separate_cifti_files

intent

Character vector indicating which brain structure(s)
to obtain: <code>"left"</code> (left cortex), <code>"right"</code> (right cortex)
and/or <code>"subcortical"</code> (subcortex and cerebellum). Can also be
<code>"all"</code> (obtain all three brain structures). Default:
<code>c("left","right")</code> (cortex only).
If a brain structure is indicated but does not exist in the CIFTI file, a
warning will occur and that brain structure will be skipped.

brainstructures

(Optional) GIFTI file names
(*.[func/label].gii) to save the [left/right] cortex data to. If not provided,
defaults to <code>"*[L/R].\[func/label\].gii"</code>, where * is the file name
component of <code>cifti_fname</code>. Will be written in <code>write_dir</code>.
dtseries and dscalar files should use "func", whereas dlabel files should
use "label".

cortexL_fname, cortexR_fname

(Optional) NIFTI file names to save
the subcortical [volume/labels] to. If not provided, defaults to
<code>"*[/.labels].nii"</code>, where * is the file name component of
<code>cifti_fname</code>. Will be written in <code>write_dir</code>.

subcortVol_fname, subcortLabs_fname

Which ROIs should be obtained? <code>"all"</code>
(default) to obtain ROIs for each of the <code>brainstructures</code>. <code>NULL</code>
to not obtain any ROIs. This should be a subset of <code>brainstructures</code>.

ROI_brainstructures

(Optional) GIFTI file names
(*.[func/label].gii) to save the [left/right] cortex ROI to. If not provided,
defaults to <code>"*ROI_[L/R].\[func/label\].gii"</code>, where * is the file name component
of <code>cifti_fname</code>. The cortical ROIs typically represent the medial wall
mask, with values of 1 for in-ROI (non-medial wall) vertices and 0 for
out-of-ROI (medial wall) vertices. Will be written in <code>write_dir</code>.
dtseries and dscalar files should use "func", whereas dlabel files should
use "label".

ROIcortexL_fname, ROIcortexR_fname

(Optional) NIFTI file names to save
the subcortical ROI to. If not provided, defaults to
<code>"*ROI.nii"</code>, where * is the file name component of
<code>cifti_fname</code>. The subcortical ROI typically represents the volumetric
mask for the entire subcortical structure, with values of 1 for in-ROI
(in subcortex) voxels and 0 for out-of-ROI (not in subcortex) voxels. Will
be written in <code>write_dir</code>.

ROIsubcortVol_fname

Where should the separated files be placed? <code>NULL</code>
(default) will write them to the current working directory.<code>write_dir</code> must already exist, or an error will occur.

write_dir

File paths for writing GIFTI and NIFTI files from a CIFTI or <code>"xifti"</code>

internal

CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.

Amanda Mejia

ciftiTools

Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

Damon Pham

John Muschelli

separate_cifti_files function

Where should the separated files be placed? <code>NULL</code>
(default) will write them to the current working directory.

<code>write_dir</code> must already exist, or an error will occur.

separate_cifti_files: Separate CIFTI: file names

Description

Usage

Arguments

Value