Whereami unavailable

AFNI Message Board
1

Hello,

I am having an issue when viewing my results in AFNI where both the whereami and “go to atlas location” functions are unavailable. when I right click, they are there but they are unhighlighted and unable to be clicked on. My results, and anatomical underlay are in MNI space, but I’ve never had this be an issue before. My understanding is that regardless of your individual template space, the whereami gives you coordinates in talairach first, with MNI template coordinates below. I’m assuming my issue might have to do with unavailable templates in my AFNI directory, though I know I at least of an MNI template because I’ve loaded it. Has anyone encountered this issue, I assume it is probably a minor adjustment that is needed. Thank you!

As a follow up, as I have not used AFNI for a while, I seem to recall needing to making an adjustment to the x and/or y coordinate that whereami outputs in order to have the coordinate agree with the region listed. I can’t recall if this is due to radiological left/right flip, or another coordinate adjustment that has to be made,

Best,
Sam

2

If you are finding this with NIFTI datasets, then you may need to reset the sform or qform codes for the dataset. For AFNI datasets, those will only appear if your datasets have the +tlrc view. You can reset the datasets (AFNI or NIFTI) with

3drefit -view tlrc mydset+orig

If the NIFTI datasets are often misformed, then you can change the AFNI_NIFTI_VIEW to tlrc.

3

3drefit solved it, thank you very much!

Sam