io_mesh¶
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nighres.io.
load_mesh_geometry
(surf_mesh)[source]¶ Load a mesh geometry into a dictionary with entries “points” and “faces”
Parameters: surf_mesh – Mesh geometry to be loaded, can be a path to a file (currently supported formats are freesurfer geometry formats, gii and ASCII-coded vtk, ply or obj) or a dictionary with the keys “points” and “faces” Returns: Dictionary with a numpy array with key “points” for a Numpy array of the x-y-z coordinates of the mesh vertices and key “faces” for a Numpy array of the the indices (into points) of the mesh faces Return type: dict Notes
Originally created as part of Laminar Python [1]_
References
[1] Huntenburg et al. (2017), Laminar Python: Tools for cortical depth-resolved analysis of high-resolution brain imaging data in Python. DOI: 10.3897/rio.3.e12346
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nighres.io.
save_mesh_geometry
(filename, surf_dict)[source]¶ Saves surface mesh geometry to file
Parameters: - filename (str) – Full path and filename under which surfaces data should be saved. The extension determines the file format. Currently supported are freesurfer geometry formats, gii and ASCII-coded vtk, obj, ply’
- surf_dict (dict) – Surface mesh geometry to be saved. Dictionary with a numpy array with key “points” for a Numpy array of the x-y-z coordinates of the mesh vertices and key “faces2 for a Numpy array of the the indices (into points) of the mesh faces
Notes
Originally created as part of Laminar Python [1]_
References
[1] Huntenburg et al. (2017), Laminar Python: Tools for cortical depth-resolved analysis of high-resolution brain imaging data in Python. DOI: 10.3897/rio.3.e12346
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nighres.io.
load_mesh_data
(surf_data, gii_darray=None)[source]¶ Loads mesh data into a Numpy array
Parameters: - surf_data – Mesh data to be loaded, can be a Numpy array or a path to a file. Currently supported formats are freesurfer data formats (mgz, curv, sulc, thickness, annot, label), nii, gii, ASCII-coded vtk and txt
- gii_darray (int, optional) – Index of gii data array to load (default is to load all)
Returns: Numpy array containing the data
Return type: np.ndarray
Notes
Originally created as part of Laminar Python [1]_
References
[1] Huntenburg et al. (2017), Laminar Python: Tools for cortical depth-resolved analysis of high-resolution brain imaging data in Python. DOI: 10.3897/rio.3.e12346
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nighres.io.
save_mesh_data
(filename, surf_data)[source]¶ Saves surface data that is a Numpy array to file
Parameters: - filename (str) – Full path and filename under which surfaces data should be saved. The extension determines the file format. Currently supported are freesurfer formats curv, thickness, sulc and ASCII-coded txt’
- surf_data (np.ndarray) – Surface data to be saved
Notes
Originally created as part of Laminar Python [1]_
References
[1] Huntenburg et al. (2017), Laminar Python: Tools for cortical depth-resolved analysis of high-resolution brain imaging data in Python. DOI: 10.3897/rio.3.e12346