Package 'oro.nifti'

Description

The AFNI class for medical imaging data.

Usage

## S4 method for signature 'afni'
show(object)

Arguments

Objects from the Class

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

Slots

.Data:

Object of class "array" contains the imaging data

DATASET_RANK:

Object of class "integer"

DATASET_DIMENSIONS:

Object of class "integer"

TYPESTRING:

Object of class "character"

SCENE_DATA:

Object of class "integer"

ORIENT_SPECIFIC:

Object of class "integer"

ORIGIN:

Object of class "numeric"

DELTA:

Object of class "numeric"

TAXIS_NUMS:

Object of class "integer"

TAXIS_FLOATS:

Object of class "numeric"

TAXIS_OFFSETS:

Object of class "numeric"

IDCODE_STRING:

Object of class "character"

IDCODE_DATE:

Object of class "character"

BYTEORDER_STRING:

Object of class "character"

BRICK_STATS:

Object of class "numeric"

BRICK_TYPES:

Object of class "integer"

BRICK_FLOAT_FACS:

Object of class "numeric"

BRICK_LABS:

Object of class "character"

BRICK_STATAUX:

Object of class "numeric"

STAT_AUX:

Object of class "numeric"

HISTORY_NOTE:

Object of class "character"

NOTES_COUNT:

Object of class "integer"

NOTE_NUMBER:

Object of class "character"

TAGALIGN_MATVEC:

Object of class "numeric"

VOLREG_MATVEC:

Object of class "array"

VOLREG_ROTCOM:

Object of class "character"

VOLREG_CENTER_OLD:

Object of class "numeric"

VOLREG_CENTER_BASE:

Object of class "numeric"

VOLREG_ROTPARENT_IDCODE:

Object of class "character"

VOLREG_ROTPARENT_NAME:

Object of class "character"

VOLREG_GRIDPARENT_IDCODE:

Object of class "character"

VOLREG_GRIDPARENT_NAME:

Object of class "character"

VOLREG_INPUT_IDCODE:

Object of class "character"

VOLREG_INPUT_NAME:

Object of class "character"

VOLREG_BASE_IDCODE:

Object of class "character"

VOLREG_BASE_NAME:

Object of class "character"

VOLREG_ROTCOM_NUM:

Object of class "integer"

IDCODE_ANAT_PARENT:

Object of class "character"

TO3D_ZPAD:

Object of class "integer"

IDCODE_WARP_PARENT:

Object of class "character"

WARP_TYPE:

Object of class "integer"

WARP_DATA:

Object of class "numeric"

MARKS_XYZ:

Object of class "numeric"

MARKS_LAB:

Object of class "character"

MARKS_HELP:

Object of class "character"

MARKS_FLAGS:

Object of class "integer"

TAGSET_NUM:

Object of class "integer"

TAGSET_FLOATS:

Object of class "numeric"

TAGSET_LABELS:

Object of class "character"

LABEL_1:

Object of class "character"

LABEL_2:

Object of class "character"

DATASET_NAME:

Object of class "character"

DATASET_KEYWORDS:

Object of class "character"

BRICK_KEYWORDS:

Object of class "character"

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.

Author(s)

Karsten Tabelow [email protected]

References

AFNI
http://afni.nimh.nih.gov/pub/dist/src/README.attributes

See Also

nifti, anlz

Examples

showClass("afni")

Description

Constructor for Analyze class objects.

Usage

anlz(img = array(0, dim = rep(1, 4)), dim, datatype = 2, ...)

Arguments

Value

An object of class anlz.

Author(s)

Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf

See Also

anlz, nifti, nifti, convert.datatype.anlz

Examples

aim <- anlz() # default

Description

The ANALYZE class for medical imaging data.

Usage

## S4 method for signature 'anlz'
show(object)

Arguments

Objects from the Class

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

hkey_un0:

Object of class "character"

dim_:

Object of class "vector" contains the dimensions of the imaging data

vox_units:

Object of class "character"

cal_units:

Object of class "character"

unused1:

Object of class "numeric"

datatype:

Object of class "numeric"

bitpix:

Object of class "numeric" contains the number of bits per voxel (pixel)

dim_un0:

Object of class "numeric"

pixdim:

Object of class "vector" contains the real-world dimensions of the imaging data

vox_offset:

Object of class "numeric"

funused1:

Object of class "numeric"

funused2:

Object of class "numeric"

funused3:

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

compressed:

Object of class "numeric"

verified:

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"

orient:

Object of class "character"

origin:

Object of class "numeric"

generated:

Object of class "character"

scannum:

Object of class "character"

patient_id:

Object of class "character"

exp_date:

Object of class "character"

exp_time:

Object of class "character"

hist_un0:

Object of class "character"

views:

Object of class "numeric"

vols_added:

Object of class "numeric"

start_field:

Object of class "numeric"

field_skip:

Object of class "numeric"

omax:

Object of class "numeric"

omin:

Object of class "numeric"

smax:

Object of class "numeric"

smin:

Object of class "numeric"

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 = "anlz"): displays the image(s).

show

signature(object = "anlz"): prints out a summary of the imaging data.

Author(s)

Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf

See Also

nifti, niftiExtension

Examples

showClass("anlz")

Description

Overloaded operators for anlz and nifti objects

Usage

## S4 method for signature 'anlz,anlz'
Ops(e1, e2)

## S4 method for signature 'anlz,numeric'
Ops(e1, e2)

## S4 method for signature 'numeric,anlz'
Ops(e1, e2)

## S4 method for signature 'nifti,anlz'
Ops(e1, e2)

## S4 method for signature 'anlz,nifti'
Ops(e1, e2)

Arguments

Author(s)

John Muschelli [email protected]

Examples

img01 <- anlz(array(1:64, c(4,4,4,1)), datatype=4)
img02 <- anlz(array(64:1, c(4,4,4,1)), datatype=4)
is.anlz(img01 + img02)
is.anlz(sqrt(2) * img01)
is.anlz(img02 / pi)

Description

Internal function that converts multidimensional arrays to ANALYZE class objects.

Usage

as.anlz(from, value = NULL, verbose = FALSE)

Arguments

Value

An object of class anlz.

Author(s)

Andrew Thornton [email protected],
Brandon Whitcher [email protected]

Description

Internal function that converts multidimensional arrays to NIfTI class objects.

Usage

as.nifti(from, value = NULL, verbose = FALSE)

Arguments

Value

An object of class nifti.

Author(s)

Andrew Thornton [email protected].
Brandon Whitcher [email protected]

Description

Facilitate the creation and modification of audit trails for NIfTI class objects.

Usage

oro.nifti.info(type)

enableAuditTrail()

getLastCallWithName(functionName)

newAuditTrail()

niftiExtensionToAuditTrail(
  nim,
  workingDirectory = NULL,
  filename = NULL,
  call = NULL
)

niftiAuditTrailSystemNode(
  type = "system-info",
  workingDirectory = NULL,
  filename = NULL,
  call = NULL
)

niftiAuditTrailSystemNodeEvent(
  trail,
  type = NULL,
  call = NULL,
  workingDirectory = NULL,
  filename = NULL,
  comment = NULL
)

niftiAuditTrailCreated(
  history = NULL,
  call = NULL,
  workingDirectory = NULL,
  filename = NULL
)

niftiAuditTrailEvent(trail, type = NULL, call = NULL, comment = NULL)

Arguments

Details

The function oro.nifti.info is used to find the ecode or the XML namespace relevant to the audit trail.

The function enableAuditTrail is turned “off” by default to minimize package dependencies. Should one wish to turn “on” the audit trail functionality, then one should set the option NIfTI.audit.trail to TRUE and call the function enableAuditTrail. Setting the option NIfTI.audit.trail to FALSE will disable the audit trail.

The function newAuditTrail returns an XMLAbstractNode representing the root node of an audit trail. This is mostly intended as an internal function.

The function niftiExtensionToAuditTrail takes an object representing a NIfTI object, casts it as a niftiAuditTrail and checks if there is an extension (a niftiExtensionSection) with ecode equal to oro.nifti.info("ecode"); i.e. has a extension with data representing a serialized audit trail. The function will then strip the object of this extension parsing the serialized edata into an audit trail and adding a ‘read’ event to the trail.

The function niftiAuditTrailToExtension takes a niftiAuditTrail and returns a niftiExtensionSection with edata containing the serialized form of the audit trail after adding a ‘saved’ event to the trail.

The function niftiAuditTrailSystemNodeEvent adds an element with name equal to type to the trail. It uses the niftiAuditTrailSystemNode function to create the node.

The function niftiAuditTrailSystemNode is an internal function creating an XMLAbstractNode element with name type and attributes giving information about the R system and library. The filename and call will also be added as attributes if available.

The function niftiAuditTrailEvent adds an element with name event to the trail. The arguments type, filename, call are added as attributes and the comment is the text value of the element.

The function niftiAuditTrailCreated will create a new audit trail containing a system node element created with the child history with the contents history. If the last element of the history given is an event with type="processing", then this node will be removed from the history and its call attribute will be used as the value of the call attribute on the created node.

The function getLastCallWithName will search the call stack for a call of the function functionName, returning last call to that function if possible. It will default to the call of the function which called the function which called getLastCallWithName if there was no such call (and if there was no such call it will return the call of itself).

Note

These functions are mostly intended to be used internally in order to document the changes that occur to NIfTI objects due to functions that are audit-trail aware. However, as the precise manner in which these functions are used is not documented anywhere else, we shall proceed to describe which functions are audit-trail aware and how they interact with the audit trail.

as.nifti and its S4 alias as(nim, "nifti") will always produce niftiAuditTrail objects if the functionality is turned on. The function niftiAuditTrailCreated will be used and if an exemplar object is provided (e.g., as.nifti(array, niftiExemplar)) then the trail of the exemplar will be used as the history.

readNIfTI and writeNIfTI also always produce niftiAuditTrail objects if the functionality is turned on. The functions niftiExtensionToAuditTrail and niftiAuditTrailToExtension are used internally by these functions to facilitate this behaviour.

Author(s)

Andrew Thornton [email protected] and Brandon Whitcher [email protected]

Examples

## A good example of the use of these functions is shown by this
## wrapper function which takes a function fun(nim, ...) returning
## lists of arrays which are nifti-ized using as(...)
options("niftiAuditTrail"=TRUE)
enableAuditTrail()

wrapper <- function(functionToWrap, nameOfCallingFunction, nim, ...) {
  if (!is(nim, "nifti")) 
    nim <- as(nim, "nifti")
  
  if (is(nim, "niftiAuditTrail")) {
    ## This will force as(...) to set the call which created the
    ## results to the calling function's call rather than
    ## as(result, nifti) as it would otherwise do
    slot(nim, "trail") <- niftiAuditTrailEvent(slot(nim, "trail"), "processing",
                                      nameOfCallingFunction)
  }
  
  result <- functionToWrap(nim, ...)
  as(result, "nifti") <- nim
  return(result)
}

## An example of how wrapper is used follows:
functionToWrap <- function(ignored, x, y) {
  return (array(1, dim=c(x,y)))
}

## The nifti-ized form
niftiizedForm <- function(nim,...) {
  return(wrapper(functionToWrap, "niftiizedForm", nim, ...))
}
 
## Not run: 
  if (isTRUE(getOption("niftiAuditTrail"))) {
    print(slot(as.nifti(functionToWrap(nifti(), 4, 4), nifti()), "trail"))
    print(slot(niftiizedForm(nifti(), 4, 4), "trail"))
  }

## End(Not run)

Description

Operators that act on the audit trail (XML) in the NIfTI header.

Usage

audit.trail(object)

## S4 method for signature 'nifti'
audit.trail(object)

audit.trail(object) <- value

## S4 replacement method for signature 'nifti'
audit.trail(object) <- value

Arguments

Methods

object = "nifti"

Extract or replace NIfTI audit trail.

Author(s)

Andrew Thornton [email protected]

Description

Methods that act on the aux_file field in the NIfTI/ANALYZE header.

Usage

aux_file(object)

## S4 method for signature 'nifti'
aux_file(object)

## S4 method for signature 'anlz'
aux_file(object)

aux_file(object) <- value

## S4 replacement method for signature 'nifti'
aux_file(object) <- value

## S4 replacement method for signature 'anlz'
aux_file(object) <- value

aux.file(object)

## S4 method for signature 'nifti'
aux.file(object)

## S4 method for signature 'anlz'
aux.file(object)

aux.file(object) <- value

## S4 replacement method for signature 'nifti'
aux.file(object) <- value

## S4 replacement method for signature 'anlz'
aux.file(object) <- value

## S4 method for signature 'niftiImage'
aux_file(object)

## S4 replacement method for signature 'niftiImage'
aux_file(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

## Not run: 
url <- "http://nifti.nimh.nih.gov/nifti-1/data/avg152T1_RL_nifti.nii.gz"
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                    "mniRL.nii.gz")
download.file(url, urlfile, quiet=TRUE)

## End(Not run)
options("niftiAuditTrail"=FALSE)

urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniRL.nii.gz")
mniRL <- readNIfTI(urlfile)
aux.file(mniRL)
aux.file(mniRL) <- "avg152T1_RL_nifti"
aux.file(mniRL)
file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
aux_file(img)
aux_file(img) = "hey"
stopifnot(aux_file(img) ==  "hey")

Description

Methods that act on the bitpix field in the NIfTI/ANALYZE header.

Usage

bitpix(object)

## S4 method for signature 'nifti'
bitpix(object)

## S4 method for signature 'anlz'
bitpix(object)

bitpix(object) <- value

## S4 replacement method for signature 'nifti'
bitpix(object) <- value

## S4 replacement method for signature 'anlz'
bitpix(object) <- value

## S4 method for signature 'niftiImage'
bitpix(object)

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
bitpix(img)

Description

Two volumes of medical imaging data are merged together in the superior-inferior (or $z$) direction. One assumes that there is at least one slice that overlaps between the two volumes.

Usage

blendVolumes(x, y, seqX, seqY, method = "linear")

## S4 method for signature 'nifti,nifti'
blend(x, y, seqX, seqY, method = "linear")

## S4 method for signature 'anlz,anlz'
blend(x, y, seqX, seqY, method = "linear")

## S4 method for signature 'anlz,nifti'
blend(x, y, seqX, seqY, method = "linear")

## S4 method for signature 'nifti,anlz'
blend(x, y, seqX, seqY, method = "linear")

Arguments

Value

A single volume that blends the voxel-wise information from x and y.

Methods

x = "nifti", y = "nifti"

Merge x and y.

x = "anlz", y = "anlz"

Merge x on y.

x = "nifti", y = "anlz"

Merge x on y.

x = "anlz", y = "nifti"

Merge x and y.

Author(s)

Brandon Whitcher [email protected]

See Also

image-methods, overlay-methods

Description

Methods that act on the cal_max field in the NIfTI/ANALYZE header.

Usage

cal_max(object)

## S4 method for signature 'nifti'
cal_max(object)

## S4 method for signature 'anlz'
cal_max(object)

cal_max(object) <- value

## S4 replacement method for signature 'nifti'
cal_max(object) <- value

## S4 replacement method for signature 'anlz'
cal_max(object) <- value

cal.max(object)

## S4 method for signature 'nifti'
cal.max(object)

## S4 method for signature 'anlz'
cal.max(object)

cal.max(object) <- value

## S4 replacement method for signature 'nifti'
cal.max(object) <- value

## S4 replacement method for signature 'anlz'
cal.max(object) <- value

## S4 method for signature 'niftiImage'
cal.max(object)

## S4 replacement method for signature 'niftiImage'
cal.max(object) <- value

## S4 method for signature 'niftiImage'
cal_max(object)

## S4 replacement method for signature 'niftiImage'
cal_max(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

## Not run: 
url <- "http://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz"
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
download.file(url, urlfile, quiet=TRUE)

## End(Not run)
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
mniLR <- readNIfTI(urlfile)
cal.max(mniLR)
file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
cal.max(img)
cal_max(img)
cal.max(img) = 2500
stopifnot(cal_max(img) == 2500)
cal_max(img) = 2500
cal.min(img)
cal.min(img) = 2
stopifnot(cal_min(img) == 2)
cal_min(img)
cal_min(img) = 0
stopifnot(cal_min(img) == 0)

Description

Methods that act on the cal_min field in the NIfTI/ANALYZE header.

Usage

cal_min(object)

## S4 method for signature 'nifti'
cal_min(object)

## S4 method for signature 'anlz'
cal_min(object)

cal_min(object) <- value

## S4 replacement method for signature 'nifti'
cal_min(object) <- value

## S4 replacement method for signature 'anlz'
cal_min(object) <- value

cal.min(object)

## S4 method for signature 'nifti'
cal.min(object)

## S4 method for signature 'anlz'
cal.min(object)

cal.min(object) <- value

## S4 replacement method for signature 'nifti'
cal.min(object) <- value

## S4 replacement method for signature 'anlz'
cal.min(object) <- value

## S4 method for signature 'niftiImage'
cal.min(object)

## S4 replacement method for signature 'niftiImage'
cal.min(object) <- value

## S4 method for signature 'niftiImage'
cal_min(object)

## S4 replacement method for signature 'niftiImage'
cal_min(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

## Not run: 
url <- "http://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz"
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
download.file(url, urlfile, quiet=TRUE)

## End(Not run)
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
mniLR <- readNIfTI(urlfile)
cal.min(mniLR)

Description

Methods that act on the cal_units field in the NIfTI/ANALYZE header.

Usage

cal_units(object)

## S4 method for signature 'anlz'
cal_units(object)

cal_units(object) <- value

## S4 replacement method for signature 'anlz'
cal_units(object) <- value

cal.units(object)

## S4 method for signature 'anlz'
cal.units(object)

cal.units(object) <- value

## S4 replacement method for signature 'anlz'
cal.units(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Rescales image cal_max and cal_min slots to be the max and min, respectively, of an object of class nifti, with na.rm = TRUE. This is so that when images are rendered/written, the values correspond to those in the array (stored in .Data slot) are plotted on correct greyscale and no error is given by writeNIfTI.

Usage

calibrateImage(img, infok = TRUE)

cal_img(img, infok = TRUE)

Arguments

Value

An object of class nifti.

Author(s)

John Muschelli [email protected]

Description

Methods for function coerce in Package ‘methods’.

Arguments

Value

An object of class anlz or nifti.

Methods

from = "anlz", to = "nifti"

An object of class anlz is coerced into a NIfTI object.

from = "array", to = "anlz"

An object of class array is coerced into an ANALYZE object.

from = "array", to = "nifti"

An object of class array is coerced into a NIfTI object.

from = "list", to = "anlz"

All objects of class array in the list are coerced into ANALYZE objects. All other objects are left alone. The original list structure is retained.

from = "list", to = "nifti"

All objects of class array in the list are coerced into NIfTI objects. All other objects are left alone. The original list structure is retained.

Author(s)

Andrew Thornton [email protected],
Brandon Whitcher [email protected]

See Also

as

Description

Methods that act on the compressed field in the NIfTI/ANALYZE header.

Usage

compressed(object)

## S4 method for signature 'anlz'
compressed(object)

compressed(object) <- value

## S4 replacement method for signature 'anlz'
compressed(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Codes that appear in the ANALYZE header are mapped to meaningful character strings.

Usage

convert.bitpix.anlz(bitpix = NULL)

convert.datatype.anlz(datatype.code = NULL)

convert.orient.anlz(orientation)

Arguments

Details

switch statements are used to map a numeric code to the appropriate string.

Value

A character string.

Author(s)

Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf

See Also

convert.datatype, convert.bitpix, convert.intent, convert.form, convert.units, convert.slice

Examples

##  4 = SIGNED_SHORT
convert.datatype.anlz(4)
## 16 = FLOAT
convert.datatype.anlz(16)
##  2 = "saggital unflipped"
convert.orient.anlz(2)
##  4 = "coronal flipped"
convert.orient.anlz(4)

Description

Codes that appear in the ANALYZE header are mapped to meaningful character strings.

Usage

convert.bitpix(bitpix = NULL)

convert.datatype(datatype.code = NULL)

convert.intent(intent.code = NULL)

convert.form(form.code)

convert.units(units, inverse = FALSE)

convert.slice(slice.code)

Arguments

Details

switch statements are used to map a numeric code to the appropriate string.

Value

A character string.

Author(s)

Brandon Whitcher [email protected]

References

Neuroimaging Informatics Technology Initiative (NIfTI)
http://nifti.nimh.nih.gov/

Examples

##  4 = SIGNED_SHORT
convert.datatype.anlz(4)
## 16 = FLOAT
convert.datatype.anlz(16)
##  2 = "saggital unflipped"
convert.orient.anlz(2)
##  4 = "coronal flipped"
convert.orient.anlz(4)

Description

Codes that appear in the AFNI header are mapped to meaningful character strings.

Usage

convert.scene(scene.data, typestring)

Arguments

Details

switch statements are used to map a numeric code to the appropriate string.

Value

A character string.

Author(s)

Karsten Tabelow [email protected]

References

AFNI
http://afni.nimh.nih.gov/pub/dist/src/README.attributes

See Also

convert.datatype.anlz, convert.orient.anlz

Examples

## 4 = CT for anatomic data
convert.scene(4, "3DIM_HEAD_ANAT")

Description

Methods that act on the data_type field in the NIfTI/ANALYZE header.

Usage

data_type(object)

## S4 method for signature 'nifti'
data_type(object)

## S4 method for signature 'anlz'
data_type(object)

data_type(object) <- value

## S4 replacement method for signature 'nifti'
data_type(object) <- value

## S4 replacement method for signature 'anlz'
data_type(object) <- value

data.type(object)

## S4 method for signature 'nifti'
data.type(object)

## S4 method for signature 'anlz'
data.type(object)

data.type(object) <- value

## S4 replacement method for signature 'nifti'
data.type(object) <- value

## S4 replacement method for signature 'anlz'
data.type(object) <- value

## S4 method for signature 'niftiImage'
data_type(object)

## S4 method for signature 'niftiImage'
datatype(object)

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
data_type(img)
datatype(img)

Description

Methods that act on the datatype field in the NIfTI/ANALYZE header.

Usage

datatype(object)

## S4 method for signature 'nifti'
datatype(object)

## S4 method for signature 'anlz'
datatype(object)

datatype(object) <- value

## S4 replacement method for signature 'nifti'
datatype(object) <- value

## S4 method for signature 'ANY'
datatype(object)

## S4 replacement method for signature 'anlz'
datatype(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the db_name field in the NIfTI/ANALYZE header.

Usage

db_name(object)

## S4 method for signature 'nifti'
db_name(object)

## S4 method for signature 'anlz'
db_name(object)

db_name(object) <- value

## S4 replacement method for signature 'nifti'
db_name(object) <- value

## S4 replacement method for signature 'anlz'
db_name(object) <- value

db.name(object)

## S4 method for signature 'nifti'
db.name(object)

## S4 method for signature 'anlz'
db.name(object)

db.name(object) <- value

## S4 replacement method for signature 'nifti'
db.name(object) <- value

## S4 replacement method for signature 'anlz'
db.name(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the descrip field in the NIfTI/ANALYZE header.

Usage

descrip(object)

## S4 method for signature 'nifti'
descrip(object)

## S4 method for signature 'anlz'
descrip(object)

descrip(object) <- value

## S4 replacement method for signature 'nifti'
descrip(object) <- value

## S4 replacement method for signature 'anlz'
descrip(object) <- value

## S4 method for signature 'niftiImage'
descrip(object)

## S4 replacement method for signature 'niftiImage'
descrip(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

## Not run: 
url <- "http://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz"
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
download.file(url, urlfile, quiet=TRUE)

## End(Not run)
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
mniLR <- readNIfTI(urlfile)
descrip(mniLR)
## Not run: 
descrip(mniLR) <- paste(descrip(mniLR), version$version.string, sep="; ")
descrip(mniLR)

## End(Not run)
file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
descrip(img)
file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
descrip(img) = "a file"
descrip(img)
stopifnot(descrip(img) == "a file")

Description

Methods that act on the dim_ field in the NIfTI/ANALYZE header.

Usage

dim_(object)

## S4 method for signature 'nifti'
dim_(object)

## S4 method for signature 'anlz'
dim_(object)

dim_(object) <- value

## S4 replacement method for signature 'nifti'
dim_(object) <- value

## S4 replacement method for signature 'anlz'
dim_(object) <- value

## S4 method for signature 'ANY'
dim_(object)

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the dim_info field in the NIfTI/ANALYZE header.

Usage

dim_info(object)

## S4 method for signature 'nifti'
dim_info(object)

dim_info(object) <- value

## S4 replacement method for signature 'nifti'
dim_info(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the dim_un0 field in the NIfTI/ANALYZE header.

Usage

dim_un0(object)

## S4 method for signature 'anlz'
dim_un0(object)

dim_un0(object) <- value

## S4 replacement method for signature 'anlz'
dim_un0(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Drops a dimension of an image that has one-dimension and sets respective values to 0 in pixdim or 1 in dim.

Usage

dropImageDimension(img, onlylast = TRUE, warn = TRUE)

drop_img_dim(img, onlylast = TRUE, warn = TRUE)

Arguments

Value

Object of class nifti

Examples

nim <- nifti(array(rnorm(10^3), dim = rep(10, 3)))
nim2 <- nifti(array(rnorm(10^3), dim = c(10, 10, 1, 10)))
dropImageDimension(nim2)
dropImageDimension(nim2, onlylast = FALSE)
nim3 <- nifti(array(rnorm(10^3), dim = c(10, 10, 10, 1)))
dropImageDimension(nim3)
dropImageDimension(nim3, onlylast = FALSE) # the same as above
nim4 <- nifti(array(rnorm(10^3), dim = c(10, 10, 10, 1, 10)))
dim(nim4[,,,1,])
dim(nim4[,,,1,,drop=TRUE])
dropImageDimension(nim4)

nim5 <- nifti(array(rnorm(10^4), dim = c(1, 10, 10, 10, 1, 10)))
dropImageDimension(nim5)
dropImageDimension(nim5, onlylast = FALSE)

nim6 <- nifti(array(rnorm(10^3), dim = c(1, 10, 10, 10, 1, 1)))
dropImageDimension(nim6)
## Not run: 
## 27 scans of Colin Holmes (MNI) brain co-registered and averaged
## NIfTI two-file format
URL <- "http://imaging.mrc-cbu.cam.ac.uk/downloads/Colin/colin_1mm.tgz"
urlfile <- file.path(tempdir(), "colin_1mm.tgz")
download.file(URL, dest=urlfile, quiet=TRUE)
untar(urlfile, exdir=tempdir())
colin <- readNIfTI(file.path(tempdir(), "colin_1mm"))
dim(colin)
dim_(colin)
pixdim(colin)
# this will error
writeNIfTI(colin, filename = tempfile())
colin <- dropImageDimension(colin)
writeNIfTI(colin, filename = tempfile())

## End(Not run)

Description

Methods that act on the exp_date field in the NIfTI/ANALYZE header.

Usage

exp_date(object)

## S4 method for signature 'anlz'
exp_date(object)

exp_date(object) <- value

## S4 replacement method for signature 'anlz'
exp_date(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the exp_time field in the NIfTI/ANALYZE header.

Usage

exp_time(object)

## S4 method for signature 'anlz'
exp_time(object)

exp_time(object) <- value

## S4 replacement method for signature 'anlz'
exp_time(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the extender field in the NIfTI/ANALYZE header.

Usage

extender(object)

## S4 method for signature 'nifti'
extender(object)

extender(object) <- value

## S4 replacement method for signature 'nifti'
extender(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the extents field in the NIfTI/ANALYZE header.

Usage

extents(object)

## S4 method for signature 'nifti'
extents(object)

## S4 method for signature 'anlz'
extents(object)

extents(object) <- value

## S4 replacement method for signature 'nifti'
extents(object) <- value

## S4 replacement method for signature 'anlz'
extents(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the field_skip field in the NIfTI/ANALYZE header.

Usage

field_skip(object)

## S4 method for signature 'anlz'
field_skip(object)

field_skip(object) <- value

## S4 replacement method for signature 'anlz'
field_skip(object) <- value

field.skip(object)

## S4 method for signature 'anlz'
field.skip(object)

field.skip(object) <- value

## S4 replacement method for signature 'anlz'
field.skip(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the funused1 field in the NIfTI/ANALYZE header.

Usage

funused1(object)

## S4 method for signature 'anlz'
funused1(object)

funused1(object) <- value

## S4 replacement method for signature 'anlz'
funused1(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the funused2 field in the NIfTI/ANALYZE header.

Usage

funused2(object)

## S4 method for signature 'anlz'
funused2(object)

funused2(object) <- value

## S4 replacement method for signature 'anlz'
funused2(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the funused3 field in the NIfTI/ANALYZE header.

Usage

funused3(object)

## S4 method for signature 'anlz'
funused3(object)

funused3(object) <- value

## S4 replacement method for signature 'anlz'
funused3(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the generated field in the NIfTI/ANALYZE header.

Usage

generated(object)

## S4 method for signature 'anlz'
generated(object)

generated(object) <- value

## S4 replacement method for signature 'anlz'
generated(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the glmax field in the NIfTI/ANALYZE header.

Usage

glmax(object)

## S4 method for signature 'nifti'
glmax(object)

## S4 method for signature 'anlz'
glmax(object)

glmax(object) <- value

## S4 replacement method for signature 'nifti'
glmax(object) <- value

## S4 replacement method for signature 'anlz'
glmax(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the glmin field in the NIfTI/ANALYZE header.

Usage

glmin(object)

## S4 method for signature 'nifti'
glmin(object)

## S4 method for signature 'anlz'
glmin(object)

glmin(object) <- value

## S4 replacement method for signature 'nifti'
glmin(object) <- value

## S4 replacement method for signature 'anlz'
glmin(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the hist_un0 field in the NIfTI/ANALYZE header.

Usage

hist_un0(object)

## S4 method for signature 'anlz'
hist_un0(object)

hist_un0(object) <- value

## S4 replacement method for signature 'anlz'
hist_un0(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the hkey_un0 field in the NIfTI/ANALYZE header.

Usage

hkey_un0(object)

## S4 method for signature 'anlz'
hkey_un0(object)

hkey_un0(object) <- value

## S4 replacement method for signature 'anlz'
hkey_un0(object) <- value

hkey.un0(object)

## S4 method for signature 'anlz'
hkey.un0(object)

hkey.un0(object) <- value

## S4 replacement method for signature 'anlz'
hkey.un0(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

The hotmetal color table patterned after the one used in Matlab.

Usage

hotmetal(n = 64)

Arguments

Details

Based on the tim.colors function in the fields package. The hotmetal function has been modified to break any dependence on code in the fields package. Spline interpolation (interpSpline) is used when the number of requested colors is not the default.

Value

A vector of character strings giving the colors in hexadecimal format.

See Also

terrain.colors, tim.colors, topo.colors

Examples

hotmetal(10) 
image(outer(1:20,1:20,"+"), col=hotmetal(75), main="hotmetal")

Description

Produce “lightbox” layout of images for nifti, anlz and afni objects.

Usage

## S4 method for signature 'nifti'
image(
  x,
  z = 1,
  w = 1,
  col = gray(0:64/64),
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  zlim = NULL,
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  ...
)

## S4 method for signature 'anlz'
image(
  x,
  z = 1,
  w = 1,
  col = gray(0:64/64),
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  zlim = NULL,
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  ...
)

## S4 method for signature 'afni'
image(x, ...)

Arguments

Details

Uses the S3 generic function image, with medical-image friendly settings, to display nifti, anlz and afni class objects in a “lightbox” layout.

Methods

x = "ANY"

Generic function: see image.

x = "nifti"

Produce images for x.

x = "anlz"

Produce images for x.

x = "afni"

Produce images for x.

Author(s)

Brandon Whitcher [email protected]

See Also

orthographic-methods, overlay-methods

Description

Methods that act on the .Data field in the NIfTI/ANALYZE header.

Usage

img_data(object)

## S4 method for signature 'nifti'
img_data(object)

## S4 method for signature 'anlz'
img_data(object)

## S4 method for signature 'character'
img_data(object)

## S4 method for signature 'ANY'
img_data(object)

img_data(object) <- value

## S4 replacement method for signature 'nifti'
img_data(object) <- value

## S4 replacement method for signature 'anlz'
img_data(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Multiplies the number of slices by the voxel resolution for each direction.

Usage

img_length(img, units = c("mm", "cm"))

Arguments

Value

Scalar numeric, one number, in mm or cm.

Examples

nim <- nifti(array(rnorm(10^3), dim = c(5, 2, 100)),
pixdim = c(1, 0.5, 0.2, 1))
img_length(nim)

Description

...

Usage

integerTranslation(nim, data, verbose = FALSE)

invertIntegerTranslation(nim, verbose = FALSE)

Arguments

Details

...

Value

...

Author(s)

Andrew Thornton [email protected]

Description

Methods that act on the intent_code field in the NIfTI/ANALYZE header.

Usage

intent_code(object)

## S4 method for signature 'nifti'
intent_code(object)

intent_code(object) <- value

## S4 replacement method for signature 'nifti'
intent_code(object) <- value

intent.code(object)

## S4 method for signature 'nifti'
intent.code(object)

intent.code(object) <- value

## S4 replacement method for signature 'nifti'
intent.code(object) <- value

## S4 method for signature 'niftiImage'
intent_code(object)

## S4 replacement method for signature 'niftiImage'
intent_code(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
intent_code(img)
intent_code(img) = 4
stopifnot(intent_code(img) == 4)

Description

Methods that act on the intent_name field in the NIfTI/ANALYZE header.

Usage

intent_name(object)

## S4 method for signature 'nifti'
intent_name(object)

intent_name(object) <- value

## S4 replacement method for signature 'nifti'
intent_name(object) <- value

intent.name(object)

## S4 method for signature 'nifti'
intent.name(object)

intent.name(object) <- value

## S4 replacement method for signature 'nifti'
intent.name(object) <- value

## S4 method for signature 'niftiImage'
intent_name(object)

## S4 replacement method for signature 'niftiImage'
intent_name(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
intent_name(img)
intent_name(img) = "hey"
stopifnot(intent_name(img) ==  "hey")

Description

Methods that act on the intent_p1 field in the NIfTI/ANALYZE header.

Usage

intent_p1(object)

## S4 method for signature 'nifti'
intent_p1(object)

intent_p1(object) <- value

## S4 replacement method for signature 'nifti'
intent_p1(object) <- value

intent.p1(object)

## S4 method for signature 'nifti'
intent.p1(object)

intent.p1(object) <- value

## S4 replacement method for signature 'nifti'
intent.p1(object) <- value

## S4 method for signature 'niftiImage'
intent_p1(object)

## S4 replacement method for signature 'niftiImage'
intent_p1(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
intent_p1(img)
intent_p1(img) = 2
stopifnot(intent_p1(img) == 2)
intent_p2(img)
intent_p2(img) = 2
stopifnot(intent_p2(img) == 2)
intent_p3(img)
intent_p3(img) = 2
stopifnot(intent_p3(img) == 2)

Description

Methods that act on the intent_p2 field in the NIfTI/ANALYZE header.

Usage

intent_p2(object)

## S4 method for signature 'nifti'
intent_p2(object)

intent_p2(object) <- value

## S4 replacement method for signature 'nifti'
intent_p2(object) <- value

intent.p2(object)

## S4 method for signature 'nifti'
intent.p2(object)

intent.p2(object) <- value

## S4 replacement method for signature 'nifti'
intent.p2(object) <- value

## S4 method for signature 'niftiImage'
intent_p2(object)

## S4 replacement method for signature 'niftiImage'
intent_p2(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the intent_p3 field in the NIfTI/ANALYZE header.

Usage

intent_p3(object)

## S4 method for signature 'nifti'
intent_p3(object)

intent_p3(object) <- value

## S4 replacement method for signature 'nifti'
intent_p3(object) <- value

intent.p3(object)

## S4 method for signature 'nifti'
intent.p3(object)

intent.p3(object) <- value

## S4 replacement method for signature 'nifti'
intent.p3(object) <- value

## S4 method for signature 'niftiImage'
intent_p3(object)

## S4 replacement method for signature 'niftiImage'
intent_p3(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

"internalImage" class

Description

Check whether object is of class afni.

Usage

is.afni(x)

Arguments

Value

Logical indicating whether object is of class afni.

Author(s)

Karsten Tabelow [email protected]

References

AFNI
http://afni.nimh.nih.gov/pub/dist/src/README.attributes

See Also

afni

Description

Check whether object is of class anlz.

Usage

is.anlz(x)

Arguments

Value

Logical indicating whether object is of class anlz.

Author(s)

Karsten Tabelow [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf

See Also

anlz

Description

Check whether object is of class nifti.

Usage

is.nifti(x)

is.niftiExtension(x)

Arguments

Value

Logical indicating whether object is of class nifti.

Author(s)

Karsten Tabelow [email protected]

References

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

See Also

nifti

Description

Methods that act on the magic field in the NIfTI/ANALYZE header.

Usage

magic(object)

## S4 method for signature 'nifti'
magic(object)

magic(object) <- value

## S4 replacement method for signature 'nifti'
magic(object) <- value

## S4 method for signature 'niftiImage'
magic(object)

## S4 replacement method for signature 'niftiImage'
magic(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

file = system.file("extdata", "example.nii.gz", package = "RNifti")
img = RNifti::readNifti(file)
magic(img)
magic(img) = "ni1"
stopifnot(magic(img) == "ni1")
magic(img) = "n+1"
stopifnot(magic(img) == "n+1")
magic(img) = "r" # bad magic
stopifnot(magic(img) == "")

Description

Constructor for NIfTI class objects.

Usage

nifti(
  img = array(0, dim = rep(1, 4)),
  dim,
  datatype = 2,
  cal.min = NULL,
  cal.max = NULL,
  pixdim = NULL,
  ...
)

Arguments

Value

An object of class nifti.

Author(s)

Brandon Whitcher [email protected]

References

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

See Also

nifti, anlz, convert.datatype

Examples

options("niftiAuditTrail"=FALSE)

nim <- nifti() # default
nim
nim <- nifti(datatype=4) # 2-byte integers
nim

Description

Methods for function [<- in Package 'base'

Methods

x = "nifti", i = "ANY", j = "ANY", value = "ANY"

Replaces the data at the provided co-ordinates with the value provided and updates the header.

x = "nifti", i = "numeric", j = "numeric", value = "ANY"

Replaces the data at the provided co-ordinates with the value provided and updates the header.

x = "nifti", i = "ANY", j = "missing", value = "ANY"

Replaces the data row i of the provided nifti object with the value provided and updates the header.

x = "nifti", i = "numeric", j = "missing", value = "ANY"

Replaces the data row i of the provided nifti object with the value provided and updates the header.

x = "nifti", i = "missing", j = "missing", value = "array"

Replaces the data of the provided nifti object with the array provided and updates the header.

Description

The NIfTI class for medical imaging data.

Usage

## S4 method for signature 'nifti'
show(object)

Arguments

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.

Author(s)

Brandon Whitcher [email protected],
Andrew Thornton [email protected]

References

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

See Also

anlz, niftiExtension, niftiAuditTrail

Examples

showClass("nifti")

Description

Overloaded operators for nifti objects

Usage

## S4 method for signature 'nifti,nifti'
Ops(e1, e2)

## S4 method for signature 'nifti,numeric'
Ops(e1, e2)

## S4 method for signature 'numeric,nifti'
Ops(e1, e2)

Arguments

Author(s)

John Muschelli [email protected]

Examples

img01 <- nifti(array(1:64, c(4,4,4,1)), datatype=4)
img02 <- nifti(array(64:1, c(4,4,4,1)), datatype=4)
is.nifti(img01 + img02)
is.nifti(sqrt(2) * img01)
is.nifti(img02 / pi)

Description

An extension of the NIfTI class that adds an audit trail in XML format.

Objects from the Class

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

Methods

show

signature(object = "niftiAuditTrail"): prints out a summary of the imaging data.

Author(s)

Andrew Thornton [email protected]

References

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

See Also

nifti, niftiExtension

Examples

showClass("niftiAuditTrail")

Description

An extension of the NIfTI class that allows “extensions” that conform to the NIfTI data standard.

Objects from the Class

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

Author(s)

Andrew Thornton [email protected]

References

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

See Also

nifti, niftiAuditTrail

Examples

showClass("niftiExtension")

Description

A niftiExtensionSection contains the fields that conform to the NIfTI standard regarding header extensions. A niftiExtension is composed of one or more of these objects.

Objects from the Class

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

Author(s)

Brandon Whitcher [email protected],
Andrew Thornton [email protected]

References

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

See Also

niftiExtension, nifti

Examples

showClass("niftiExtensionSection")

Description

"niftiImage" class

Description

Converts a niftiImage from RNifti to a nifti object from the oro.nifti package

Usage

nii2oro(image)

Arguments

Value

Object of class nifti

Description

Functions to extract the higher dimensions from ANALYZE/NIfTI data.

Usage

nsli(x)

NSLI(x)

ntim(x)

NTIM(x)

Arguments

Details

Simple calls to dim to replicate the functionality of nrow and ncol for higher dimensions of an array that are commonly required when manipulating medical imaging data.

Value

Third (slice) or fourth (time) dimension of the array.

Author(s)

Brandon Whitcher [email protected]

See Also

readNIfTI, readANALYZE

Description

Methods that act on the omax field in the NIfTI/ANALYZE header.

Usage

omax(object)

## S4 method for signature 'anlz'
omax(object)

omax(object) <- value

## S4 replacement method for signature 'anlz'
omax(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the omin field in the NIfTI/ANALYZE header.

Usage

omin(object)

## S4 method for signature 'anlz'
omin(object)

omin(object) <- value

## S4 replacement method for signature 'anlz'
omin(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Changes the magic and vox_offset slots to be consistent with the onefile option in writeNIfTI. As of version 0.4.0, oro.nifti did not support the "ni1" magic type for output.

Usage

onefile(img)

Arguments

Value

Object of class nifti.

Author(s)

John Muschelli [email protected]

References

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

Description

Methods that act on the orient field in the NIfTI/ANALYZE header.

Usage

orient(object)

## S4 method for signature 'anlz'
orient(object)

orient(object) <- value

## S4 replacement method for signature 'anlz'
orient(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Description

Methods that act on the “qform” and “sform” information in the NIfTI header.

Usage

sform(object)

## S4 method for signature 'nifti'
sform(object)

qform(object)

## S4 method for signature 'nifti'
qform(object)

Arguments

Methods

object = "nifti"

Extract or replace NIfTI description.

Author(s)

Brandon Whitcher [email protected]

Examples

## Not run: 
url <- "http://nifti.nimh.nih.gov/nifti-1/data/avg152T1_LR_nifti.nii.gz"
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
download.file(url, urlfile, quiet=TRUE)

## End(Not run)
urlfile <- file.path(system.file("nifti", package="oro.nifti"),
                     "mniLR.nii.gz")
mniLR <- readNIfTI(urlfile)
sform(mniLR)

Description

Methods that act on the origin field in the NIfTI/ANALYZE header.

Usage

origin(object)

## S4 method for signature 'nifti'
origin(object)

## S4 method for signature 'anlz'
origin(object)

## S4 method for signature 'ANY'
origin(object)

origin(object) <- value

## S4 replacement method for signature 'anlz'
origin(object) <- value

## S4 replacement method for signature 'nifti'
origin(object) <- value

Arguments

Details

See documentation on the ANALYZE and/or NIfTI data standards for more details.

Author(s)

John Muschelli [email protected],
Brandon Whitcher [email protected]

References

ANALYZE 7.5
http://eeg.sourceforge.net/ANALYZE75.pdf
NIfTI-1
http://nifti.nimh.nih.gov/

Examples

fname = system.file("nifti", "mniRL.nii.gz", 
package = "oro.nifti")
img = readNIfTI(fname)
oimg = origin(img)
stopifnot(all(oimg == c(-90, -126, -72)))
zero_img = img
origin(zero_img) = rep(0, 3)
stopifnot(all(origin(zero_img) == 0))

Description

Converts a nifti from oro.nifti to a niftiImage object from the RNifti package

Usage

oro2nii(image, verbose = FALSE)

Arguments

Value

Object of class niftiImage

Description

Produce orthographic display for nifti, anlz and afni objects.

Usage

orthographic.nifti(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

orthographic(x, ...)

## S4 method for signature 'nifti'
orthographic(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

## S4 method for signature 'anlz'
orthographic(
  x,
  y = NULL,
  xyz = NULL,
  w = 1,
  col = gray(0:64/64),
  col.y = hotmetal(),
  zlim = NULL,
  zlim.y = NULL,
  crosshairs = TRUE,
  col.crosshairs = "red",
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  text = NULL,
  text.color = "white",
  text.cex = 2,
  ...
)

## S4 method for signature 'array'
orthographic(x, ...)

## S4 method for signature 'afni'
orthographic(x, ...)

Arguments

Methods

x = "afni"

Produce orthographic display for x.

x = "anlz"

Produce orthographic display for x.

x = "array"

Produce orthographic display for x.

x = "nifti"

Produce orthographic display for x.

Author(s)

Brandon Whitcher [email protected]

See Also

image-methods, overlay-methods

Examples

fname = system.file(
file.path("nifti", "mniRL.nii.gz"),
package = "oro.nifti")
eve = readNIfTI(fname)
orthographic(eve)

image(eve, z = 45)
image(eve, z = 45, plot.type = "single")
image(eve, z = c(45, 50), plot.type = "single")

Description

Methods for function overlay

Usage

overlay.nifti(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

overlay(x, y, ...)

## S4 method for signature 'nifti,missing'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'nifti,nifti'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'anlz,anlz'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'anlz,nifti'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'nifti,anlz'
overlay(
  x,
  y,
  z = 1,
  w = 1,
  col.x = gray(0:64/64),
  col.y = hotmetal(),
  zlim.x = NULL,
  zlim.y = NULL,
  plane = c("axial", "coronal", "sagittal"),
  plot.type = c("multiple", "single"),
  xlab = "",
  ylab = "",
  axes = FALSE,
  oma = rep(0, 4),
  mar = rep(0, 4),
  bg = "black",
  NA.x = FALSE,
  NA.y = FALSE,
  ...
)

## S4 method for signature 'array,array'
overlay(x, y, ...)

## S4 method for signature 'array,nifti'
overlay(x, y, ...)

## S4 method for signature 'nifti,array'
overlay(x, y, ...)

## S4 method for signature 'array,anlz'
overlay(x, y, ...)

## S4 method for signature 'anlz,array'
overlay(x, y, ...)

## S4 method for signature 'afni,afni'
overlay(x, y, ...)

## S4 method for signature 'afni,array'
overlay(x, y, ...)

Arguments