macapype.nodes.extract_brain.AtlasBREX

class macapype.nodes.extract_brain.AtlasBREX(command=None, terminal_output=None, **inputs)

Description: Atlas based BrainExtraction

Inputs:

Mandatory:

script_atlas_BREX:

File, ‘atlasBREX script’

NMT_SS_file:

File, ‘Skullstriped version of the template’,

NMT_file:

File, ‘template img’

t1_restored_file:

File, ‘T1 image to map’

f:

Float, default = 0.5, f

reg :

Enum, default = 1,0,2,3, “Method: 0 = FNIRT w/ bending, 1 (default) = FNIRT membrane-energy regularization, 2 = ANTs/SyN w/, 3 = w/o N4Bias”

w:

String, default = “10,10,10”, “w”

msk:

String, default = “a,0,0”, “msk”,

Outputs:

brain_file:

File, “extracted brain from atlas_brex”

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.extract_brain.AtlasBREXInputSpec
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.extract_brain.AtlasBREXOutputSpec
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