Hi Babak,

Thank you for creating the ART tools! I have had great success with them so far, but I am occationally encountering a problem. I have been working to adapt registration tools to the confocal microscopy images of the honey bee brain, and it generally works. So far, I have successfully registered 23 of 25 brains. However, like your previous correspondent, two of the 25 brains show significantly altered intensity values at the end of the registration process using 3dwarper.  I looked in the program, and it appears that the -nn option doesn't exist as an option under -help for 3dwarper. Can you make any suggestions?

Here is my code:

3dwarper -s 10 -trg 20120416PER4_256to4_3dwarper_256_blur.nii -sub $basename""_HBS_10blur_PER4_3dAllineate9x2.nii -o $basename""_HBS_10blur_PER4_3dAllineate9x2_searchwindow10_3dwarped.nii

As you can guess, the input brains are ones that I have previous run through the AFNI program 3dAllineate using the poly9 subfunction. This pre-registration, registration, step makes a big difference in how well the 3dwarper function works.
Thanks very much. I really appreciate any help you can offer!
Matt