oro.nifti v0.11.0

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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 in oro.nifti

Name Description
Audit Trails Facilitate the Creation and Modification of Audit Trails
anlz-nifti-ops Operations for Objects in the ANALYZE and NIfTI classes
afni-class Class "afni"
bitpix-methods Extract Image Attribute bitpix
as.anlz as.anlz
anlz Constructor for Analyze
aux_file-methods Extract Image Attribute aux_file
audit.trail-methods Extract or Replace NIfTI Audit Trail
anlz-class Class "anlz"
as.nifti as.nifti
Convert ANALYZE Codes Convert ANALYZE Codes
coerce-methods Force an Object to Belong to the ANALYZE or NIfTI Class
descrip-methods Extract Image Attribute descrip
convert.scene Convert AFNI data codes
xyzt2space Bitwise Conversion Subroutines
funused1-methods Extract Image Attribute funused1
dim_-methods Extract Image Attribute dim_
exp_date-methods Extract Image Attribute exp_date
blend 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
calibrateImage Set Minimum/Maximum Values for NIfTI data
magic-methods 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
is.nifti check object
is.anlz check object
orthographic-methods Methods for Function `orthographic' in Package `dcemriS4'
field_skip-methods Extract Image Attribute field_skip
orient-methods Extract Image Attribute orient
nifti-operators Operations for NIfTI Objects
nsli 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
is.afni check object
data_type-methods Extract Image Attribute data_type
glmax-methods 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
nii2oro Convert RNifti niftiImage to oro.nifti nifti object
img_length 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
nifti Constructor for NIfTI
nifti-class Class "nifti"
glmin-methods Extract Image Attribute glmin
niftiAuditTrail-class Class "niftiAuditTrail"
niftiExtension-class Class "niftiExtension"
omax-methods 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
onefile Creates the onefile Specification for NIfTI
oro2nii Convert oro.nifti nifti to RNifti niftiImage object
omin-methods Extract Image Attribute omin
origin-methods 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
pixdim-methods Extract Image Attribute pixdim
hotmetal 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
image-methods Methods for Function `image'
niftiExtensionSection-class Class "niftiExtensionSection"
vox_units-methods Extract Image Attribute vox_units
niftiImage-class "niftiImage" class
readNIfTI readNIfTI
readANALYZE readANALYZE
slice-methods Methods for Function `slice'
reorient Reorient Image using NIfTI header
quatern_d-methods Extract Image Attribute quatern_d
scannum-methods Extract Image Attribute scannum
srow_y-methods Extract Image Attribute srow_y
slice_start-methods Extract Image Attribute slice_start
smax-methods Extract Image Attribute smax
rmniigz Remove File Extensions Around the NIfTI/ANALYZE Formats
qform_code-methods Extract Image Attribute qform_code
voxres Gets Voxel Resolution
voxdim Gets Voxel Dimensions
smin-methods Extract Image Attribute smin
scl_inter-methods Extract Image Attribute scl_inter
srow_z-methods Extract Image Attribute srow_z
quaternion2rotation Convert Quaternion into a Rotation Matrix
readAFNI readAFNI
srow_x-methods 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
views-methods Extract Image Attribute views
scl_slope-methods Extract Image Attribute scl_slope
writeNIfTI-methods writeNIfTI
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.colors Tim's Useful Color Table
start_field-methods Extract Image Attribute start_field
writeANALYZE-methods writeANALYZE
writeAFNI-methods writeAFNI
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License BSD_3_clause + file LICENSE
BugReports https://github.com/bjw34032/oro.nifti/issues
URL http://rig.oro.us.com, http://rigorousanalytics.blogspot.com
LazyData true
LazyDataCompression gzip
Collate 'auditTrail.R' 'niftiS4.R' 'analyzeS4.R' 'afniS4.R' 'is.R' 'nifti_assign.R' 'coerce.R' 'writeS4.R' 'convert_anlz.R' 'convert_nifti.R' 'cal_img.R' 'drop_img_dim.R' 'hotmetal.R' 'miscellaneous.R' 'plot.R' 'slice.R' 'slice_overlay.R' 'blend.R' 'readS4.R' 'remove.R' 'tim_colors.R' 'transform.R' 'wrappers.R' 'onefile.R' 'voxdim.R' 'anlz_Operators.R' 'Operators.R' 'zero_trans.R' 'aux_file.R' 'cal_max.R' 'cal_min.R' 'descrip.R' 'glmax.R' 'glmin.R' 'pixdim.R' 'qform_code.R' 'scl_inter.R' 'scl_slope.R' 'sform_code.R' 'vox_offset.R' 'bitpix.R' 'data_type.R' 'datatype.R' 'db_name.R' 'dim_.R' 'dim_info.R' 'extender.R' 'extents.R' 'img_data.R' 'intent_code.R' 'intent_name.R' 'intent_p1.R' 'intent_p2.R' 'intent_p3.R' 'magic.R' 'qoffset_x.R' 'qoffset_y.R' 'qoffset_z.R' 'quatern_b.R' 'quatern_c.R' 'quatern_d.R' 'quaternion.R' 'regular.R' 'session_error.R' 'sizeof_hdr.R' 'slice_code.R' 'slice_duration.R' 'slice_end.R' 'slice_start.R' 'srow_x.R' 'srow_y.R' 'srow_z.R' 'toffset.R' 'xyzt_units.R' 'cal_units.R' 'compressed.R' 'dim_un0.R' 'exp_date.R' 'exp_time.R' 'field_skip.R' 'funused1.R' 'funused2.R' 'funused3.R' 'generated.R' 'hist_un0.R' 'hkey_un0.R' 'niftiImage_class.R' 'nii2oro.R' 'oro2nii.R' 'omax.R' 'omin.R' 'orient.R' 'origin.R' 'patient_id.R' 'scannum.R' 'smax.R' 'smin.R' 'start_field.R' 'unused1.R' 'verified.R' 'views.R' 'vols_added.R' 'vox_units.R' 'voxres.R' 'img_length.R' 'zzz.R' 'zzz_niftiImage.R'
RoxygenNote 7.1.1
Encoding UTF-8
NeedsCompilation no
Packaged 2020-09-07 16:02:13 UTC; johnmuschelli
Repository CRAN
Date/Publication 2020-09-08 13:10:10 UTC

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