T1 Processing
- Paul Macey (admin)
Owned by Paul Macey (admin)
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:
| prob > 0.5 | prob > 0.1 | prob > 0.1, close with sphere r = 7 |
|---|---|---|
|
|
|
brainmask_*.nii | brainmasklots_*.nii (pre-2017-08) | brainmasklots_*.nii |
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);