Inter-species correspondences in primates' cortical morphology
Here are the scripts resulting from the 7 weeks-internship I had the chance to do with Olivier COULON and Kep Kee LOH in the Methods and Computational Anatomy (MeCA) team at the Institut de Neurosciences de la Timone, Marseille in June 2020.
Using the Cortical Surface toolbox that the team has developed and which is available on the software BrainVisa (http://meca-brain.org/software/) my goal was to develop a computational tool that would enable inter-species cortical surface matching. Meaning that given the sulci-induced HIPHOP parameterization models of different primate species, the code is to rescale the longitude and latitude textures of the primate we want to map a texture (of another species) onto, so that next we can obtain a spherical mesh from it that still needs to be resampled and then remeshed to a cortical mesh. The overall idea is detailed in the report of the internship that you will find in this repository.
More specifically, here is what the different scripts do:
- read_file.py contains functions that read text files such that HIP-HOP models (read_model) in their default generated format, correspondence tables (read_corr), and the affine transformations text files that are returned by the present code (read_affine). This code is called by the other ones and has no use on its own.
- PrimateToPrimate.py was the first version of the code and can be ignored. It is however functional. It computes the affine transformations and use them to rescale the corresponding longitudes and latitudes all at once.
- Affine_transformations.py Given two models and a correspondences text file, it returns the two text files of the affine transformations from one primate to the other and the other way around. It must be called by 'Affine_transformations.py 'speciesA' 'speciesB' 'side'' (the order of species A and speciesB does not matter, 'side' can be 'L' or 'R')
- Rescale.py uses the affine transformations returned in the text files to rescale the longitude and latitude textures of the corresponding primate. It must be called by 'Rescale.py PrimateA' 'PrimateB' 'side'' (the order of PrimateA and ¨PrimateB matters as it will rescale speciesB textures to match soeciesA). However it does not work with the database format, hence files will need to be renamed to match the affine transformations files to rescale individual textures.
- Affine_trans_compo.py is a more sophisticated version of Affine_transformations.py as it uses an intermediary model to compute the affine transformations. Hence it needs three models and three correpondences text files as inputs. For instance, it can help reparameterizing the macaque's cortical mesh thanks to the putative sulci correspondences between the human and the macaque, the macaque and the chimpanzee and the chimpanzee and the human. It must be called by 'Affine_trans_compo.py 'speciesA' 'speciesB' 'speciesC' 'side'' and will write the affine transformations to rescale speciesC to match speciesA using correspondences with speciesB as well (the order matters as, contrary to Affine_transformation.py, it computes only one way).
- Iterate.py must be called as It must be called by 'Iterate.py 'speciesA' 'speciesB' 'side'' or 'Iterate.py 'speciesA' 'speciesC' 'side' 'speciesB'' if used for the composition. It enables to rescale the longitude and latitude textures of all individuals of a model, in a Database that has the following shape:
where speciesA, speciesB, speciesC are for instance 'macaque', 'chimp' or 'human' and ind_a can be 'cerimed_cesar' or any other individual of speciesA, or even 'average_macaque'. The examples are written for the left hemisphere but it suffies to replace 'L' with 'R' in the files' names to obtain the right hemisphere files.
The directories for the different species are necessary and need to be complete, as well as the correspondence text files, however all other directories and files are created by the code if used in the right order (Affine_transformations.py or Affine_trans_compo.py before Iterate.py), while Rescale.py needs to be in the same directory as all the files needed (initial textures and affine transformations) and writes the new textures where the code is (basically it does not use the database format).