Workflow: 'FreeSurfer' surface reconstruction

Runs 'FreeSurfer' recon-all command underneath; must have 'FreeSurfer' installed.

Usage

cmd_run_freesurfer_recon_all(
  subject,
  mri_path,
  args = c("-all", "-autorecon1", "-autorecon2", "-autorecon3", "-autorecon2-cp",
    "-autorecon2-wm", "-autorecon2-pial"),
  work_path = NULL,
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run
)

cmd_run_freesurfer_recon_all_clinical(
  subject,
  mri_path,
  work_path = NULL,
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run,
  ...
)

Arguments

subject

'RAVE' subject or subject ID

mri_path

path to 'T1'-weighted 'MRI', must be a 'NIfTI' file

args

type of workflow; see 'FreeSurfer' recon-all command documentation; default choice is '-all' to run all workflows

work_path

working directory; 'FreeSurfer' errors out when working directory contains white spaces. By default, 'RAVE' automatically creates a symbolic link to a path that contains no white space. Do not set this input manually unless you know what you are doing

overwrite

whether to overwrite existing work by deleting the folder; default is false. In case of errors, set this to true to restart the workflow; make sure you back up the files first.

command_path

'FreeSurfer' home directory. In some cases, 'RAVE' might not be able to find environment variable 'FREESURFER_HOME'. Please manually set the path if the workflow fails. Alternatively, you can manually set FreeSurfer' home directory via 'RAVE' options raveio_setopt("freesurfer_path", "/path/to/freesurfer/home") prior to running the script

dry_run

avoid running the code, but print the process instead

verbose

print messages

...

ignored

Value

A list of shell command set.

Examples

# Requires `FreeSurfer` and only works on MacOS or Linux
# as `FreeSurfer` does not support Windows

if (FALSE) { # \dontrun{

# Create subject instance; strict=FALSE means it's OK if the subject
# is missing
subject <- as_rave_subject("YAEL/s01", strict = FALSE)

cmd_run_freesurfer_recon_all(
  subject = subject,
  mri_path = "/path/to/T1.nii.gz"
)

} # }