Created in T1 preprocessing folder, for example
Z:\Analysis\Preprocess\ChronicMigraine_7T\T1preprocess\Chronic Migraineurs\Subject_2117\T1_ref_vox0.75_bb_min_-90_-126_-72_max_90_90_108
The brain mask is based on the gray matter (GM) and white matter (WM) files (“c1…”, “c2…” for DARTEL/new segment, “p1…”, “p2…” for CAT). These files are probabilities, and “brain” is classified where GM + WM >= 0.5. In other words, a voxel is “brain” if the sum of probabilities of being gray and white matter is 50% or more.
So:
brainmask = (GM + WM) > 0.5
The brainmasklots is the brainmask that has been dilated, which means expanded - puffed out is a good analogy.
Troubleshooting
If brainmask/brainmasklots look bad, check the c1 & c2 files (or p1 & p2). Here is an example:
Looking at the gray and white matter files, we see the problem - incorrect gray matter segmentation:
When we look at the CSF image (c3), we see the problem - gray matter has been classified as CSF:
