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
February 07, 2023 11:16AM
Partial images can be particularly difficult. If the data starts out this far apart, it seems there is something off in the coordinates. Try "-giant_move" to overcome that and allow movement a long distance. Cost functions like lpc+ZZ, lpc and nmi may be used too (-cost ...). There are options for partial coverage, but that assumes movement mostly within the planes of the acquisition, and that doesn't appear to be the case. I would remove the deobliquing step except as a test to check for appropriate coordinates and use the original data to avoid interpolating the EPI data twice.
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Subject Author Posted

How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)? Attachments

shjung February 06, 2023 01:41PM

Re: How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)?

Daniel Glen February 07, 2023 11:16AM

Re: How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)? Attachments

shjung February 08, 2023 02:17PM

Re: How can I align a partial 3d image (Turbo-spin echo) to a whole brain 3d image (T1)?

Daniel Glen February 08, 2023 11:33PM