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miykael / atlasreader

Python interface for generating coordinate tables and region labels from statistical MRI images
BSD 3-Clause "New" or "Revised" License
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Ideas for other atlases? #57

Open miykael opened 5 years ago

miykael commented 5 years ago

During a discussion with a colleague, I was asked if atlasreader also gives out all the brodmann areas. In this context, he also told me that he would be interested in the colin27, Conte69, and PALS atlas.

Without too much overloading the data/atlas folder, which other atlases do you think we should include?

Does anyone know where we can easily and without license issue get the colin27, conte69 or PALS atlas? Or one that has all BA in MNI space?

miykael commented 5 years ago

I just saw that the Talairach atlas would also include BA. FSL provides a Talairach atlas that is in MNI space, but I have no idea how good it actually is: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases

Should we include this one as well?

miykael commented 5 years ago

Amendment: https://github.com/miykael/atlasreader/pull/67 will add the talairach atlas, as well as the AICHA atlas.

miykael commented 5 years ago

Looking through Table 1 of Eickhoff, Yeo & Genon (2018). Imaging-based parcellations of the human brain, I think it would be good if we coud also include the MarsAtlas (i.e. MarsAtlas-Colin27-MNI). But I wasn't able to access the mentioned homepage: http://meca-brain.org/software/marsatlas-colin27/

Does anyone of you have more luck or can provide the atals directly?

miykael commented 5 years ago

I was able to download the MarsAtlas in the meantime and created a PR to add it to atlasreader. In my opinion, we can close this issue, after merging/closing of PR https://github.com/miykael/atlasreader/pull/78.

PeerHerholz commented 5 years ago

Sounds good to me. From my experience within ALPACA I think that a certain variety of atlases is helpful and informative, but can, of course, become overwhelming quite easily. However, including atlases based on different modalities (e.g., functional, structural, resting state, etc.) is IMHO important. That being said, how about using the HCP atlas? There's a FreeSurfer fsaverage and MNI152 version. If folks are interested, I'm happy to implement them.

miykael commented 5 years ago

Would be great if you could implement the HCP atlas. As we try to have everything MNI152 conform, I think it makes sense to use this version.

And you're right, so far I've tried to avoid functional and resting state atlases (not my field of expertise). But it probably makes sense to also include the most prominent of them. Additionally to the HCP atlas, which ones would that be and would you like to do this? (I think the Shen et al. (2013) and Power et al. (2011) (the 17 parcellations one) atlases might be easy to implement.

The only problem I see is that some of well known atlases (Yeo,) are surface-based which might not be ideal for atlasreader, for example.

danjgale commented 5 years ago

Another potential atlas is the Glasser parcelation. I'm not sure how broadly it is used in the literature, but we have had success with it in our lab. When my schedule gets less crazy after SfN I could look to implement this.

seralouk commented 2 years ago

Another potential atlas is the Glasser parcelation. I'm not sure how broadly it is used in the literature, but we have had success with it in our lab. When my schedule gets less crazy after SfN I could look to implement this.

Integration of the Glasser atlas in this module would be great. Glasser remains one of the state of the art atlases in the field.