Cluster labelling with nilearn

1

Hi everyone,
I would like to know if nilearn (or any other related package) has a function to assign anatomical label to clusters similar to atlasquery in FSL. If this exist I would prefer this not to be a wrapper around fsl or spm since I would like it to be platform independent.
Thanks in advance for any suggestion

F.

2

Hey @fednem,

maybe atlasquerpy (python version of FSL’s atlasquery) and fslpy might be helpful? As far as I know, nilearn has great functionality wrt extracting and creating ROIs from atlases and brain activations (e.g. here). I’m not aware of something related to your question. But I’m sure others will have more pointers / ideas.

HTH, best, Peer

1 Like
3

Thanks a lot for your answer, I will dig in the libraries you mentioned.

Best

F.

4

Hi Peer,

I’ve got a grouplevel correlation map that I have thresholded , which has resulted in several clusters. No I would like to write out each of those clusters as a map. Can this be done with the same function from nilearn or would you know of other functionality that could accomplish this?

Thanks,

Sebastian

5

Hi @Sebastian , did you figure out a solution to this? Thanks!

6

Hi,

I dug into the get_cluster_tables and found where the label maps are made. I have added a pull request to Nilearn to have these saved out with get_cluster_tables. See the PR here: [ENH] Add label maps as output to get_cluster_tables by smeisler · Pull Request #3477 · nilearn/nilearn · GitHub

Best,
Steven