Package 'cifti'

Extract Brain Structures from CIFTI Brain Models

Description

Extracts the BrainStructure attribute from a BrainModel in a cifti object

Usage

cifti_brain_structs(file)

Arguments

file	cifti object

Value

A vector of brain structure names

---

Map CIFTI values to Coordinates using GIFTI

Description

Maps the data portion of CIFTI data set from a Brain Model to the xyz coordinate triangles

Usage

cifti_coords_gifti(file, gii_file, structure, add_one = TRUE)

Arguments

file	filename of CIFTI file or cifti object
gii_file	filename of corresponding GIFTI file or gifti object
structure	Structure to map, must be one of the brain models in the CIFTI
add_one	should 1 be added to indices (1-based vs. 0-based)

Value

List of coordinates and values

---

Extract CIFTI data from file

Description

Extracts the data after the CIFTI XML information

Usage

cifti_data(fname, nim = NULL)

Arguments

fname	Filename of CIFTI
nim	NIfTI-2 header, if already parsed. If NULL, nifti_2_hdr will be run on the CIFTI.

Value

Array of values

---

Read characters with embedded nulls

Description

Simple wrapper for reading in character values with embedded nulls in a binary file

Usage

cifti_read_char(fid, n, to = "UTF-8")

Arguments

fid	identifier of the open file connection
n	number of elements to read
to	A character string describing the target encoding.

Value

Character vector

---

Extract CIFTI XML

Description

Extracts CIFTI XML from the CIFTI file

Usage

cifti_xml_txt(fname, nim = NULL)

cifti_xml(...)

Arguments

fname	filename of CIFTI
nim	NIfTI-2 header, if already parsed. If NULL, nifti_2_hdr will be run on the CIFTI.
...	arguments to pass to cifti_xml

Value

Character string of XML information

---

Download CIFTI Test Data

Description

Downloads CIFTI test data from https://www.nitrc.org/frs/download.php/8541/cifti-2_test_data-1.2.zip

Usage

download_cifti_data(
  outdir = system.file(package = "cifti"),
  overwrite = FALSE,
  ...
)

Arguments

outdir	Output directory for test file directory
overwrite	Should files be overwritten if already exist?
...	additional arguments to download.file

Value

Vector of file names

---

Get Generic CIFTI Type

Description

Wrapper for multiple types of CIFTI XML types.

Usage

get_cifti_type(
  fname,
  type = c("Volume", "Surface", "Parcel", "NamedMap", "BrainModel"),
  verbose = TRUE
)

cifti_as_list(
  fname,
  type = c("Volume", "Surface", "Parcel", "NamedMap", "BrainModel")
)

Arguments

fname	File name of CIFTI file
type	type of data to extract from CIFTI XML
verbose	print diagnostic messages

Value

List of output from each type

---

Check Presence of CIFTI Test Data

Description

Checks if CIFTI test data is downloaded

Usage

have_cifti_test_data(outdir = system.file(package = "cifti"))

Arguments

outdir

Output directory for test file directory

Value

Logical indicator

---

Test of numeric CIFTI field

Description

Wrapper of CIFTI fields for easy logical test

Usage

is_cifti_numeric(x)

Arguments

x	character vector of names

Value

Logical of length same as x

---

Test if CIFTI

Description

Simple wrapper to determine if class is CIFTI

Usage

is.cifti(x)

Arguments

x	object to test

Value

Logical if x is CIFTI

---

Extract MatrixIndicesMap nodes from CIFTI

Description

Extracts the nodes from a CIFTI-2 file corresponding to the MatrixIndicesMap branch

Usage

matrix_ind_map_nodes(fname)

Arguments

fname

File of CIFTI data

Value

Nodes of class xml_nodeset

---

Read NIfTI-2 Header

Description

Reads a NIfTI-2 header from a filename

Usage

nifti_2_hdr(fname, verbose = FALSE, warn = -1)

Arguments

fname	Filename
verbose	Print diagnostic messages
warn	Should warnings be printed? Passed to options

Value

Object of class nifti

Note

The unused_str part of the header is not returned, but is an empty string of 15 characters. This code was adapted by the oro.nifti package

---

Parse BrainModel from CIFTI

Description

Extracts information about BrainModels from CIFTI file

Usage

parse_brain_model(nodeset)

get_brain_model(fname, verbose = TRUE)

Arguments

nodeset	Set of XML nodes corresponding to BrainModel
fname	filename of CIFTI file
verbose	print diagnostic messages

Value

List of values

Examples

## Not run: 
doc = cifti_xml(fname)
nodes = xml_find_all(doc, "/CIFTI/Matrix/MatrixIndicesMap")
nodeset = xml_find_all(nodes, "./BrainModel")

## End(Not run)

---

Parse Named Map from CIFTI

Description

Extracts information about Named Maps from CIFTI file

Usage

parse_named_map(nodeset)

get_named_map(fname, verbose = TRUE)

Arguments

nodeset	Set of XML nodes corresponding to NamedMap
fname	filename of CIFTI file
verbose	print diagnostic messages

Value

List of values

Examples

## Not run: 
doc = cifti_xml(fname)
nodes = xml_find_all(doc, "/CIFTI/Matrix/MatrixIndicesMap")
nodeset = xml_find_all(nodes, "./NamedMap")
parse_named_map(nodeset)

## End(Not run)

---

Parse Parcel from CIFTI

Description

Extracts information about Parcels from CIFTI file

Usage

parse_parcel(nodeset)

get_parcel(fname, verbose = TRUE)

Arguments

nodeset	Set of XML nodes corresponding to Parcel
fname	filename of CIFTI file
verbose	print diagnostic messages

Value

List of values

---

Parse Surface from CIFTI

Description

Extracts information about Surfaces from CIFTI file

Usage

parse_surface(nodeset)

get_surface(fname, verbose = TRUE)

Arguments

nodeset	Set of XML nodes corresponding to Surface
fname	filename of CIFTI file
verbose	print diagnostic messages

Value

List of values

Examples

## Not run: 
doc = cifti_xml(fname)
nodes = xml_find_all(doc, "/CIFTI/Matrix/MatrixIndicesMap")
nodeset = xml_find_all(nodes, "./Surface")
parse_volume(nodeset)

## End(Not run)

---

Parse Volume from CIFTI

Description

Extracts information about Volumes from CIFTI file

Usage

parse_volume(nodeset)

get_volume(fname, verbose = TRUE)

Arguments

nodeset	Set of XML nodes corresponding to Volume
fname	filename of CIFTI file
verbose	print diagnostic messages

Value

List of values

Examples

## Not run: 
doc = cifti_xml(fname)
nodes = xml_find_all(doc, "/CIFTI/Matrix/MatrixIndicesMap")
nodeset = xml_find_all(nodes, "./Volume")
parse_volume(nodeset)

## End(Not run)

---

Read CIFTI File

Description

Reads CIFTI Files

Usage

read_cifti(fname, drop_data = TRUE, trans_data = TRUE, verbose = TRUE)

readCIFTI(fname, drop_data = TRUE, trans_data = TRUE)

readcii(fname, drop_data = TRUE, trans_data = TRUE)

Arguments

fname	file name of CIFTI file
drop_data	Should the empty data dimensions be dropped?
trans_data	Should the data be transposed
verbose	print diagnostic messages

Value

List of information from the CIFTI file

Examples

outdir = tempdir()
if (have_cifti_test_data(outdir = outdir)) {
   files = download_cifti_data(outdir = outdir)
   fname = grep("MyelinAndCorrThickness.32k_fs_LR.dscalar",
   files, value = TRUE)
   res = read_cifti(fname)
}

---