Mesh-to-NIfTI conversion using the SimNIBS Python API.
Wraps simnibs.transformations so that the simulation pipeline can
convert .msh meshes to volumetric NIfTI files without shelling out
to bash scripts.
msh_to_nifti
Convert a single mesh to subject-space NIfTI.
msh_to_mni
Convert a single mesh to MNI-space NIfTI.
convert_mesh_dir
Batch-convert every .msh file in a directory.
tit.tools.nifti_to_mesh : Inverse operation (NIfTI to surface mesh).
tit.tools.field_extract : Extract tissue sub-meshes before conversion.
msh_to_nifti(mesh_path: str, m2m_dir: str, output_path: str, fields: list[str] | None = None) -> None
Convert a mesh file to subject-space NIfTI.
mesh_path : str
Path to the .msh file.
m2m_dir : str
Path to the m2m_{subject} directory (used as reference grid).
output_path : str
Output file prefix. SimNIBS appends the field name
(e.g. prefix_magnE.nii.gz).
fields : list[str] | None
If given, only these fields are written. Otherwise all fields in the
mesh are converted.
Source code in tit/tools/mesh2nii.py
| def msh_to_nifti(
mesh_path: str,
m2m_dir: str,
output_path: str,
fields: list[str] | None = None,
) -> None:
"""Convert a mesh file to subject-space NIfTI.
Parameters
----------
mesh_path : str
Path to the ``.msh`` file.
m2m_dir : str
Path to the ``m2m_{subject}`` directory (used as reference grid).
output_path : str
Output file prefix. SimNIBS appends the field name
(e.g. ``prefix_magnE.nii.gz``).
fields : list[str] | None
If given, only these fields are written. Otherwise all fields in the
mesh are converted.
"""
mesh = mesh_io.read_msh(mesh_path)
if fields:
mesh = _filter_mesh_fields(mesh, fields)
transformations.interpolate_to_volume(mesh, m2m_dir, output_path)
|
msh_to_mni(mesh_path: str, m2m_dir: str, output_path: str, fields: list[str] | None = None) -> None
Convert a mesh file to MNI-space NIfTI.
mesh_path : str
Path to the .msh file.
m2m_dir : str
Path to the m2m_{subject} directory.
output_path : str
Output file prefix. SimNIBS appends the field name
(e.g. prefix_magnE.nii.gz).
fields : list[str] | None
If given, only these fields are written.
Source code in tit/tools/mesh2nii.py
| def msh_to_mni(
mesh_path: str,
m2m_dir: str,
output_path: str,
fields: list[str] | None = None,
) -> None:
"""Convert a mesh file to MNI-space NIfTI.
Parameters
----------
mesh_path : str
Path to the ``.msh`` file.
m2m_dir : str
Path to the ``m2m_{subject}`` directory.
output_path : str
Output file prefix. SimNIBS appends the field name
(e.g. ``prefix_magnE.nii.gz``).
fields : list[str] | None
If given, only these fields are written.
"""
if fields:
mesh = mesh_io.read_msh(mesh_path)
mesh = _filter_mesh_fields(mesh, fields)
mesh_path = _write_temp_mesh(mesh)
transformations.warp_volume(mesh_path, m2m_dir, output_path)
|
convert_mesh_dir(mesh_dir: str, output_dir: str, m2m_dir: str, fields: list[str] | None = None, skip_patterns: list[str] | None = None) -> None
Batch-convert every .msh file in mesh_dir to NIfTI.
For each mesh two NIfTI sets are produced:
{basename}_subject_{field}.nii.gz – subject space{basename}_MNI_{field}.nii.gz – MNI space
mesh_dir : str
Directory containing .msh files.
output_dir : str
Where the NIfTI files are written.
m2m_dir : str
Path to the m2m_{subject} directory.
fields : list[str] | None
If given, only these fields are converted.
skip_patterns : list[str] | None
Basenames containing any of these substrings are skipped.
Defaults to ["normal"] (surface-only meshes have no volume
elements).
Source code in tit/tools/mesh2nii.py
| def convert_mesh_dir(
mesh_dir: str,
output_dir: str,
m2m_dir: str,
fields: list[str] | None = None,
skip_patterns: list[str] | None = None,
) -> None:
"""Batch-convert every ``.msh`` file in *mesh_dir* to NIfTI.
For each mesh two NIfTI sets are produced:
* ``{basename}_subject_{field}.nii.gz`` – subject space
* ``{basename}_MNI_{field}.nii.gz`` – MNI space
Parameters
----------
mesh_dir : str
Directory containing ``.msh`` files.
output_dir : str
Where the NIfTI files are written.
m2m_dir : str
Path to the ``m2m_{subject}`` directory.
fields : list[str] | None
If given, only these fields are converted.
skip_patterns : list[str] | None
Basenames containing any of these substrings are skipped.
Defaults to ``["normal"]`` (surface-only meshes have no volume
elements).
"""
if skip_patterns is None:
skip_patterns = ["normal"]
os.makedirs(output_dir, exist_ok=True)
msh_files = sorted(f for f in os.listdir(mesh_dir) if f.endswith(".msh"))
if not msh_files:
logger.warning("No .msh files found in %s", mesh_dir)
return
for fname in msh_files:
base = os.path.splitext(fname)[0]
if any(p in base for p in skip_patterns):
logger.debug("Skipping surface mesh: %s", fname)
continue
mesh_path = os.path.join(mesh_dir, fname)
mesh = mesh_io.read_msh(mesh_path)
# When filtering fields, write a temp mesh for warp_volume
# (it only accepts file paths, not in-memory mesh objects).
warp_path = mesh_path
if fields:
mesh = _filter_mesh_fields(mesh, fields)
warp_path = _write_temp_mesh(mesh)
subject_prefix = os.path.join(output_dir, f"{base}_subject")
mni_prefix = os.path.join(output_dir, f"{base}_MNI")
logger.debug("Converting %s → subject space", fname)
transformations.interpolate_to_volume(mesh, m2m_dir, subject_prefix)
logger.debug("Converting %s → MNI space", fname)
transformations.warp_volume(warp_path, m2m_dir, mni_prefix)
if warp_path != mesh_path:
os.unlink(warp_path)
logger.info("NIfTI conversion complete: %s", output_dir)
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