Create a 'YAEL' imaging processing instance — as_yael

Image registration across different modals. Normalize brain 'T1'-weighted 'MRI' to template brain and generate subject-level atlas files. See cmd_run_yael_preprocess to see how to run a built-in workflow

Usage

as_yael_process(subject, ..., engine = c("rpyANTs", "native"))

Arguments

subject: character (subject code, or project name with subject code), or RAVESubject instance.
...: internally used
engine: which implementation to use: 'rpyANTs' (default, YAELProcess, which runs ANTs through 'Python') or 'native' (YAELNativeProcess, built on ravetools without 'Python'). Both have the same methods and read and write the same files

Value

A processing instance, see YAELProcess and YAELNativeProcess

Examples


process <- as_yael_process("YAEL/test_subject")

# the same process without 'Python'
process_native <- as_yael_process("YAEL/test_subject", engine = "native")

if (FALSE) { # \dontrun{

# Import and set original T1w MRI and CT
process$set_input_image("/path/to/T1w_MRI.nii", type = "T1w")
process$set_input_image("/path/to/CT.nii.gz", type = "CT")

# Co-register CT to MRI
process$register_to_T1w(image_type = "CT")

# Morph T1w MRI to 0.5 mm^3 MNI152 template
process$map_to_template(
  template_name = "mni_icbm152_nlin_asym_09b",
  native_type = "T1w"
)

} # }