macapype.nodes.segment.AtroposN4

class macapype.nodes.segment.AtroposN4(command=None, terminal_output=None, **inputs)

Description: Wrap of antsAtroposN4.sh

Inputs:

Mandatory:

dimension

Int, default=3 , ‘Dimension’

brain_file

File, ‘brain_file’

brainmask_file

File, ‘brainmask_file’

numberOfClasses

Int, default=3, ‘numberOfClasses’

out_pref:

String, default = “segment_”, “output prefix”

Optional:

priors

List of Files, ‘priors’ (not used, will be replaced by template file)

prior_weight:

Float, default = 0, “Atropos prior segmentation weight”

Outputs:

brain_file:

File, “extracted brain from AtroposN4.sh”

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)

terminal_output

version

interfaces should implement a version property

Methods

aggregate_outputs([runtime, needed_outputs])	Collate expected outputs and apply output traits validation.
help([returnhelp])	Prints class help
input_spec	alias of macapype.nodes.segment.AtroposN4InputSpec
load_inputs_from_json(json_file[, overwrite])	A convenient way to load pre-set inputs from a JSON file.
output_spec	alias of macapype.nodes.segment.AtroposN4OutputSpec
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.

raise_exception
version_from_command

__init__(command=None, terminal_output=None, **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
references_
resource_monitor
terminal_output
version	interfaces should implement a version property