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!

It is not that uncommon for the automatic alignment to fail, particular when a larger portion of the phase and neck  is visible. One possibility is to reduce the image content by masking out face & neck regions prior to running the automatic alignment. 

You would also have more issues with alignment if the age settings between template and the data is off, e.g. adult template used with infant MRI data. The differences in size will make automatic 6DOF alignment difficult. So make sure to use the age appropriate ICBM template.

Finally, an alternative is to do the ACPC alignment manually. Several existing tools will allow you to do that. I usually use 3DSlicer load both the template and the dataset and then manually adjust the alignment transform (using the Transform module in 3D Slicer). Btw, the General Registration module in 3D Slicer is the same tool (BRAINSFit) used by AutoEACSF to do the alignment, so you could also use a good manual transform as an initialization for the General Registration module

Martin

Dear Dr. Styner,

I see, thank you very much for your reply and helpful suggestions! I forgot to mention that my data is adult images so the age between the template and data are matching. I will give it a try and see what works best for my data. 

Best wishes,
Jane