-check_flip

AFNI Message Board
1

Hi all,
I recently read your article (Glen et al., 2020). I have a question based on it/check_flip.

I have images that were acquired in RPI orientation (verified with a vitamin E capsule. When I ran align_epi_anat.py, I get the outcome NO_FLIP (using the raw images as input). So far, so good.

However, previously, I had reoriented the mprage and epi images to RAI (as I know that is the afni default) and then deobliqued them. I reoriented them using 3drefit -orient RAI. When I use THESE Images as the input to align_epi_anat.py, the outcome is DO_FLIP.

Could you please explain why this might happen?
Thanks,
Matt

2

Hi, Matt-

Glad the article was of interest!

I think the main thing happening is noting the distinct usage of 2 AFNI programs for adjusting header information and datasets:

  • 3dresample is useful when the current header information is correct (in the sense that the data on disk is consistent with the header info), and when you change a header property like orientation, the data also gets changed to stay correct.
  • 3drefit is useful when the current header information is incorrect, and you want to change a header property like orientation, and the data will not be changed simultaneously.
    As a corollary, if your data starts correct and you change the header property of orientation with 3drefit, then it will change to be incorrect.

If I understand correctly, that is what has happened in your case?

–pt

3

Aside from Paul’s sage advice, another important point is that RAI is not really the “default” in AFNI. There is no default, so you could use any orientation.

4

Ugh, I had it wrong. I DID use 3dresample to reorient the images. However, as I just tested it and found that the outcome was still DO_FLIP.

5

One other thing to note is that these are multiband images. Not sure that should make a difference, just letting you know. However, I think the EPI image may have gotten corrupted because it showed up as being in TLRC template space, which is incorrect, so I think we’re probably ok, though I have no idea how the corruption occurred.

6

I understand.