meegpype.interfaces.freesurfer.mri_watershed module🔗

class meegpype.interfaces.freesurfer.mri_watershed.MRIWatershed(**inputs)🔗

Bases: FSCommand

Wrapped executable: mri_watershed.

Mandatory Inputs:

  • invol (a pathlike object or string representing an existing file) – Input volume. Maps to a command-line argument: %s (position: -2).

  • outvol (a pathlike object or string representing a file) – Output volume. Maps to a command-line argument: %s (position: -1).

Optional Inputs:

  • T1 (a boolean) – Specify T1 input volume (T1 grey value = 110). Maps to a command-line argument: -T1.

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

  • 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: {})

  • h (a float) – Precize the preflooding height (in percent). Maps to a command-line argument: -h %f.

  • n (a boolean) – Not use the watershed analyze process. Maps to a command-line argument: -n.

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

  • surf (a string) – Save the BEM surfaces. Maps to a command-line argument: -surf %s.

  • useSRAS (a boolean) – Use the SRAS coordinate system. Maps to a command-line argument: -useSRAS.

Outputs:

  • brainvol (a pathlike object or string representing an existing file) – Skull stripped brain volume.

  • surf_brain_surface (a pathlike object or string representing an existing file) – Brain surface.

  • surf_inner_skull_surface (a pathlike object or string representing an existing file) – Inner skull surface.

  • surf_outer_skin_surface (a pathlike object or string representing an existing file) – Outer skin surface.

  • surf_outer_skull_surface (a pathlike object or string representing an existing file) – Outer skull surface.