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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jgoold
January 16, 2020 04:01PM
Hello PT,

Thank you for your help with this. I tried align_epi_anat.py with ginormous move, anat_has_skull no, and epi_strip None and still didn't have luck with good alignment (see image).

align_epi_anat.py -epi2anat \
-epi pb02.sub002.r01.despike+orig \
-anat sub002t1_ns+orig \
-epi_strip None \
-anat_has_skull no \
-epi_base 0 -volreg off -tshift off \
-ginormous_move \
-cost lpc -multi_cost lpa lpc+ZZ mi

The raw scans have better alignment than the processed ones (but still not good).

I'm going to try your other suggestion of SSwarper next and see how that goes. Will keep you posted.

Best,
Jessi
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EPI to Anat alignment issues Attachments

jgoold January 13, 2020 08:15PM

Re: EPI to Anat alignment issues

ptaylor January 13, 2020 08:44PM

Re: EPI to Anat alignment issues Attachments

jgoold January 16, 2020 04:01PM

Re: EPI to Anat alignment issues

ptaylor January 16, 2020 10:26PM