afni.nimh.nih.gov

Hi Cesar,

I'm not clear as to what you want to do. I'll provide options that hopefully will give clues.

1. 3dAllineate does allow for an identity matrix, mostly for the purpose of resampling. Both -1Dparam_apply and -1Dmatrix_apply can take "IDENTITY".
2. 3dBlurInMask can be used specifically with a mask.
3. 3danisosmooth also smooths within a mask. You can set the fraction of gaussian smoothing.

Let us know if I'm completely off track with these suggestions.