- 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
- 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).
- 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").
- 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").
- 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:
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