AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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February 02, 2023 04:11PM
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?
Attachments:
open | download - Screen Shot 2023-02-02 at 15.51.02.png (496.5 KB)
Subject Author Posted

impose -orient_code on DICOM conversion on Dimon Attachments

Pawel February 02, 2023 04:11PM

Re: impose -orient_code on DICOM conversion on Dimon

rick reynolds February 02, 2023 05:24PM

Re: impose -orient_code on DICOM conversion on Dimon

Pawel February 02, 2023 05:40PM