Hi guys:

Please forgive this very specific question. I just attended an AFNI Bootcamp (best 5 days of my life) where as part of the handouts you guys provided us with some "c" and "p" scripts in an "AFNI_pamenc" folder.

I was enthralled by how streamlined these scripts made things so have edited them for my own purposes. I have had some registration issues, though, so I basically re-wrote "c.ss.1.sswarper" to perform 3dQwarp after some anatomical manipulation Daniel helped me with because he is wonderful and I love him. I then applied the requisite manipulation to the "c.ss.3.AP.pamenc" script and everything runs fine.

The problem is that with 3dQwarp you don't actually supply the aff12.1D file that is the first entry to cat_matvec because the T1 -> MNI registration warp you get out of 3dQwarp includes both the affine and nonlinear transformation.

My question is - if using these scripts is there any easy way you can think of that can be added or amended to the "c" or "p" script to remove this line from the cat_matvec command? Since the "p" script calls the "c" script which created AND calls the proc script my current solution is to run the "p" script to generate the proc script then quit the program, edit the proc script and then directly call the proc script after editing but this defeats the whole purpose of the "p" and "c" scripts and if I'm going to do this I should just use the proc command on its own. I haven't found anything in the proc. help regarding cat_matvec so just figured I could ask because these "p" and "c" scripts have really streamlined things for me and I'd hate to let them go so easily.

Thanks so much for your wonderful resources and help. You're all amazing.

Lauren