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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Daniel Glen
December 18, 2009 01:51PM
Probably. You can use 3dWarp to match obliquities. See this link for details.

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

You can also use align_epi_anat.py to match EPI and anatomical datasets together. The obliquity is handled as part of the alignment by default.

align_epi_anat.py -anat anat+orig -epi epi+orig -epi_base 0

Matching the obliquity information assumes the transformations are correct in the header of the data. If they are not correct, the output of either of these methods will not be correct either. In that case, add "-giant_move -deoblique off"
to the align_epi_anat.py command. See the help for each of these commands for more details.
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Subject Author Posted

Very Poor ANAT/EPI alignment

Anita Cservenka December 18, 2009 02:21AM

Re: Very Poor ANAT/EPI alignment

rick reynolds December 18, 2009 09:34AM

Re: Very Poor ANAT/EPI alignment

Anita Cservenka December 18, 2009 12:20PM

Re: Very Poor ANAT/EPI alignment

Daniel Glen December 18, 2009 01:51PM