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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Sarah Jacobson
July 29, 2009 11:03PM
Hi Rick,

Thank you for your reply.

I did as you suggested: 3dcopy, @align_centers with anat and epi only, 3dWarp -deoblique both anat and epi, then for the align_epi_anat.py I ran the following:

align_epi_anat.py -anat $sub.anat_deob_ns+orig. \
-epi $sub.MID_shft_deob+orig. -epi2anat -epi_base 2 -anat_has_skull \
no -verb 1 -save_vr -giant_move

Although the alignment is now correct, the top part of the brain has been cut off. Could you please take a look at the transformed anat and epi in zipped folder "SarahJ.tgz" and please let me know if there are any other options I could use to correct for this issue?

Thank you very much for your advice.

Sarah
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Subject Author Posted

Bad Alignment

Sarah Jacobson July 29, 2009 10:40AM

Re: Bad Alignment

rick reynolds July 29, 2009 05:29PM

Re: Bad Alignment

Sarah Jacobson July 29, 2009 11:03PM

Re: Bad Alignment

rick reynolds July 30, 2009 09:38AM

Re: Bad Alignment

Sarah Jacobson July 30, 2009 03:15PM

Re: Bad Alignment

Daniel Glen August 03, 2009 05:03PM