Home · Quickstart · Documentation · Citation · NiPy

# interfaces.meshfix

## MeshFix

Link to code

Wraps command meshfix

MeshFix v1.2-alpha - by Marco Attene, Mirko Windhoff, Axel Thielscher.

See also

http://jmeshlib.sourceforge.net
  Sourceforge page
http://simnibs.de/installation/meshfixandgetfem
  Ubuntu installation instructions

If MeshFix is used for research purposes, please cite the following paper: M. Attene - A lightweight approach to repairing digitized polygon meshes. The Visual Computer, 2010. (c) Springer.

Accepted input formats are OFF, PLY and STL. Other formats (like .msh for gmsh) are supported only partially.

### Example

    >>> import nipype.interfaces.meshfix as mf
    >>> fix = mf.MeshFix()
    >>> fix.inputs.in_file1 = 'lh-pial.stl'
    >>> fix.inputs.in_file2 = 'rh-pial.stl'
    >>> fix.run()

Inputs:

    [Mandatory]
    in_file1: (an existing file name)
    terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
            Control terminal output

    [Optional]
    args: (a string)
            Additional parameters to the command
    cut_inner: (an integer)
            Remove triangles of 1st that are inside of the 2nd shell. Dilate 2nd by N; Fill holes
            and keep only 1st afterwards.
    cut_outer: (an integer)
            Remove triangles of 1st that are outside of the 2nd shell.
    decouple_inin: (an integer)
            Treat 1st file as inner, 2nd file as outer component.Resolve overlaps by moving inners
            triangles inwards. Constrain the min distance between the components > d.
    decouple_outin: (an integer)
            Treat 1st file as outer, 2nd file as inner component.Resolve overlaps by moving outers
            triangles inwards. Constrain the min distance between the components > d.
    decouple_outout: (an integer)
            Treat 1st file as outer, 2nd file as inner component.Resolve overlaps by moving outers
            triangles outwards. Constrain the min distance between the components > d.
    dilation: (an integer)
            Dilate the surface by d. d < 0 means shrinking.
    dont_clean: (a boolean)
            Don't Clean
    environ: (a dictionary with keys which are a value of type 'str' and with values which
             are a value of type 'str', nipype default value: {})
            Environment variables
    epsilon_angle: (a float)
            Epsilon angle in degrees (must be between 0 and 2)
    finetuning_distance: (a float)
            Used to fine-tune the minimal distance between surfaces.A minimal distance d is ensured,
            and reached in n substeps. When using the surfaces for subsequent volume meshing by
            gmsh, this step prevent too flat tetrahedra2)
    finetuning_inwards: (a boolean)
    finetuning_outwards: (a boolean)
            Similar to finetuning_inwards, but ensures minimal distance in the other direction
            mutually_exclusive: finetuning_inwards
    finetuning_substeps: (an integer)
            Used to fine-tune the minimal distance between surfaces.A minimal distance d is ensured,
            and reached in n substeps. When using the surfaces for subsequent volume meshing by
            gmsh, this step prevent too flat tetrahedra2)
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the interface fails to
            run
    in_file2: (an existing file name)
    join_closest_components: (a boolean)
            Join the closest pair of components.
            mutually_exclusive: join_closest_components
    join_overlapping_largest_components: (a boolean)
            Join 2 biggest components if they overlap, remove the rest.
            mutually_exclusive: join_closest_components
    laplacian_smoothing_steps: (an integer)
            The number of laplacian smoothing steps to apply
    number_of_biggest_shells: (an integer)
            Only the N biggest shells are kept
    out_filename: (a file name)
            The output filename for the fixed mesh file
    output_type: ('stl' or 'msh' or 'wrl' or 'vrml' or 'fs' or 'off', nipype default value:
             off)
            The output type to save the file as.
    quiet_mode: (a boolean)
            Quiet mode, don't write much to stdout.
    remove_handles: (a boolean)
            Remove handles
    save_as_freesurfer_mesh: (a boolean)
            Result is saved in freesurfer mesh format
            mutually_exclusive: save_as_vrml, save_as_stl
    save_as_stl: (a boolean)
            Result is saved in stereolithographic format (.stl)
            mutually_exclusive: save_as_vmrl, save_as_freesurfer_mesh
    save_as_vmrl: (a boolean)
            Result is saved in VRML1.0 format (.wrl)
            mutually_exclusive: save_as_stl, save_as_freesurfer_mesh
    set_intersections_to_one: (a boolean)
            If the mesh contains intersections, return value = 1.If saved in gmsh format,
            intersections will be highlighted.
    uniform_remeshing_steps: (an integer)
            Number of steps for uniform remeshing of the whole mesh
    uniform_remeshing_vertices: (an integer)
            Constrains the number of vertices.Must be used with uniform_remeshing_steps
    x_shift: (an integer)
            Shifts the coordinates of the vertices when saving. Output must be in FreeSurfer format

Outputs:

    mesh_file: (an existing file name)
            The output mesh file