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oro.nifti (version 0.11.0)

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

Description

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.

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Version

Install

install.packages('oro.nifti')

Monthly Downloads

1,843

Version

0.11.0

License

BSD_3_clause + file LICENSE

Homepage

http://rig.oro.us.com

Maintainer

Brandon Whitcher

Last Published

September 8th, 2020

Functions in oro.nifti (0.11.0)

Facilitate the Creation and Modification of Audit Trails

Operations for Objects in the ANALYZE and NIfTI classes

Extract Image Attribute bitpix

Constructor for Analyze

aux_file-methods

Extract Image Attribute aux_file

audit.trail-methods

Extract or Replace NIfTI Audit Trail

Convert ANALYZE Codes

Convert ANALYZE Codes

Force an Object to Belong to the ANALYZE or NIfTI Class

descrip-methods

Extract Image Attribute descrip

Convert AFNI data codes

Bitwise Conversion Subroutines

funused1-methods

Extract Image Attribute funused1

Extract Image Attribute dim_

exp_date-methods

Extract Image Attribute exp_date

Merge Two NIfTI or ANALYZE Volumes

dropImageDimension

Drop Image Dimension

cal_min-methods

Extract Image Attribute cal_min

funused2-methods

Extract Image Attribute funused2

integerTranslation

integerTranslation

intent_name-methods

Extract Image Attribute intent_name

intent_code-methods

Extract Image Attribute intent_code

Set Minimum/Maximum Values for NIfTI data

Extract Image Attribute magic

compressed-methods

Extract Image Attribute compressed

extents-methods

Extract Image Attribute extents

cal_max-methods

Extract Image Attribute cal_max

cal_units-methods

Extract Image Attribute cal_units

db_name-methods

Extract Image Attribute db_name

datatype-methods

Extract Image Attribute datatype

intent_p1-methods

Extract Image Attribute intent_p1

dim_info-methods

Extract Image Attribute dim_info

orthographic-methods

Methods for Function `orthographic' in Package `dcemriS4'

field_skip-methods

Extract Image Attribute field_skip

Extract Image Attribute orient

nifti-operators

Operations for NIfTI Objects

Dimension Accessor Functions

hist_un0-methods

Extract Image Attribute hist_un0

nifti_assign-methods

Methods for Function [<- in Package 'base'

hkey_un0-methods

Extract Image Attribute hkey_un0

internalImage-class

"internalImage" class

generated-methods

Extract Image Attribute generated

funused3-methods

Extract Image Attribute funused3

data_type-methods

Extract Image Attribute data_type

Extract Image Attribute glmax

Convert NIfTI Codes

Convert NIfTI Codes

orientation-methods

Extract NIfTI 3D Image Orientation

dim_un0-methods

Extract Image Attribute dim_un0

extender-methods

Extract Image Attribute extender

Convert RNifti niftiImage to oro.nifti nifti object

Gets Image Length in Each Dimension

img_data-methods

Extract Image Attribute .Data

exp_time-methods

Extract Image Attribute exp_time

quatern_c-methods

Extract Image Attribute quatern_c

Constructor for NIfTI

Extract Image Attribute glmin

niftiAuditTrail-class

Class "niftiAuditTrail"

niftiExtension-class

Class "niftiExtension"

Extract Image Attribute omax

performPermutation

Transform array with orthogonal permutation matrix

patient_id-methods

Extract Image Attribute patient_id

qoffset_z-methods

Extract Image Attribute qoffset_z

quatern_b-methods

Extract Image Attribute quatern_b

Creates the onefile Specification for NIfTI

Convert oro.nifti nifti to RNifti niftiImage object

Extract Image Attribute omin

Extract Image Attribute origin

regular-methods

Extract Image Attribute regular

overlay-methods

Methods for Function overlay

qoffset_x-methods

Extract Image Attribute qoffset_x

qoffset_y-methods

Extract Image Attribute qoffset_y

vox_offset-methods

Extract Image Attribute vox_offset

Extract Image Attribute pixdim

Hot Metal Color Table

intent_p3-methods

Extract Image Attribute intent_p3

intent_p2-methods

Extract Image Attribute intent_p2

sizeof_hdr-methods

Extract Image Attribute sizeof_hdr

Methods for Function `image'

niftiExtensionSection-class

Class "niftiExtensionSection"

vox_units-methods

Extract Image Attribute vox_units

niftiImage-class

"niftiImage" class

Methods for Function `slice'

Reorient Image using NIfTI header

quatern_d-methods

Extract Image Attribute quatern_d

scannum-methods

Extract Image Attribute scannum

Extract Image Attribute srow_y

slice_start-methods

Extract Image Attribute slice_start

Extract Image Attribute smax

Remove File Extensions Around the NIfTI/ANALYZE Formats

qform_code-methods

Extract Image Attribute qform_code

Gets Voxel Resolution

Gets Voxel Dimensions

Extract Image Attribute smin

scl_inter-methods

Extract Image Attribute scl_inter

Extract Image Attribute srow_z

quaternion2rotation

Convert Quaternion into a Rotation Matrix

Extract Image Attribute srow_x

session_error-methods

Extract Image Attribute session_error

toffset-methods

Extract Image Attribute toffset

slice_end-methods

Extract Image Attribute slice_end

sform_code-methods

Extract Image Attribute sform_code

translateCoordinate

Translate Voxel Coordinates

slice_overlay-methods

Methods for Function slice_overlay

vols_added-methods

Extract Image Attribute vols_added

Extract Image Attribute views

scl_slope-methods

Extract Image Attribute scl_slope

writeNIfTI-methods

slice_code-methods

Extract Image Attribute slice_code

xyzt_units-methods

Extract Image Attribute xyzt_units

resetSlopeIntercept

Change Intercept to 0 and Slope to 1 in NIfTI Object

verified-methods

Extract Image Attribute verified

unused1-methods

Extract Image Attribute unused1

slice_duration-methods

Extract Image Attribute slice_duration

Tim's Useful Color Table

start_field-methods

Extract Image Attribute start_field

writeANALYZE-methods

writeAFNI-methods