x and y axis reversed

AFNI Message Board
1

hello

I am new to afni and after running my first level models I am seeing the x axis is reversed (which is not that unusual) however I am also seeing the y axis is reversed. for example I am showing the left caudate at -16 -14 12 instead of 16 14 12 (it is the y axis reversed that has me most concerned)

is there a way I can correct for these reversals or at least correct for the y axis? I would prefer my data to be in neurological format. The data comes from the scanner is radiological format.

thank you for your help

jef

2

Hi, jef-

There are two issues here:

  1. Is the left of the image also the leftside of the displayed brain (default convention) or the right side (switchable)?
  2. Are x-values to the left of the coordinate origin positive (RAI-DICOM notation) or negative (LPI/SPM ordering)?
    Each of these is a convention, and you can choose to set what you prefer. Each of these can be changed either temporarily or longterm in the GUI with environment variables. (Each of these should be reported in papers when you display your information, so everybody else knows, too!)

Re. #2:
Some background resources on this are available here on the AFNI Bootcamp channel:
https://www.youtube.com/watch?v=fWDPMi_r2z0&list=PL_CD549H9kgqwHr0EDtvAU8hylsOj30OK
… and in the Bootcamp slide on dataset properties and GUI visualization, pg 27ff from here (this will download+open the named afni*.pdf presentation):


afni_open -aw afni30_vol_dset_basics.pdf

To change this as a one-off in the GUI, as the link above states, you can go to the upper left of the GUI where the corodinates are shown, right-click, and change the ordering (basically, adjusting what the signs mean for various coordinate components).

To do this more permanently, you can open the ~/.afnirc settings file that you should have on your computer from your AFNI installation (if you don’t see one there, then run “afni_system_check.py -check_all”, and in the “Please fix” section at the bottom, you will see how to populate a default one). The environment variable of interest is called AFNI_ORIENT, it is described here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/readme_env_vars.html
The default in the distributed ~/.afnirc is uncommented, but the default is basically this:


AFNI_ORIENT                = RAI  // coordinate order

You can set it to look like:


AFNI_ORIENT                = LPI  // coordinate order

Once you save this setting (or any other) in the ~/.afnirc file, the next time you open the GUI up, it should be active. Here, you should see a different “order” label in the upper left of the GUI.

Re. #1:
To change this temporarily in the GUI, hover the mouse over the axial or coronal image, and hit the “l” (=ell, like the letter between k & m). You will see the brain left-right swap, and the label below the image should change from “left=left” to “left=right”.

To change this more permanently–youuuuu guessed it–you can set an environment variable in the ~/.afnirc file! This one is cleverly called “AFNI_LEFT_IS_LEFT”, and you can set it to “NO”:


AFNI_LEFT_IS_LEFT        = NO  // YES==show human left on screen left

–pt

3

thank you that was very helpful

all the best