aslprep.interfaces.freesurfer module

SynthStrip interfaces

class FixHeaderSynthStrip(**inputs)

Bases: SynthStrip

Wrapped executable: mri_synthstrip.

Mandatory Inputs:

input_image (a pathlike object or string representing an existing file) – Maps to a command-line argument: -i %s.

Optional Inputs:

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

• border (an integer) – Mask border threshold in mm. Default is 1. Maps to a command-line argument: -b %d.

• 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: {})

• gpu (a boolean) – Maps to a command-line argument: -g.

• no_csf (a boolean) – Exclude CSF from brain border. Maps to a command-line argument: --no-csf.

• num_threads (an integer) – Allows for specifying more threads.

• out_brain (a pathlike object or string representing a file) – Skull stripped image with corrupt sform. Maps to a command-line argument: -o %s.

• out_brain_mask (a pathlike object or string representing a file) – Mask image with corrupt sform. Maps to a command-line argument: -m %s.

• subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

Outputs:

• out_brain (a pathlike object or string representing an existing file)

• out_brain_mask (a pathlike object or string representing an existing file)

class MockSynthStrip(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

input_image (a pathlike object or string representing an existing file) – Maps to a command-line argument: -i %s.

Optional Inputs:

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

• border (an integer) – Mask border threshold in mm. Default is 1. Maps to a command-line argument: -b %d.

• 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: {})

• gpu (a boolean) – Maps to a command-line argument: -g.

• no_csf (a boolean) – Exclude CSF from brain border. Maps to a command-line argument: --no-csf.

• num_threads (an integer) – Allows for specifying more threads.

• out_brain (a pathlike object or string representing a file) – Skull stripped image with corrupt sform. Maps to a command-line argument: -o %s.

• out_brain_mask (a pathlike object or string representing a file) – Mask image with corrupt sform. Maps to a command-line argument: -m %s.

• subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

Outputs:

• out_brain (a pathlike object or string representing an existing file)

• out_brain_mask (a pathlike object or string representing an existing file)

class PrepareSynthStripGrid(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

input_image (a pathlike object or string representing an existing file)

Outputs:

prepared_image (a pathlike object or string representing an existing file)

class SynthStrip(**inputs)

Bases: FSCommandOpenMP

Wrapped executable: mri_synthstrip.

Mandatory Inputs:

input_image (a pathlike object or string representing an existing file) – Maps to a command-line argument: -i %s.

Optional Inputs:

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

• border (an integer) – Mask border threshold in mm. Default is 1. Maps to a command-line argument: -b %d.

• 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: {})

• gpu (a boolean) – Maps to a command-line argument: -g.

• no_csf (a boolean) – Exclude CSF from brain border. Maps to a command-line argument: --no-csf.

• num_threads (an integer) – Allows for specifying more threads.

• out_brain (a pathlike object or string representing a file) – Skull stripped image with corrupt sform. Maps to a command-line argument: -o %s.

• out_brain_mask (a pathlike object or string representing a file) – Mask image with corrupt sform. Maps to a command-line argument: -m %s.

• subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

Outputs:

• out_brain (a pathlike object or string representing an existing file)

• out_brain_mask (a pathlike object or string representing an existing file)