search

CoBrALab / RABIES

fMRI preprocessing pipeline and analysis tools adapted for rodent images. Visit the full documentation at https://rabies.readthedocs.io/en/stable/
Other
34 stars 14 forks source link

Generate a commonspace mask excluding empty voxels #215

Open Gab-D-G opened 2 years ago

Gab-D-G commented 2 years ago

When EPI are not covering the whole brain, they may be empty voxels within the brain mask from the atlas. Should take a median across subjects at each voxel within the brain mask in commonspace to remove voxels which are empty.

gdevenyi commented 2 years ago

Voxelwise and will produce a mask with only value 1 at every subject.

Gab-D-G commented 2 years ago

Additionally, during network modeling with dual regression, when evaluating the network amplitude/variance, it may be biased by the number of brain voxels present. So generating a commonspace mask which only includes voxels with brain coverage across >90% subjects may be a good idea for downstream analysis as well. Ideally all voxels that have an empty value in at least one sample should be ignored.