Class

The NIfTI class for medical imaging data.

# S4 method for nifti
show(object)

Arguments

object	An object of class `nifti`.

Objects from the Class

Objects can be created by calls of the form new("nifti", data, dim, dimnames, ...) or by calling the nifti function.

Slots

.Data:: Object of class "array" contains the imaging data
sizeof_hdr:: Object of class "numeric" contains the size of the header (= 348)
data_type:: Object of class "character"
db_name:: Object of class "character"
extents:: Object of class "numeric"
session_error:: Object of class "numeric"
regular:: Object of class "character"
dim_info:: Object of class "numeric" contains MRI slice ordering
dim_:: Object of class "vector" contains the dimensions of the imaging data
intent_p1:: Object of class "numeric"
intent_p2:: Object of class "numeric"
intent_p3:: Object of class "numeric"
intent_code:: Object of class "numeric"
datatype:: Object of class "numeric"
bitpix:: Object of class "numeric" contains the number of bits per voxel (pixel)
slice_start:: Object of class "numeric"
pixdim:: Object of class "vector" contains the real-world dimensions of the imaging data
vox_offset:: Object of class "numeric" contains the voxel offset (= 352 when no extensions exist)
scl_slope:: Object of class "numeric"
scl_inter:: Object of class "numeric"
slice_end:: Object of class "numeric"
slice_code:: Object of class "numeric"
xyzt_units:: Object of class "numeric"
cal_max:: Object of class "numeric" contains the maximum display intensity
cal_min:: Object of class "numeric" contains the minimum display intensity
slice_duration:: Object of class "numeric"
toffset:: Object of class "numeric"
glmax:: Object of class "numeric"
glmin:: Object of class "numeric"
descrip:: Object of class "character"
aux_file:: Object of class "character"
qform_code:: Object of class "numeric"
sform_code:: Object of class "numeric"
quatern_b:: Object of class "numeric"
quatern_c:: Object of class "numeric"
quatern_d:: Object of class "numeric"
qoffset_x:: Object of class "numeric"
qoffset_y:: Object of class "numeric"
qoffset_z:: Object of class "numeric"
srow_x:: Object of class "vector"
srow_y:: Object of class "vector"
srow_z:: Object of class "vector"
intent_name:: Object of class "character"
magic:: Object of class "character"
extender:: Object of class "vector"
reoriented:: Object of class "logical"

Extends

Class "array", from data part.
Class "matrix", by class “array”, distance 2, with explicit test and coerce.
Class "structure", by class “array”, distance 2.
Class "vector", by class “array”, distance 3, with explicit coerce.
Class "vector", by class “array”, distance 5, with explicit test and coerce.

Methods

image: signature(x = "nifti"): displays the image(s).
orthographic: signature(x = "nifti"): displays the image(s).
overlay: signature(x = "nifti", y = "nifti"): displays the image(s).
show: signature(object = "nifti"): prints out a summary of the imaging data.

References

NIfTI-1
http://nifti.nimh.nih.gov/

Author

Brandon Whitcher bwhitcher@gmail.com,
Andrew Thornton zeripath@users.sourcefore.net

Examples


showClass("nifti")
#> Class "nifti" [package "oro.nifti"]
#> 
#> Slots:
#>                                                                   
#> Name:           .Data     sizeof_hdr      data_type        db_name
#> Class:          array        numeric      character      character
#>                                                                   
#> Name:         extents  session_error        regular       dim_info
#> Class:        numeric        numeric      character      character
#>                                                                   
#> Name:            dim_      intent_p1      intent_p2      intent_p3
#> Class:         vector        numeric        numeric        numeric
#>                                                                   
#> Name:     intent_code       datatype         bitpix    slice_start
#> Class:        numeric        numeric        numeric        numeric
#>                                                                   
#> Name:          pixdim     vox_offset      scl_slope      scl_inter
#> Class:         vector        numeric        numeric        numeric
#>                                                                   
#> Name:       slice_end     slice_code     xyzt_units        cal_max
#> Class:        numeric        numeric        numeric        numeric
#>                                                                   
#> Name:         cal_min slice_duration        toffset          glmax
#> Class:        numeric        numeric        numeric        numeric
#>                                                                   
#> Name:           glmin        descrip       aux_file     qform_code
#> Class:        numeric      character      character        numeric
#>                                                                   
#> Name:      sform_code      quatern_b      quatern_c      quatern_d
#> Class:        numeric        numeric        numeric        numeric
#>                                                                   
#> Name:       qoffset_x      qoffset_y      qoffset_z         srow_x
#> Class:        numeric        numeric        numeric         vector
#>                                                                   
#> Name:          srow_y         srow_z    intent_name          magic
#> Class:         vector         vector      character      character
#>                                     
#> Name:        extender     reoriented
#> Class:         vector        logical
#> 
#> Extends: 
#> Class "array", from data part
#> Class "structure", by class "array", distance 2
#> Class "vector", by class "array", distance 3, with explicit coerce
#> 
#> Known Subclasses: 
#> Class "niftiExtension", directly
#> Class "niftiAuditTrail", by class "niftiExtension", distance 2

Class "nifti"