Hi Rick,

Thanks for your reply.

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So you will be reporting individual subject results in original space?

Yes, we are going to get ROIs in original space for other analysis: 1, extract information in these ROIs, then do some correlation and group comparison; 2, DTI tractography, which needs precise ROI location.

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But still, such a mask need not be applied until actually clustering or otherwise correcting the results. The orig space linear regression need not be masked, for example.

I didn't fully understand what you mean. The differences between proc scripts produced by afni_proc with and without mask_apply epi option are:
1, In the scale step, full_mask vs mask_extents;
2, In the regress step, full_mask vs no mask.
In the later blur estimation step, both proc scripts use full_mask for correcting for multiple comparisons.


Thank you again.
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