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

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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.

Author
Brandon Whitcher [aut, cre], Volker Schmid [aut], Andrew Thornton [aut], Karsten Tabelow [ctb], Jon Clayden [ctb], John Muschelli [ctb]
Date of publication
2016-07-24 01:16:58
Maintainer
Brandon Whitcher <bwhitcher@gmail.com>
License
BSD_3_clause + file LICENSE
Version
0.5.5.2
URLs

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'
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
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'
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/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/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/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/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/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/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