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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.

Functions (127)

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_-methods

Extract Image Attribute dim_

dim_info-methods

Extract Image Attribute dim_info

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

img_length

Gets Image Length in Each Dimension

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

internalImage-class

"internalImage" class

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-class

Class "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'

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

orient-methods

Extract Image Attribute orient

orientation-methods

Extract NIfTI 3D Image Orientation

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-methods

Methods for Function ‘slice’

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_overlay-methods

Methods for Function slice_overlay

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

vox_offset-methods

Extract Image Attribute vox_offset

vox_units-methods

Extract Image Attribute vox_units

voxdim

Gets Voxel Dimensions

voxres

Gets Voxel Resolution

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

oro.nifti

Rigorous - 'NIfTI' + 'ANALYZE' + 'AFNI' : Input / Output

v0.11.0

BSD_3_clause + file LICENSE

Authors

Brandon Whitcher [aut, cre], Volker Schmid [aut], Andrew Thornton [aut], Karsten Tabelow [ctb], Jon Clayden [ctb], John Muschelli [aut]

Initial release

oro.nifti

Functions (127)

oro.nifti

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