General mapping between volume and surface.
Subclasses have to implement node2voxels
Methods
coordinates_to_grey_distance_mm(nodes, xyz) | Computes the grey position of coordinates in metric units | ||
get_node2voxels_mapping() |
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get_parameter_dict() | Returns a dictionary with the most important parameters | ||
surf_project_nodewise(xyz) | Projects coordinates on lines connecting pial and white matter. | ||
surf_project_weights(nodes, xyz) | Computes relative position of xyz on lines from pial to white matter. | ||
surf_project_weights_nodewise(xyz) | Computes relative position of xyz on lines from pial to white matter. | ||
surf_unproject_weights_nodewise(weights) | Maps relative positions in grey matter to coordinates | ||
voxel_count_nifti_image() | Returns a NIFTI image indicating how often each voxel is selected. |
Parameters: | volgeom: volgeom.VolGeom :
white: surf.Surface :
pial: surf.Surface :
intermediate: surf.Surface (default: None). :
nsteps: int (default: 10) :
start_fr: float (default: 0) :
stop_fr: float (default: 1) :
start_mm: float (default: 0) :
stop_mm: float (default: 0) :
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Notes
‘pial’ and ‘white’ should have the same topology.
Methods
coordinates_to_grey_distance_mm(nodes, xyz) | Computes the grey position of coordinates in metric units | ||
get_node2voxels_mapping() |
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get_parameter_dict() | Returns a dictionary with the most important parameters | ||
surf_project_nodewise(xyz) | Projects coordinates on lines connecting pial and white matter. | ||
surf_project_weights(nodes, xyz) | Computes relative position of xyz on lines from pial to white matter. | ||
surf_project_weights_nodewise(xyz) | Computes relative position of xyz on lines from pial to white matter. | ||
surf_unproject_weights_nodewise(weights) | Maps relative positions in grey matter to coordinates | ||
voxel_count_nifti_image() | Returns a NIFTI image indicating how often each voxel is selected. |
Returns: | n2v: dict : A mapping from node indices to voxels. In this mapping, the : ‘i’-th node is associated with ‘n2v[i]=v2p’ which contains the : mapping from linear voxel indices to grey matter positions. In : other words, ‘n2v[i][idx]=v2p[idx]=pos’ means that the voxel with : linear index ‘idx’ is associated with node ‘i’ and has has : relative position ‘pos’ in the gray matter. : If node ‘i’ is outside the volume, then ‘n2v[i]=None’. : |
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Notes
The typical use case is selecting voxels in the grey matter. The rationale of this method is that (assuming a sufficient dense cortical surface mesh, combined with a sufficient number of nsteps, the grey matter is sampled dense enough so that ‘no voxels are left out’.
Returns a dictionary with the most important parameters of this instance
Returns a NIFTI image indicating how often each voxel is selected.
Parameters: | n2v: dict :
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Returns: | img: nifti.Nifti1Image :
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