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
June 02, 2020 12:42PM
Not completely sure of what is going on, but a few scattered ideas:

1.Cluster these images first (3dClusterize/3dclust/3dmerge/3dkmeans) if the gadolinium is separable from the head. Motion correction on each cluster separately (3dvolreg/align_epi_anat.py/3dWarpDrive/3dAllineate) and then join them back together at the end (3dcalc).

2. Since these are T1 images, you might try a rigid or rigid_equiv alignment to a template (@auto_tlrc/align_epi_anat.py).

3. Skullstrip each volume first (@SSwarper/3dSkullstrip) to separate the brain from the gadolinium or 3dAutomask.
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independent volreg on brain and phantom in same acquisition smoking smiley

paul.hamilton May 28, 2020 12:31PM

Re: independent volreg on brain and phantom in same acquisition smoking smiley

Daniel Glen June 02, 2020 12:42PM

Re: independent volreg on brain and phantom in same acquisition smoking smiley Attachments

paul.hamilton June 08, 2020 12:06PM

Re: independent volreg on brain and phantom in same acquisition smoking smiley

Daniel Glen June 10, 2020 06:19PM