Pulling ICA network from nifit file on nibabel

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1

I have a nifti file with the following colormap.

0 NONE 0 0 0 0
1 7Networks_1 120 18 134 0
2 7Networks_2 70 130 180 0
3 7Networks_3 0 118 14 0
4 7Networks_4 196 58 250 0
5 7Networks_5 220 248 164 0
6 7Networks_6 230 148 34 0
7 7Networks_7 205 62 78 0

Once I load the file with nibabel.load() then get_fdata() how can I pull the MNI coordinate of a voxel with one of those values?

2

you can go from voxel indices to millimeters by multiplying by the inverse of the image affine matrix

https://nilearn.github.io/auto_examples/04_manipulating_images/plot_affine_transformation.html#sphx-glr-auto-examples-04-manipulating-images-plot-affine-transformation-py

3

Thank you I am not trying to go from MNI to millimeters and I understand how to transform between them I am trying to get separate networks out so I want the set of voxels considered to be a part of each of these networks as a list or array.

4

In this case since ICA components are continuous maps you need to threshold them and identify connected components in the thresholded maps. you can do it easily using nilearn.regions.RegionExtractor:
https://nilearn.github.io/modules/generated/nilearn.regions.RegionExtractor.html#nilearn.regions.RegionExtractor
see these examples: https://nilearn.github.io/auto_examples/03_connectivity/plot_extract_regions_dictlearning_maps.html and https://nilearn.github.io/auto_examples/04_manipulating_images/plot_extract_rois_smith_atlas.html

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5

What if I don’t have an image affine? I have a set of real mri coordinates and a set of MNI coordinates can I calculate the affine from that data to go to mm space?

6

As far as I know the registration of the MRI image to the MNI template is not necessarily affine?