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 |
| imports | abind , bitops , graphics , grDevices , methods , RNifti (>= 0.9.0) , splines , stats , utils |
| suggests | covr , knitr , rmarkdown , rticles , testthat , XML |
| enhances | fmri , oro.dicom |
| depends | R (>= 2.14.0) |
| Contributors | Jon Clayden, Volker Schmid, Andrew Thornton, John Muschelli, Karsten Tabelow |
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