Open AhmetNSimsek opened 6 months ago
Thank you for the request, @AhmetNSimsek. It would be very interesting to integrate this into openMINDS.
I had a look at the resources you linked here and additional ones that I found online. To me, it seems that the MarsAtlas is a model/a parcellation scheme. It is not a complete brain atlas in itself. We have registered parcellation schemes (i.e., Brodman) in openMINDS, so we should be able to do this in a similar way for the MarsAtlas.
I am curious about the resources that you linked and how these have been produced. colin27-marsatlas-labelled.json seems to be a representation of the MarsAtlas parcellation scheme in the MNI Colin 27 space. Has the MarsAtlas model been applied to the template data to produce the volume (https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/temp/MarsAtlas/colin27_MNI_MarsAtlas.nii)? Or has a pre-existing volume been transform into the MNI space?
@UlrikeS91 thanks for pushing this. @AhmetNSimsek as discussed MarsAtlas is a deterministic brain atlas (normally autogenerated on a subject space). For openMINDS we will register MarsAtlas with Colin27 as common coordinate space. @AhmetNSimsek what is the status? do you need help? we can meet to further discuss.
Thank you @UlrikeS91 and @lzehl. Excuse me for returning to you so late.
To me, it seems that the MarsAtlas is a model/a parcellation scheme. It is not a complete brain atlas in itself
I am not sure how do you differentiate a complete atlas and a parcellation scheme. Could you elaborate?
colin27-marsatlas-labelled.json seems to be a representation of the MarsAtlas parcellation scheme in the MNI Colin 27 space
The jsons I linked are configuration files made for siibra-toolsuite. We create such files for parcellations, atlases, features, spaces and more. So these files are generated from original source material to be in the format siibra can digest.
The nifti file you are referring to is available at http://meca-brain.org/software/marsatlas-colin27. We just stored it in a data-proxy due to the way it was stored (technical limitations).
For openMINDS we will register MarsAtlas with Colin27 as common coordinate space.
Maybe we should have a short meeting to discuss this because from what I understand, it is not a common coordinate space.
EDIT: Perhaps MarsAtlas is not a good starting point due to these ambiguities. We could take a look at another parcellations that are supported in siibra but not registered in openMINDS yet.
To clarify a bit:
Brain atlases according to the Atlas Ontology Model (AtOM) must have:
The MarsAtlas fulfills all these requirements:
The usual use case, would require us to register one MarsAtlas version for each patient. However, as a generic example MarsAtlas provides one application to the coordinate space and reference data of the Colin27 reference brain.
So for the atlas registration in openMINDS we only register the Colin27 case
Thank you for the clarification and discussion on Zoom, @lzehl. Based on our conversation, it is easier for me to continue in the following order: 1) Convert the AAL atlas from openMINDS to siibra configuration. (tracked here). I will create a script as generic as possible for this purpose. 2) Create a PR to openMINDS for MarsAtlas on Colin27. 3) Recreate the siibra configuration for MarsAtlas using the script from 1.
siibra team created MarsAtlas based on http://meca-brain.org/software/marsatlas/. The color map and the subcortical structures are taken from http://meca-brain.org/software/marsatlas-subcortical/. Could we validate and integrate it to openMINDS?
Publication: MarsAtlas: A cortical parcellation atlas for functional mapping