Hello,

I would like to use the rigid registration provided in the toolbox to ensure that my T1 image is in the correct space and the ACPC line is cut correctly. I used the t1 template from AdultAtlas_ICBM_152_2009a_sym as the template. However, for one of my subjects, the output of the rigid registration does not look good, it is tilted in the coronal view (left side of attached). I then tried to register using FSL's FLIRT outside of the toolbox, using linear registration with 6 DOF, but in this case, the coronal view looks ok and the sagittal view looks a little too tilted and does not look parallel to the ACPC line (right side of attached). I was wondering if there is any recommendation on what to do when the rigid registration from the toolbox is not ideal and how to assess if the registration is good when performing the rigid registration outside the toolbox? Thank you!