Source code for osl_dynamics.utils.filenames
"""Filename containers for M/EEG processing pipelines."""
import os
from typing import Optional
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class SurfaceFilenames:
"""Container for surface extraction file paths.
Parameters
----------
root : str
Root directory for surface files.
"""
def __init__(self, root: str):
os.makedirs(root, exist_ok=True)
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self.fsl_dir = os.environ["FSLDIR"]
# Nifti files
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self.mri_file = f"{root}/smri.nii.gz"
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self.std_brain = f"{self.fsl_dir}/data/standard/MNI152_T1_1mm_brain.nii.gz"
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self.std_brain_bigfov = (
f"{self.fsl_dir}/data/standard/MNI152_T1_1mm_BigFoV_facemask.nii.gz"
)
# Transformations
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self.mni_mri_t_file = f"{root}/mni_mri-trans.fif"
# BET mesh / surfaces
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self.bet_outskin_mesh_vtk_file = f"{root}/outskin_mesh.vtk"
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self.bet_inskull_mesh_vtk_file = f"{root}/inskull_mesh.vtk"
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self.bet_outskull_mesh_vtk_file = f"{root}/outskull_mesh.vtk"
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self.bet_outskin_mesh_file = f"{root}/outskin_mesh.nii.gz"
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self.bet_outskin_plus_nose_mesh_file = f"{root}/outskin_plus_nose_mesh.nii.gz"
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self.bet_inskull_mesh_file = f"{root}/inskull_mesh.nii.gz"
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self.bet_outskull_mesh_file = f"{root}/outskull_mesh.nii.gz"
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class CoregFilenames:
"""Container for coregistration file paths.
Parameters
----------
root : str
Root directory for coregistration files.
"""
def __init__(self, root: str):
os.makedirs(root, exist_ok=True)
# Nifti files
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self.mri_file = f"{root}/scaled_mri.nii.gz"
# Fif files
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self.info_fif_file = f"{root}/info-raw.fif"
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self.head_scaledmri_t_file = f"{root}/head_scaledmri-trans.fif"
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self.head_mri_t_file = f"{root}/head_mri-trans.fif"
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self.ctf_head_mri_t_file = f"{root}/ctf_head_mri-trans.fif"
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self.mrivoxel_scaledmri_t_file = f"{root}/mrivoxel_scaledmri_t_file-trans.fif"
# Fiducials / headshape points
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self.mri_nasion_file = f"{root}/mri_nasion.txt"
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self.mri_rpa_file = f"{root}/mri_rpa.txt"
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self.mri_lpa_file = f"{root}/mri_lpa.txt"
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self.head_nasion_file = f"{root}/head_nasion.txt"
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self.head_rpa_file = f"{root}/head_rpa.txt"
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self.head_lpa_file = f"{root}/head_lpa.txt"
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self.head_headshape_file = f"{root}/head_headshape.txt"
# Freesurfer mesh in native space
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self.bet_outskin_surf_file = f"{root}/scaled_outskin.surf"
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self.bet_outskin_plus_nose_surf_file = f"{root}/scaled_outskin_plus_nose.surf"
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self.bet_inskull_surf_file = f"{root}/scaled_inskull.surf"
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self.bet_outskull_surf_file = f"{root}/scaled_outskull.surf"
# BET mesh / surfaces in native space
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self.bet_outskin_mesh_vtk_file = f"{root}/scaled_outskin_mesh.vtk"
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self.bet_inskull_mesh_vtk_file = f"{root}/scaled_inskull_mesh.vtk"
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self.bet_outskull_mesh_vtk_file = f"{root}/scaled_outskull_mesh.vtk"
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self.bet_outskin_mesh_file = f"{root}/scaled_outskin_mesh.nii.gz"
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self.bet_outskin_plus_nose_mesh_file = (
f"{root}/scaled_outskin_plus_nose_mesh.nii.gz"
)
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self.bet_inskull_mesh_file = f"{root}/scaled_inskull_mesh.nii.gz"
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self.bet_outskull_mesh_file = f"{root}/scaled_outskull_mesh.nii.gz"
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class OSLFilenames:
"""Container for all pipeline file paths for processing a single M/EEG session.
Parameters
----------
outdir : str
Base output directory.
id : str
Session identifier.
preproc_file : str
Path to the preprocessed data file.
surfaces_dir : str
Path to the surfaces directory.
pos_file : str, optional
Path to a .pos file (only needed for CTF data).
elc_file : str, optional
Path to an .elc file (alternative format for head shape points
from CTF data).
"""
def __init__(
self,
outdir: str,
id: str,
preproc_file: str,
surfaces_dir: str,
pos_file: Optional[str] = None,
elc_file: Optional[str] = None,
):
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self.preproc_file = preproc_file
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self.surfaces_dir = surfaces_dir
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self.surfaces = SurfaceFilenames(surfaces_dir)
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self.bem_dir = f"{outdir}/{id}/bem"
os.makedirs(self.bem_dir, exist_ok=True)
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self.coreg_dir = f"{outdir}/{id}/coreg"
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self.coreg = CoregFilenames(self.coreg_dir)
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self.fwd_model = f"{self.coreg_dir}/model-fwd.fif"
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self.pos_file = pos_file
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self.elc_file = elc_file
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self.src_dir = f"{outdir}/{id}/src"
os.makedirs(self.src_dir, exist_ok=True)
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self.filters = f"{self.src_dir}/filters-lcmv.h5"
def __str__(self) -> str:
lines = [
f"OSLFilenames for {self.id}:",
f" Output directory: {self.outdir}",
f" Preprocessed file: {self.preproc_file}",
f" Surfaces directory: {self.surfaces_dir}",
f" BEM directory: {self.bem_dir}",
f" Coreg directory: {self.coreg_dir}",
f" \u2514\u2500 Forward model: {self.fwd_model}",
f" Source directory: {self.src_dir}",
f" \u2514\u2500 lcmv filters: {self.filters}",
]
if self.pos_file is not None:
lines += [
f" pos file: {self.pos_file}",
]
if self.elc_file is not None:
lines += [
f" elc file: {self.elc_file}",
]
return "\n".join(lines)
def __repr__(self) -> str:
return f"<OSLFilenames id='{self.id}' outdir='{self.outdir}'>"
