Creating a mask of one ICA component with nilearn

1

Hello everyone,

I am relatively new to nilearn and have a few questions.

  1. I did a canICA via nilearn with my resting state data and now i would like to create a mask out of only one component (e.g. the default mode network) but i do not now how to do that properly. Can somebody help?

  2. Later on, i would like to combine my mask of the ICA component with regions from an atlas to get the functional connectivity matrices of these regions altogether. Is it possible to create a combined mask out of atlas regions and ica components?

It would be awesome if somebody could help me!

Best,
Maria

2

Hi,

I did a canICA via nilearn with my resting state data and now i would like to create a mask out of only one component (e.g. the default mode network) but i do not now how to do that properly. Can somebody help?

Since this would be a continuous valued map and unthresholded, I advice to use some form of threshold that component image using nilearn.image.threshold_img and use nilearn.masking.compute_background_mask on the thresholded image to get a mask of network that survived this threshold.

Later on, i would like to combine my mask of the ICA component with regions from an atlas to get the functional connectivity matrices of these regions altogether. Is it possible to create a combined mask out of atlas regions and ica components?

What sort of atlas is it? Is it ICA-like or regions that are defined as labels (integers)?

Hope this helps atleast partially

Best wishes

3

Thanks for your help !

I will try that. But i guess, it would be probably easier to just use an ICA component from an available atlas?

I was thinking of regions which are defined as labels because i wanted to use limbic structures.

4

I think you may be find this interesting: Dictionaries of multiple dimensions | DiFuMo

This gives you ICA-like maps + the regions (Neuroanatomy nomenclature) that could be found in the limbic systems after searching from a high-dimensional atlas.

Best,
Kamalakar

1 Like
5

Thanks for the suggestion! I used the atlas now and it is exactly what i have been looking for.

Best,
Maria