Hi,

for example, in /quality control/ output directory of niak, obtained from the fMRI preprocessing of a group of subjects,
we have func_mask_group_stereonl.mnc.

If I want to generate this mask only for the gray matter, or only for the cortical region (without the brain stem, cerebellum, etc),
what is the best way?

Thanks in advance

**I've been using AAL template resampled for func_mask_group_stereonl.mnc to generate the cortical mask, however, it involves some redundant voxels at the boundary. that's why I'm asking for any better strategy.

Dear Kangjoo,

The modified AAL template which ships with NIAK is based on a gray matter segmentation. It includes all voxels with substantial overalp with grey matter at the group level, which turns out to be quite extensive. You can try to restrict the regions to grey matter at the individual level. You have the individual segmentation results in the anat folder, which you will need to resample at the functional resolution. 

I hope this helps. Best,