Aligning to minimum outlier vs first TR

AFNI Message Board
1

Hi all,

I had a quick question on the afni_proc.py alignment options. I work with some projects which align to the first TR and some which align to the minimum outlier. If the first TR is censored due to motion, would aligning to the first TR align to this later censored TR or would it go ahead and align to the first “non-censored” TR from later in the run? I’m assuming that it is aligning to a TR that is later censored during 3dDeconvolve since alignment occurs first but I wanted to make sure this was the case and that I’m not missing something. If so, I’ll be editing my scripts to align to the minimum outlier as that sounds like the current recommendation.

Best,
Walker

2

Hi Walker,

You are correct. Censoring is not decided upon until the regress block. In fact, it is the result of volreg that later determines censoring.

This is a good example of why aligning to the MIN_OUTLIER is preferable. The point of using the MIN_OUTLIER is that it should be a low-motion volume. A censored volume is just a special case were motion seems particularly high.

  • rick
3

That makes sense. Alignment has definitely improved using the minimum outlier. Thanks, Rick!

Best,
Walker