macapype.nodes.correct_bias.T1xT2BiasFieldCorrection

class macapype.nodes.correct_bias.T1xT2BiasFieldCorrection(command=None, terminal_output=None, **inputs)

Description: Bias field correction using T1w & T2w images.

Provides an attempt of brain extration if wanted.

Inputs:

Mandatory:

t1_file

Whole-head T1w image

t2_file

Whole-head T2w image (use -aT2 if T2w image is not in the T1w space)

Optional:

os

Suffix for the bias field corrected images (default is “_debiased”)

aT2

Will coregrister T2w to T1w using flirt. Output will have the suffix provided. Will only work for spatially close images.

opt_as

Suffix for T2w to T1w registration (“-in-T1w” if not specified)

s

size of gauss kernel in mm when performing mean filtering (default=4)argstr=”-s %d”, mandatory=False)

b

Brain mask file. Will also output bias corrected brain files with the format “output_prefix_brain.nii.gz”

bet

Will try to “smart” BET the anat files to get a brain mask: n = the number of iterations BET will be run to find center of gravity (default=0, will not BET if option -b has been specified).

bs

Suffix for the BET masked images (default is “_BET”)

f

-f options of BET: fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline

estimates

g

-g options of BET: vertical gradient in fractional intensity threshold

(-1->1); default=0; positive values give larger brain outline at bottom, smaller at top

k

Will keep temporary files

p

Prefix for running FSL functions (can be a path or just a prefix)

Outputs:

t1_debiased_file

debiased T1

t2_debiased_file

debiased T2

t2_coreg_file

T2 on T1

t1_debiased_brain_file

debiased bet T1

t2_debiased_brain_file

debiased bet T2

debiased_mask_file

debiased bet mask

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.correct_bias.T1xT2BiasFieldCorrectionInputSpec
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.correct_bias.T1xT2BiasFieldCorrectionOutputSpec
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
package_directory
references_
resource_monitor
terminal_output
version	interfaces should implement a version property