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

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marven
October 22, 2018 09:05AM
Hello AFNI experts,

Apologies if the question has been asked before but I could not find an answer.

I was wondering if there is an easy way to preserve the obliquity with 3dZeroPad/3dAllineate, i.e. if I run 3dZeroPad on a volume with "Data Axes Tilt: Oblique (30.600 deg. from plumb)" the output is "Data Axes Tilt: Plumb".

The same happens if I register an oblique source to an oblique base, the output is Plumb.

I have run ' 3drefit -atrfloat IJK_TO_DICOM_REAL ' in the past if so that after I run -card2oblique with 3dWarp the oblique matrix in the nii volume is preserved, but I don't know how to proceed when there is padding/rotations being applied.

I appreciate that staying within the AFNI format would avoid the problem, but I need to use the output as nii for subsequent analysis...

Many thanks,

Marcello
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preserving obliquity with 3dZeroPad/3dAllineate

marven October 22, 2018 09:05AM