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Documentation request: how are the files in cortical_coordinates generated? #44
Dear contributors to the
I am looking for a specific information about the files located in cortical_coordinates.
The process by which a curved cortical coordinate system has been obtained is documented on pages 6 and 7 of the technical white paper:
Although I find the above process clear, I cannot infer from this description how the pia and the white matter surfaces have been flattened to fit in a 2D numpy array such as those of
Many thanks in advance for your help,
As a side note:
The returned shape doesn't match the expected value of (132, 114) that is indicated in cortical_map.py.
Thanks for your questions. As for how the paths were generated, this was not part of our work but something that the team of @lydiang carried out. So I'm afraid I do not know exactly what process occured besides what you've mentioned in the whitepaper.
As for the size of
This appears to be a documentation error in
Thanks to a colleague of mine, Sirio Puchet (Blue Brain Project), I have now more insight on this question. Indeed, Sirio pointed out that some details on the flattening process are available in the section Creation of the cortical top-down and flattened views of the CCFv3 for data visualization of Hierarchical organization of cortical and thalamic connectivity (https://www.nature.com/articles/s41586-019-1716-z):
 Oliveira, G. N., Torchelsen, R. P., Comba, J. L. D., Walter, M. & Bastos, R. Geotextures: a multi-source geodesic distance field approach for procedural texturing of complex meshes. 2010 23rd SIBGRAPI Conf. Graphics, Patterns and Images 126–133 (IEEE, 2010).