separate_cifti_wrapper

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separate_cifti wrapper

Calls separate_cifti using the file names listed in the argument sep_fnames.

Keywords
internal
Usage
separate_cifti_wrapper(
  cifti_fname,
  brainstructures = NULL,
  ROI_brainstructures = NULL,
  sep_fnames = NULL,
  write_dir = NULL,
  wb_path = NULL
)
Arguments
cifti_fname

File path of CIFTI-format data (ending in ".d*.nii").

brainstructures

Character vector indicating which brain structure(s) to obtain: "left" (left cortical surface), "right" (right cortical surface) and/or "subcortical" (subcortical and cerebellar gray matter). Can also be "all" (obtain all three brain structures). Default: c("left","right") (cortical surface only).

If a brain structure is indicated but does not exist, a warning will be raised and that brain structure will be skipped.

ROI_brainstructures

Character vector indicating which ROIs should be obtained. NULL (default) to not get any ROIs. Otherwise, this should be a subset of the brainstructures argument.

ROIs are typically the medial wall mask for the cortex and subcortical mask for the subcortex.

sep_fnames

(Optional) Where to write the separated files (override their default file names). This is a named list where each entry's name is a file type label, and each entry's value is a file name indicating where to write the corresponding separated file. The recognized file type labels are: "cortexL", "cortexR", "ROIcortexL", "ROIcortexR", "subcortVol", and "subcortLabs".

Entry values can be NULL, in which case a default file name will be used: see cifti_component_suffix. Default file names will also be used for files that need to be separated/written but without a corresponding entry in sep_fnames.

Entries in sep_fnames will be ignored if they are not needed based on [ROI_]brainstructures. For example, if brainstructures="left", then sep_fnames$cortexR will be ignored if specified.

The write_dir argument can be used to place each separated file in the same directory.

write_dir

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

write_dir must already exist, or an error will occur.

wb_path

(Optional) Path to Connectome Workbench folder or executable. If not provided, should be set with ciftiTools.setOption("wb_path", "path/to/workbench").

Details

Currently used by read_cifti and resample_cifti.

Value

The return value of the separate_cifti call

Aliases
  • separate_cifti_wrapper
Documentation reproduced from package ciftiTools, version 0.1.6.0, License: GPL-3

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