R: Resample a GIFTI file (with its ROI)

resample_gifti {ciftiTools}

R Documentation

Resample a GIFTI file (with its ROI)

Description

Perform spatial resampling of GIFTI data on the cortical surface (metric and label), or of GIFTI surface geometry data itself.

Usage

resample_gifti(
  original_fname,
  target_fname,
  hemisphere = c("left", "right"),
  file_type = NULL,
  original_res = NULL,
  resamp_res = NULL,
  resamp_method = c("barycentric", "adaptive"),
  area_original_fname = NULL,
  area_target_fname = NULL,
  ROIcortex_original_fname = NULL,
  ROIcortex_target_fname = NULL,
  sphere_original_fname = NULL,
  sphere_target_fname = NULL,
  read_dir = NULL,
  write_dir = NULL
)

resampleGIfTI(
  original_fname,
  target_fname,
  hemisphere,
  file_type = NULL,
  original_res = NULL,
  resamp_res,
  ROIcortex_original_fname = NULL,
  ROIcortex_target_fname = NULL,
  read_dir = NULL,
  write_dir = NULL
)

resamplegii(
  original_fname,
  target_fname,
  hemisphere,
  file_type = NULL,
  original_res = NULL,
  resamp_res,
  ROIcortex_original_fname = NULL,
  ROIcortex_target_fname = NULL,
  read_dir = NULL,
  write_dir = NULL
)

Arguments

`original_fname`	The GIFTI file to resample.
`target_fname`	Where to save the resampled file.
`hemisphere`	`"left"` (default) or `"right"`. An error will occur if the hemisphere indicated in the GIFTI metadata does not match.
`file_type`	`"metric"`, `"label"`, `"surf"`, or `NULL` (default) to infer from `original_fname`.
`original_res`	The resolution of the original file. If `NULL` (default), infer from the file. Alternatively, provide `sphere_original_fname` which will override `original_res`. In general, `original_res` should be used when the original file is in registration with the spheres created by the Workbench command `-surface-create-sphere`, and `sphere_original_fname` should be used when it is not compatible.
`resamp_res`	Target resolution for resampling (number of cortical surface vertices per hemisphere). Alternatively, provide `sphere_target_fname` which will override `resamp_res`. In general, `resamp_res` should be used when the target file will be in registration with the spheres created by the Workbench command `-surface-create-sphere`, and `sphere_target_fname` should be used when it is not compatible.
`resamp_method`	`"barycentric"` (default) or `"adaptive"` resampling. These options correspond to the Workbench command options `"BARYCENTRIC"` and `"ADAP_BARY_AREA"`, respectively. While adaptive resampling is recommended for metric or label data, it requires that `area_original_fname` be provided.
`area_original_fname`, `area_target_fname`	File paths to the surfaces to use for vertex area correction during adaptive resampling. (Ignored if resampling with the barycentric method.) `area_original_fname` should match the current resolution of the data, and `area_target_fname` should match `resamp_res`. If `area_target_fname` is not provided, `area_original_fname` will be resampled with the barycentric method, and the result will be used as `area_target_fname`.
`ROIcortex_original_fname`	The name of the ROI file corresponding to `original_fname`. Leave as `NULL` (default) if this doesn't exist or shouldn't be resampled.
`ROIcortex_target_fname`	The name of the resampled ROI file. Only applicable if `ROIcortex_original_fname` is provided.
`sphere_original_fname`, `sphere_target_fname`	File paths to the sphere surfaces in the original and target resolutions. If possible, the simpler arguments `original_res` and `resamp_res` can be used instead. But those depend on the surface being compatible with that created by `-surface-create-sphere`, which isn't always true. Therefore `sphere_original_fname` and `sphere_target_fname` can be used if needed.
`read_dir`	Directory to append to the path of every file name in `original_fname` and `ROIcortex_original_fname`. If `NULL` (default), do not append any directory to the path.
`write_dir`	Directory to append to the path of every file name in `target_fname` and `ROIcortex_target_fname`. If `NULL` (default), do not append any directory to the path.

Value

The resampled GIFTI file name, invisibly

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