fmri.data-class: arf3DS4 "fmri.data" class

In arf3DS4: Activated Region Fitting, fMRI data analysis (3D).

Description

The arf3DS4 "fmri.data" class contains the header information and data of an ANALYZE/NIFTI functional volume. It is essentially a nifti.header object with an added "datavec" slot.

Objects

Objects can be created by calls of the form new("fmri.data", ...).

Slots

datavec:

Vector containing the actual fMRI data.

sizeof_hdr:

<nifti> Size of the header file.

data_type:

<nifti> Type of data (representation).

db_name:

<nifti> db_name.

extents:

<nifti> extents

session_error:

<nifti> session error.

regular:

<nifti> regular

dim_info:

<nifti> MRI slice ordering.

dims:

<nifti> Data array dimensions.

intent_p1:

<nifti> 1st intent parameter.

intent_p2:

<nifti> 2nd intent parameter.

intent_p3:

<nifti> 3rd intent parameter.

intent_code:

<nifti> Intent code.

datatype:

<nifti> Data type.

bitpix:

<nifti> Number of bits per voxel.

slice_start:

<nifti> First slice index.

pixdim:

<nifti> Grid spacing (single voxel dimensions).

vox_offset:

<nifti> Offset in the .nii file.

scl_slope:

<nifti> Data scaling, slope.

scl_inter:

<nifti> Data scaling, offset.

slice_end:

<nifti> Last slice index.

slice_code:

<nifti> Slice timing order.

xyzt_units:

<nifti> Units of single voxel dimensions.

cal_max:

<nifti> Maximum display intensity.

cal_min:

<nifti> Minimum display intensity.

slice_duration:

<nifti> Time for one slice (TR).

toffset:

<nifti> Shift in time.

glmax:

<nifti> glmax.

glmin:

<nifti> glmin.

descrip:

<nifti> Description of file.

aux_file:

<nifti> An auxilliary filename.

qform_code:

<nifti> q_form code.

sform_code:

<nifti> s_form code.

quatern_b:

<nifti> quaternion b parameter.

quatern_c:

<nifti> quaternion c parameter.

quatern_d:

<nifti> quaternion d parameter.

qoffset_x:

<nifti> q offset x parameter.

qoffset_y:

<nifti> q offset y parameter.

qoffset_z:

<nifti> q offset z parameter.

srow_x:

<nifti> 1st row affine transformation.

srow_y:

<nifti> 2nd row affine transformation.

srow_z:

<nifti> 3rd row affine transformation.

intent_name:

<nifti> Meaning of data.

magic:

<nifti> nifti magicstring.

data.type:

<arf3DS4> Data type.

data.signed:

<arf3DS4> Signed data.

fullpath:

<arf3DS4> Full path of datafile.

filename:

<arf3DS4> Filename.

filetype:

<arf3DS4> Type of file.

extension:

<arf3DS4> File extension.

gzipped:

<arf3DS4> Is the file gzipped?

endian:

<arf3DS4> Endianness of file.

version:

Object of class "version" (see version)

Extends

Class "nifti.header", directly. Class "nifti.fileinfo", by class "nifti.header".

Methods

Standard arf3DS4 accessor and replacement functions can be used to access and replace slots.

access

.classname.slotname(object)

replace

.classname.slotname(object)<-

plot

signature(x = "fmri.data", y = "missing"): ...

show

signature(object = "fmri.data"): ...

summary

signature(object = "fmri.data"): ...

In this case classname is "fmri.data" and slotname is for example "dims". So to access the "dims" slot of an r-object "myfmridata" (of class "fmri.data") type .fmri.data.dims(myfmridata).

Author(s)

Wouter D. Weeda - [e-mail]

References

See the Nifti homepage (http://nifti.nimh.nih.gov/) for more information on the nifti filetype.

See Also

nifti.header,nifti.fileinfo

Examples

showClass("fmri.data")

arf3DS4 documentation built on May 2, 2019, 5:16 p.m.