ICA components have grey shadow around each brain after upgrade, and different components

I’m not sure specifically how this happened, but I have two guesses. Between v23 & 24 we changed to using nilearn to display the images. Our old version was very simplistic and just plotted the a colormap of each matrix. nilearn is using information, like the voxel sizes.

Guess 1. Our color scale goes from the 2nd percentile to the 98th percentile. If nilearn.plot_stat_map is plotting values below the 2nd percentile as gray rather than white, then perhaps there are a bunch of voxels that are rounding errors about zero rather than exactly zero and are appearing as gray. You can test this by opening desc-ICA_components.nii.gz directly and checking what the values actually are.

Guess 2. We define the underlay as bg_img=None so there shouldn’t be any underlay, but there definitely is something there. There is a default atlas (MNI152TEMPLATE) to use if bg_img is undefined. Perhaps something is being set as a background image even when this parameter is set to None? Are your data aligned to a template space? If not, maybe this is the issue.