# Generating mesh with svmtk

**URL:** <https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247>\
**Category:** mesh\
**Tags:** mesh, gmsh\
**Created:** [October 2, 2025, 5:12pm UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247 "2025-10-02T17:12:33Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![Chris\_S](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/chris_s/32/7041_2.png) [@Chris\_S](https://fenicsproject.discourse.group/u/Chris_S)\
**Post date:** [October 2, 2025, 5:12pm UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/1 "2025-10-02T17:12:33Z")

</div>

I have trouble generating a subdomain mesh as outline in an svmtk tutorial. I have been following the svmtk tutorials here “Mathematical Modeling of the Human Brain From Magnetic Resonance Images to Finite Element Simulation“ ([Mathematical Modeling of the Human Brain: From Magnetic Resonance Images to Finite Element Simulation | SpringerLink](https://link.springer.com/book/10.1007/978-3-030-95136-8)) and got the tutorial files from zenodo ( [Software for Mathematical modeling of the human brain - from magnetic resonance images to finite element simulation](https://zenodo.org/records/4899490) ). When I run “two-domain-tagged.py“ from Chapter 4, I do not get the same mesh “ernie-gw.mesh“ as provided. Instead of having two domains (green and orange) it is a single domain (orange) (see attached screenshots). I installed svmtk using conda and as outlined here: [GitHub - SVMTK/SVMTK](https://github.com/SVMTK/SVMTK) .

```auto
# two-domain-tagged.py Chapter 4
# %%
import SVMTK as svmtk 

def create_gw_mesh(pial_stl, white_stl, output):
    # Load the surfaces into SVM-Tk and combine in list
    pial = svmtk.Surface(pial_stl)
    white = svmtk.Surface(white_stl)
    surfaces = [pial, white]
    
    # Create a map for the subdomains with tags
    # 1 for inside the first and outside the second ("10")
    # 2 for inside the first and inside the second ("11")
    smap = svmtk.SubdomainMap()
    smap.add("10", 1)
    smap.add("11", 2)

    # Create a tagged domain from the list of surfaces
    # and the map
    domain = svmtk.Domain(surfaces, smap)
       
    # Create and save the volume mesh 
    resolution = 32
    domain.create_mesh(resolution)
    domain.save(output) 

create_gw_mesh("lh.pial.stl", "lh.white.stl", "ernie-gw.mesh")

# %%

```

 ![code_rerun](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/8/87474562d11ac41157aeb3a9aa6eed41b5efa584.jpeg)

 ![provided_by_zenodo](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/6/6026d5b35656e3dd9a44edb99a191a9a28344d61.jpeg)

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<div class="post-metadata">

**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\
**Post date:** [October 3, 2025, 7:30pm UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/2 "2025-10-03T19:30:23Z")

</div>

I would suggest converting the `.mesh` file with `msh` into `xdmf`, and try to visualize it in Paraview.  
As far as I am aware, GMSH doesn’t support all `.mesh` files.

---

<div class="post-metadata">

**Author:** ![Lars\_Magnus\_Valnes](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/lars_magnus_valnes/32/8901_2.png) [@Lars\_Magnus\_Valnes](https://fenicsproject.discourse.group/u/Lars_Magnus_Valnes)\
**Post date:** [October 4, 2025, 11:40am UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/3 "2025-10-04T11:40:44Z")

</div>

The CGAL/SVMTK mesh format is not compatible with GMSH. If you want to visualize it with gmsh,  
you should convert it by using e.g. meshio (v5.3.5):

```bash
meshio convert ernie-gw.mesh ernie-gw.msh --output-format gmsh22

```

If you want to visualize it in Paraview, I recommend using the conversion in the book.

---

<div class="post-metadata">

**Author:** ![Chris\_S](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/chris_s/32/7041_2.png) [@Chris\_S](https://fenicsproject.discourse.group/u/Chris_S)\
**Post date:** [October 6, 2025, 8:07pm UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/4 "2025-10-06T20:07:55Z")

</div>

Great that worked well! I am now trying to import into fenicsx but I noticed that the bounding surface aren’t properly associated when I have multidomain geometries. How do I get the geometry alongside all the surfaces ready for fenicsx use?

```auto
(base) chris@gondor:/mnt/shared/chris/Projects/2024_PhysicsAug/code/svmtk_meshing/stl_files$ meshio convert combined_final.mesh combined_final.msh --output-format gmsh22
Warning: Appending zeros to replace the missing physical tag data.
Warning: Appending zeros to replace the missing geometrical tag data.

```

---

<div class="post-metadata">

**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\
**Post date:** [October 6, 2025, 8:25pm UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/5 "2025-10-06T20:25:24Z")

</div>

I would have a look at:  
[mri2fem-ii-chapter-3-code/meshing at main · mhornkjol/mri2fem-ii-chapter-3-code · GitHub](https://github.com/mhornkjol/mri2fem-ii-chapter-3-code/tree/main/meshing) (Create and convert mesh) and [mri2fem-ii-chapter-3-code/dolfinx\_implementation/stokes\_solver.py at main · mhornkjol/mri2fem-ii-chapter-3-code · GitHub](https://github.com/mhornkjol/mri2fem-ii-chapter-3-code/blob/main/dolfinx_implementation/stokes_solver.py#L334)  
These scripts are from the upcoming book mri2fem -part 2

---

<div class="post-metadata">

**Author:** ![Chris\_S](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/chris_s/32/7041_2.png) [@Chris\_S](https://fenicsproject.discourse.group/u/Chris_S)\
**Post date:** [October 7, 2025, 3:47pm UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/6 "2025-10-07T15:47:50Z")

</div>

Thanks so much, looking forward to the new book!

Just FYI, I am getting couple syntax errors when trying to run create\_mesh.py:

```auto
line 75
    aqueduct.clip(clp1, invert=True ))
                                     ^
SyntaxError: unmatched ')'

line 41, in <module>
    white = svm.Surface(Z.white) 
NameError: name 'Z' is not defined

```

---

<div class="post-metadata">

**Author:** ![Chris\_S](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/chris_s/32/7041_2.png) [@Chris\_S](https://fenicsproject.discourse.group/u/Chris_S)\
**Post date:** [October 9, 2025, 5:17am UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/7 "2025-10-09T05:17:08Z")

</div>

Thanks for the help. Here is the pipeline I used for others to follow

1. Generate mesh from stl files using svmtk
2. convert .mesh file to xdmf
3. Use xdmf for fenics simulation

Step2: Conversion

```auto
import meshio
import argparse
from pathlib import Path

def convert_mesh(infile: Path, outfile: Path):
    msh = meshio.read(infile)

    # try:
    tmp_dir = Path(".tmp")
    tmp_dir.mkdir(exist_ok=True)

    cell_mesh = meshio.Mesh(
        points=msh.points,
        cells={"tetra": msh.cells_dict["tetra"]},
        cell_data={"subdomains": [msh.cell_data_dict["medit:ref"]["tetra"]]},
    )

    meshio.write(outfile.with_suffix(".xdmf"), cell_mesh)

    facet_mesh = meshio.Mesh(
        points=msh.points,
        cells={"triangle": msh.cells_dict["triangle"]},
        cell_data={"patches": [msh.cell_data_dict["medit:ref"]["triangle"]]},
    )
    facet_file = (
        outfile.with_stem(outfile.stem + "_facets").with_suffix(".xdmf").absolute().as_posix()
    )
    meshio.write(facet_file, facet_mesh)

if __name__ == " __main__":
    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument(
        "-i",
        "--input",
        type=Path,
        dest="infile",
        help="Path to input mesh file",
        default="./stl_files/combined_final.mesh",
    )
    parser.add_argument(
        "-o",
        "--output",
        type=Path,
        dest="outfile",
        help="Path to output mesh file",
        default="./stl_files/combined_final.xdmf",
    )

    parsed_args = parser.parse_args()
    convert_mesh(parsed_args.infile, parsed_args.outfile)

```

---

<div class="post-metadata">

**Author:** ![Lars\_Magnus\_Valnes](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/lars_magnus_valnes/32/8901_2.png) [@Lars\_Magnus\_Valnes](https://fenicsproject.discourse.group/u/Lars_Magnus_Valnes)\
**Post date:** [October 10, 2025, 9:45am UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/8 "2025-10-10T09:45:10Z")

</div>

Thanks for sharing, much appreciated ! Working on fixing the problems.

---

<div class="post-metadata">

**Author:** ![Chris\_S](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/chris_s/32/7041_2.png) [@Chris\_S](https://fenicsproject.discourse.group/u/Chris_S)\
**Post date:** [October 13, 2025, 4:53am UTC](https://fenicsproject.discourse.group/t/generating-mesh-with-svmtk/18247/9 "2025-10-13T04:53:59Z")

</div>

Thank you! I saw couple changes on the repo and tried running it, it all runs great (I think there was import argparse missing in one). The meshes come out well but I have trouble getting well formed boundaries, with boundaries not aligning with the volumes