Quick start

  1. To align a data file containing one or more time points, specify the individual volume(s) in one file, the template volume(s) in another file, and one or more brain masks in an overlay file list that masks the brain in the template space:

align individual.nii -t template.nii -o brain-mask.dat

  1.  If the orientation does not match the template orientation, use the "orientation" parameters to manually rotate by ± 90 or 180 degrees around one or more axes, or swap the slice direction (which changes handedness).
  2. The capture range is not great, especially when using the rolloff filter, so manually adjust the orientation to within about FOV/4 and then click the "auto-align affine" button (or hit "a").
  3. If desired, go to the non-linear alignment panel using right clicks on the right panel, and adjust selected distortion fields by clicking on "auto-align non-lin" button (or hit "a").
  4. When one quits the program gracefully ("q"), an output file named "align.com" is generated. Use this file in conjunction with the "jip" program to register one or more time points as follows:

      forward.com                              inverse.com

      read align.com                           read align.com

      read individual.nii                       read target-space  # a file registered by align.com

      register                                       inverse-register     # go the opposite way

      write target-space.nii                 write original-space.nii

      bye                                             bye

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard