Creating mask for group level analysis

Dear AFNI experts,

I have used other neuroimaging software package to preprocess ASL data and would like to use AFNI’s 3dMVM for the group analysis. My question is that how can I create the mask for the group analysis. I have MNI space registered absolute CBF map and FreeSurfer processed T1 images for each participant. I would like to create the whole brain map (i.e., not just focusing on gray matter regions but gray matter plus white matter regions). Please advise.


Hi JW,

Sorry we did not get back to you on this.

It is preferable to make the masks based on the functional data. Alternatively, you could start with the brain mask datasets output by FreeSurfer and interect, fractionally intersect or take the union of them using 3dmask_tool.

What we like to do is create masks from the functional data intersected with those of the anatomical images, just to keep them tight.

Note that masking can be applied after 3dMVM. It is nice to scrutinize group results for oddities or artifacts, and not just see masked results from the beginning. Masking could be applied as you correct for multiple comparisons.

Do the ASL volumes lend themselves to reasonable masking (e.g. with 3dAutomask)?

  • rick