RegionOfInterest

Used for the definition of regions of interests on surfaces and in volumes. Please see also roi_definition.py and roi_definition.m in examples/utilities for usage examples.

Initialization

• Python

  from simnibs import opt_struct
  
  # TmsFlexOptimization
  opt = opt_struct.TmsFlexOptimization()
  roi = opt.add_region_of_interest()
  
  # TesFlexOptimization
  opt = opt_struct.TesFlexOptimization()
  roi = opt.add_roi()
  

• MATLAB

  % TmsFlexOptimization
  opt = opt_struct('TmsFlexOptimization');
  opt.roi{1} = opt_struct('RegionOfInterest');
  
  % TesFlexOptimization
  opt = opt_struct('TesFlexOptimization');
  opt.roi{1} = opt_struct('RegionOfInterest');
  

Parameters and attributes

class simnibs.utils.region_of_interest.RegionOfInterest(settings_dict=None)

A class describing a region of Interest in a volume mesh or a surface mesh.

Parameters:

settings_dict: (optional) dict

Dictionary containing parameter as key value pairs

method: str

The method to create the ROI {“manual”, “custom”, “surface”, “volume”, “volume_from_surface”, “mesh+mask”}

subpath: str | None

Path to the m2m folder of the subject (example: “path/to/m2m”)

mesh: str | Msh | None

Path to a mesh or a mesh instance (example: “path/to/msh” | mesh_instance)

mask_space: str | list[str] | None

The space the mask is defined in, method = “surface” : {“subject”, “subject_lh”, “fs_avg_lh”, “subject_rh”, “fs_avg_rh”, “mni”} | method = “volume” : {“subject”, “mni”}

mask_path: str | list[str] | None

The path to the mask, method = “surface” : (label, annot, curv, nifti) | method = “volume” : (nifti) (example: “path/to/file”)

mask_value: int | list[int] | None

The values that are considered as the mask in the mask files, default 1 (example: 1 | [1, 2])

mask_operator: str | list[str] | None

The operator to combine the mask with the ROI {“union”, “intersection”, “difference”}, default “union”

roi_sphere_center: list[float] | list[list[float]] | None

Sphere center coordinates for spherical masks in mm (example: [0,0,0] | [[1,2,3], [4,5,6]])

roi_sphere_radius: float | list[float] | None

The radius of the spherical masks in mm (example: 5 | [3, 45])

roi_sphere_center_space: str | list[str] | None

The space the center coordinates of the spheres are defined in {“subject”, “mni”}

roi_sphere_operator: str | list[str] | None

The operator to combine the mask with the ROI {“union”, “intersection”, “difference”}, default “union”

nodes: list[list[float]] | None

Only for method = “custom” -> a custom list of node coordinates (example: [[1.1, 2.2, 3.3], [4.4, 5.5, 6.6]])

surface_type: str | None

Only for method = “surface” -> Weather the surface is the subject specific central gm surface or a custom surface {“central”, “custom”}

surface_path: str | None

Only for method = “surface” -> Only for surface_type = “custom” -> The path to a custom surface (msh, freesurfer, gifti)

tissues: int | list[int] | ElementTags | list[ElementTags] | None

Only for method = “volume” -> a number of volume tissue tags, default 2 (example: ElementTags.GM | [ElementTags.WM, ElementTags.GM])

surface_inclusion_radius: float | None

Only for method = “volume_from_surface” -> The radius from the surface nodes at which the volume elements should be included in mm (example: 5)

node_mask: list[bool] | None

Only for method = “mesh+mask” -> a boolean node mask (exclusive with elm_mask) (example: [True, …, False])

elm_mask: list[bool] | None

Only for method = “mesh+mask” -> a boolean node mask (exclusive with node_mask) (example: [True, …, False])