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  

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October 18, 2021 01:57PM
Adding on to Pete's useful advice, I would recommend trying "lpa+ZZ" or "lpa" cost functions for EPI data where it's hard to distinguish CSF. For data that may be very bright on the edge of the brain, you could use "-perc 99" to increase the ceiling percentile value in the EPI used for alignment.
Subject Author Posted

Cannot get good alignment with align_epi_anat.py or 3dAllineate

hdempseyjones October 18, 2021 12:25AM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

Peter Molfese October 18, 2021 10:39AM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

hdempseyjones October 19, 2021 07:22PM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

Daniel Glen October 18, 2021 01:57PM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

hdempseyjones October 25, 2021 03:29AM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

ptaylor October 25, 2021 10:25AM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate Attachments

hdempseyjones October 25, 2021 09:57PM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

ptaylor October 26, 2021 08:23AM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

hdempseyjones November 22, 2021 11:57PM

Re: Cannot get good alignment with align_epi_anat.py or 3dAllineate

Daniel Glen November 23, 2021 10:34AM