xcp_d.interfaces.workbench.ApplyWarpfield

class xcp_d.interfaces.workbench.ApplyWarpfield(command=None, terminal_output=None, write_cmdline=False, **inputs)

Wrapped executable: wb_command -surface-apply-warpfield.

Apply warpfield to surface file.

wb_command -surface-apply-warpfield
    <in-surf> - the surface to transform
    <warpfield> - the INVERSE warpfield
    <out-surf> - output - the output transformed surface

    [-fnirt] - MUST be used if using a fnirt warpfield
        <forward-warp> - the forward warpfield

Warping a surface requires the INVERSE of the warpfield used to warp the volume it lines up with. The header of the forward warp is needed by the -fnirt option in order to correctly interpret the displacements in the fnirt warpfield.

If the -fnirt option is not present, the warpfield must be a nifti ‘world’ warpfield, which can be obtained with the -convert-warpfield command.

Mandatory Inputs:

• in_file (a pathlike object or string representing an existing file) – The input file. Maps to a command-line argument: %s (position: 0).

• warpfield (a pathlike object or string representing an existing file) – The warpfield file. Maps to a command-line argument: %s (position: 1).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

• forward_warp (a pathlike object or string representing a file) – Fnirt forward warpfield. Maps to a command-line argument: -fnirt %s (position: 3).

• out_file (a pathlike object or string representing a file) – Maps to a command-line argument: %s (position: 2).

Outputs:

out_file (a pathlike object or string representing an existing file) – Output file.

__init__(command=None, terminal_output=None, write_cmdline=False, **inputs)

Subclasses must implement __init__

Methods

__init__([command, terminal_output, ...])	Subclasses must implement __init__
aggregate_outputs([runtime, needed_outputs])	Collate expected outputs and apply output traits validation.
help([returnhelp])	Prints class help
load_inputs_from_json(json_file[, overwrite])	A convenient way to load pre-set inputs from a JSON file.
raise_exception(runtime)
run([cwd, ignore_exception])	Execute this interface.
save_inputs_to_json(json_file)	A convenient way to save current inputs to a JSON file.
set_default_terminal_output(output_type)	Set the default terminal output for CommandLine Interfaces.
version_from_command([flag, cmd])

Attributes

always_run	Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.
can_resume	Defines if the interface can reuse partial results after interruption.
cmd	sets base command, immutable
cmdline	command plus any arguments (args) validates arguments and generates command line
resource_monitor
terminal_output
version	interfaces should implement a version property
write_cmdline