When  using the -acpc -A options in ART, it computes an initial affine transformation followed by a non-linear transformation. It then combines the two transformations (the affine and the non-linear) into a single non-linear transformation and stores the results as a displacement field in the warp.nii file. How can I get only the affine transformation not the non-linear transformation?. Is it possible?.

Hi Abdur,

At the moment the only way to save the affine transformation is to use the -v (verbose) options with 3dwarper and then copy/paste the affine transformation matrix to a text file.  I future version of the program we will save those automatically.

Babak