impose -orient_code on DICOM conversion on Dimon

Hello good AFNI people!

I am converting NHP DICOM files to AFNI. These are anatomical T1 and T2 volumes from more than 1 scanner.

NHPs are oriented differently from humans in the scanner, they are scanned in the sphinx position, the scanner does not know that, so I need to fix the orientation while converting. I have been doing it using -orient_code in to3d, I figured out what code I need to use depending on the scanner that was used, like -orient_code IAR, or -orient_code RIP

Now the newest scans I have do not convert correctly with to3d (example attached), even though last-year’s scans from the same scanner do. Looks like a problem with slice ordering. (I will try to figure it out with the scanner people but even if they made a change that they could revert for the future, I won’t re-do this scan)

to3d has been always bugging me to use Dimon instead, so I gave it a try, and indeed I am not getting the slice-ordering problem. But the orientation is wrong, and I cannot find an option Dimon that would allow me to impose specific orientation, or to pass an -orient-code option to to3d which Dimon internally calls?

What is the best way to solve it?

For this you might run Dimon (or dcm2niix_afni) first and just let them assume the orientation is correct.
Then run 3drefit -orient afterwards to set the orientation to what it should be.

Note that right vs left might be hard to verify. Hopefully you have a method to be sure of which side is which.

Does that seem reasonable?

  • rick

Thank you, this seems like a great solution. Yes I verify L/R independently