Read a CIFTI file by writing each component into a GIFTI and NIFTI file
(separate_cifti), optionally resampling the GIFTIs,
(resample_gifti), and then reading each separated
component into R (make_xifti). Surfaces can also be provided;
they will be resampled along with the CIFTI for viewing.
read_cifti_separate(
cifti_fname,
surfL_fname = NULL,
surfR_fname = NULL,
brainstructures = c("left", "right"),
resamp_res = NULL,
mwall_values = c(NA, NaN),
verbose = TRUE
)File path of CIFTI-format data (ending in ".d*.nii").
(Optional) File path of GIFTI surface geometry file representing the left cortex.
(Optional) File path of GIFTI surface geometry file representing the right cortex.
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.
(Optional) Target resolution for resampling (number of
cortical surface vertices per hemisphere). If NULL (default) or
FALSE, do not perform resampling.
If the medial wall locations are not indicated in the
CIFTI, use these values to infer the medial wall mask. Default:
c(NA, NaN). If NULL, do not attempt to infer the medial wall.
Should occasional updates be printed? Default: TRUE.
A "xifti" object. See is.xifti.
This function uses a system wrapper for the 'wb_command' executable. The user must first download and install the Connectome Workbench, available from https://www.humanconnectome.org/software/get-connectome-workbench .
The subcortical component (NIFTI) is not resampled.