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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March 10, 2023 03:54PM
Hi Ian,

Try adding the afni_proc.py option "-align_epi_strip_method 3dSkullStrip".

It looks like 3dAutomask is not doing a good job of removing the skull area of the EPI (which is pretty apparent in your data), and 3dSkullStrip will probably do a better job.

- rick
Subject Author Posted

Anat-EPI Alignment Troubleshooting Attachments

brainboi March 10, 2023 02:36PM

Re: Anat-EPI Alignment Troubleshooting

rick reynolds March 10, 2023 03:54PM

Re: Anat-EPI Alignment Troubleshooting

brainboi March 11, 2023 11:19AM

Re: Anat-EPI Alignment Troubleshooting

ptaylor March 12, 2023 08:57AM

Re: Anat-EPI Alignment Troubleshooting Attachments

brainboi March 20, 2023 06:05PM

Re: Anat-EPI Alignment Troubleshooting

ptaylor March 20, 2023 08:10PM

Re: Anat-EPI Alignment Troubleshooting

ptaylor March 21, 2023 09:23AM

Re: Anat-EPI Alignment Troubleshooting

brainboi March 23, 2023 06:48PM