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  

Previous Message Next Message
Message List New Topic Print View
|
Daniel Glen
July 08, 2010 05:08PM
The simplest thing to do is rotate the volume 30 degrees with 3drotate. AFNI will detect some DICOM files as "oblique" which I guess is something similar to the gantry tilt of the CT scans. For oblique data, you can deoblique this data with 3dWarp. This transformation requires an IJK_TO_DICOM_REAL transformation matrix that describes the transformation from the IJK coordinates to RAI xyz position. You can read more about obliquity handling here:

[afni.nimh.nih.gov]
[afni.nimh.nih.gov]

If you would like to match an MRI volume, you can use align_epi_anat.py to do this. Most likely you would use "-giant_move" and "-dset1", "-dset2" options.
Reply Quote
RSS
Subject Author Posted

Gantry Tilt

Chad July 08, 2010 04:30PM

Re: Gantry Tilt

Daniel Glen July 08, 2010 05:08PM

Re: Gantry Tilt

Chad July 08, 2010 05:38PM

Re: Gantry Tilt

Daniel Glen July 08, 2010 06:03PM

Re: Gantry Tilt

Chad July 09, 2010 09:04AM

Re: Gantry Tilt

Daniel Glen July 22, 2010 12:33PM

Re: Gantry Tilt

Chad July 23, 2010 11:46AM