macapype.nodes.extract_brain.T1xT2BET

class macapype.nodes.extract_brain.T1xT2BET(**inputs)

Description: Brain extraction using T1 and T2 images

Inputs:

Mandatory:

t1_file

Whole-head T1w image

t2_file

Whole-head T2w image

Optional:

opt_os

Suffix for the brain masked images (default is _BET)

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)

n

the number of iterations BET will be run to find center of gravity (n=1 if option -n is absent)

m

Will output the BET mask at the format output_prefixT1_mask.nii.gz)

ms

Suffix for the mask (default is _mask)

c

Will crop the inputs & outputs after brain extraction. c is the space between the brain and the limits of the crop box expressed in percentage of the brain size (eg. if the brain size is 200 voxels in one dimension and c=10: the sides of the brain in this dimension will be 20 voxels away from the borders of the resulting crop box in this dimension)

cs

Suffix for the cropped images (default is _cropped)

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

cog

For difficult cases, you can directly provide a center of gravity. Only one iteration will be performed.

k

Will keep temporary files

p

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

Outputs:

t1_brain_file

extracted brain from T1

t2_brain_file

extracted brain from T2

t2_coreg_file

coreg T2 from T1

mask_file

extracted mask from T1

t1_cropped_file

extracted cropped brain from T1

t2_cropped_file

extracted cropped brain from T2

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.T1xT2BETInputSpec
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.T1xT2BETOutputSpec
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_output_type(output_type)	Set the default output type for FSL classes.
set_default_terminal_output(output_type)	Set the default terminal output for CommandLine Interfaces.

raise_exception
version_from_command

__init__(**inputs)

Subclasses must implement __init__

Methods

__init__(**inputs)	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_output_type(output_type)	Set the default output type for FSL classes.
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