T1 Processing

Brain mask

The T1 image is segmented into probability maps and brain masks. The basic brain mask is where gray matter is prob > 0.05, and a liberal "brainmasklots" is created for use as a mask in analyses. This is initially set with prob > 0.1, but that actually does not make a huge difference:

Files are in T1preprocess\GROUP\Study\T1ref_.... Created in cspm_xbrain.m:

Vo = spm_create_vol(Vo);
brmask = br>0.1;
se = strel('sphere',7);
brmask = imclose(brmask,se);
spm_write_vol(Vo,brmask);