro.nifti/R/drop_img_dim.R oro.nifti/R/nifti_assign.R oro.nifti/R/orient.R oro.nifti/R/convert_nifti.R oro.nifti/R/miscellaneous.R oro.nifti/R/sizeof_hdr.R oro.nifti/R/glmax.R oro.nifti/R/bitpix.R oro.nifti/R/funused3.R oro.nifti/R/afniS4.R oro.nifti/R/aux_file.R oro.nifti/R/magic.R oro.nifti/R/datatype.R oro.nifti/R/quaternion.R oro.nifti/R/wrappers.R oro.nifti/R/glmin.R oro.nifti/R/qoffset_y.R oro.nifti/R/quatern_b.R oro.nifti/R/unused1.R oro.nifti/R/oro2nii.R oro.nifti/R/convert_anlz.R oro.nifti/R/analyzeS4.R oro.nifti/R/quatern_d.R oro.nifti/R/origin.R oro.nifti/R/hotmetal.R oro.nifti/R/intent_p3.R oro.nifti/R/cal_min.R oro.nifti/R/remove.R oro.nifti/R/vox_units.R oro.nifti/R/slice_duration.R oro.nifti/R/intent_p1.R oro.nifti/R/patient_id.R oro.nifti/R/dim_.R oro.nifti/R/sform_code.R oro.nifti/R/zero_trans.R oro.nifti/R/cal_img.R oro.nifti/R/niftiS4.R oro.nifti/R/xyzt_units.R oro.nifti/R/tim_colors.R oro.nifti/R/slice_end.R oro.nifti/R/dim_info.R oro.nifti/R/img_data.R oro.nifti/R/is.R oro.nifti/R/smin.R oro.nifti/R/db_name.R oro.nifti/R/anlz_Operators.R oro.nifti/R/slice_start.R oro.nifti/R/intent_name.R oro.nifti/R/qoffset_x.R oro.nifti/R/data_type.R oro.nifti/R/blend.R oro.nifti/R/omax.R oro.nifti/R/Operators.R oro.nifti/R/dim_un0.R oro.nifti/R/funused2.R oro.nifti/R/quatern_c.R oro.nifti/R/hist_un0.R oro.nifti/R/hkey_un0.R oro.nifti/R/scl_slope.R oro.nifti/R/vox_offset.R oro.nifti/R/field_skip.R oro.nifti/R/slice_code.R oro.nifti/R/auditTrail.R oro.nifti/R/srow_x.R oro.nifti/R/start_field.R oro.nifti/R/transform.R oro.nifti/R/voxdim.R oro.nifti/R/scannum.R oro.nifti/R/funused1.R oro.nifti/R/toffset.R oro.nifti/R/pixdim.R oro.nifti/R/compressed.R oro.nifti/R/verified.R oro.nifti/R/readS4.R oro.nifti/R/onefile.R oro.nifti/R/nii2oro.R oro.nifti/R/exp_date.R oro.nifti/R/cal_units.R oro.nifti/R/intent_p2.R oro.nifti/R/zzz.R oro.nifti/R/writeS4.R oro.nifti/R/cal_max.R oro.nifti/R/qform_code.R oro.nifti/R/descrip.R
oro.nifti/vignettes
oro.nifti/vignettes/nifti.Rnw
oro.nifti/vignettes/nifti.bib
oro.nifti/MD5
oro.nifti/build
oro.nifti/build/vignette.rds
oro.nifti/DESCRIPTION
oro.nifti/man
oro.nifti/man/drop_img_dim.Rd oro.nifti/man/tim_colors.Rd oro.nifti/man/compressed-methods.Rd oro.nifti/man/omin-methods.Rd oro.nifti/man/qoffset_y-methods.Rd oro.nifti/man/remove.Rd oro.nifti/man/dim_info-methods.Rd oro.nifti/man/vox_offset-methods.Rd oro.nifti/man/cal_units-methods.Rd oro.nifti/man/hotmetal.Rd oro.nifti/man/funused1-methods.Rd oro.nifti/man/views-methods.Rd oro.nifti/man/quatern_c-methods.Rd oro.nifti/man/qoffset_x-methods.Rd oro.nifti/man/intent_code-methods.Rd oro.nifti/man/generated-methods.Rd oro.nifti/man/unused1-methods.Rd oro.nifti/man/cal_min-methods.Rd oro.nifti/man/performPermutation.Rd oro.nifti/man/quatern_d-methods.Rd oro.nifti/man/convert_nifti.Rd oro.nifti/man/img_data-methods.Rd oro.nifti/man/aux_file-methods.Rd oro.nifti/man/sform_code-methods.Rd oro.nifti/man/funused3-methods.Rd oro.nifti/man/transformCoordinate.Rd oro.nifti/man/dim_-methods.Rd oro.nifti/man/niftiAuditTrail-class.Rd oro.nifti/man/voxdim.Rd oro.nifti/man/start_field-methods.Rd oro.nifti/man/niftiExtension-class.Rd oro.nifti/man/as.nifti.Rd oro.nifti/man/as.anlz.Rd oro.nifti/man/read_nifti.Rd oro.nifti/man/descrip-methods.Rd oro.nifti/man/convert_anlz.Rd oro.nifti/man/onefile.Rd oro.nifti/man/anlz-class.Rd oro.nifti/man/bitwise.Rd oro.nifti/man/sizeof_hdr-methods.Rd oro.nifti/man/exp_time-methods.Rd oro.nifti/man/field_skip-methods.Rd oro.nifti/man/xyzt_units-methods.Rd oro.nifti/man/write_nifti.Rd oro.nifti/man/vox_units-methods.Rd oro.nifti/man/nifti.Rd oro.nifti/man/datatype-methods.Rd oro.nifti/man/db_name-methods.Rd oro.nifti/man/scl_slope-methods.Rd oro.nifti/man/qform_code-methods.Rd oro.nifti/man/funused2-methods.Rd oro.nifti/man/slice_code-methods.Rd oro.nifti/man/slice_end-methods.Rd oro.nifti/man/extender-methods.Rd oro.nifti/man/vols_added-methods.Rd oro.nifti/man/regular-methods.Rd oro.nifti/man/image-methods.Rd oro.nifti/man/intent_name-methods.Rd oro.nifti/man/niftiops.Rd oro.nifti/man/read_anlz.Rd oro.nifti/man/dim_un0-methods.Rd oro.nifti/man/audit_trail-methods.Rd oro.nifti/man/srow_z-methods.Rd oro.nifti/man/orthographic-methods.Rd oro.nifti/man/srow_y-methods.Rd oro.nifti/man/exp_date-methods.Rd oro.nifti/man/orientation-methods.Rd oro.nifti/man/session_error-methods.Rd oro.nifti/man/hkey_un0-methods.Rd oro.nifti/man/is_afni.Rd oro.nifti/man/orient-methods.Rd oro.nifti/man/glmax-methods.Rd oro.nifti/man/omax-methods.Rd oro.nifti/man/hist_un0-methods.Rd oro.nifti/man/write_anlz.Rd oro.nifti/man/smax-methods.Rd oro.nifti/man/data_type-methods.Rd oro.nifti/man/quatern_b-methods.Rd oro.nifti/man/miscellaneous.Rd oro.nifti/man/oro2nii.Rd oro.nifti/man/voxres.Rd oro.nifti/man/read_afni.Rd oro.nifti/man/niftiExtensionSection-class.Rd oro.nifti/man/magic-methods.Rd oro.nifti/man/coerce-methods.Rd oro.nifti/man/glmin-methods.Rd oro.nifti/man/integerTranslation.Rd oro.nifti/man/cal_max-methods.Rd oro.nifti/man/patient_id-methods.Rd oro.nifti/man/nifti-class.Rd oro.nifti/man/qoffset_z-methods.Rd oro.nifti/man/srow_x-methods.Rd oro.nifti/man/anlz-nifti-ops.Rd oro.nifti/man/zero_trans.Rd oro.nifti/man/is_nifti.Rd oro.nifti/man/anlz.Rd oro.nifti/man/convert_afni.Rd oro.nifti/man/nii2oro.Rd oro.nifti/man/is_anlz.Rd oro.nifti/man/quaternion2rotation.Rd oro.nifti/man/overlay-methods.Rd oro.nifti/man/slice_duration-methods.Rd oro.nifti/man/bitpix-methods.Rd oro.nifti/man/intent_p2-methods.Rd oro.nifti/man/scl_inter-methods.Rd oro.nifti/man/audit_trail.Rd oro.nifti/man/blend-methods.Rd oro.nifti/man/toffset-methods.Rd oro.nifti/man/extents-methods.Rd oro.nifti/man/pixdim-methods.Rd oro.nifti/man/intent_p3-methods.Rd oro.nifti/man/write_afni-methods.Rd oro.nifti/man/cal_img.Rd oro.nifti/man/reorient.Rd oro.nifti/man/nifti_assign-methods.Rd oro.nifti/man/verified-methods.Rd oro.nifti/man/smin-methods.Rd oro.nifti/man/intent_p1-methods.Rd oro.nifti/man/afni-class.Rd oro.nifti/man/scannum-methods.Rd oro.nifti/man/slice_start-methods.Rd oro.nifti/man/origin-methods.Rd
oro.nifti/LICENSE

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