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
December 21, 2009 03:29PM
3dresample forces the grids to match, but doesn't align the data. It might be useful to find out why @auto_tlrc failed for this dataset. @auto_tlrc should be used with template that is a similar modality to the dataset. If a different type of data is used the alignment to the template won't work well. Also the skull stripping part of the data can fail for some datasets if you are using skull stripping in the @auto_tlrc. You can try skull stripping separately with 3dSkullStrip and then try @auto_tlrc with -no_ss.

You can also align to templates using some align_epi_anat.py or 3dAllineate. For either, you may want to use lpa cost function. See the alignment across sessions page here for some ideas.

[afni.nimh.nih.gov]
[afni.nimh.nih.gov]

If all else fails, you can upload the data, and I can take a look.
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Subject Author Posted

Grid mismatch problem

Haisam December 21, 2009 12:15PM

Re: Grid mismatch problem

Haisam December 21, 2009 12:44PM

Re: Grid mismatch problem

Daniel Glen December 21, 2009 01:08PM

Re: Grid mismatch problem

Haisam December 21, 2009 01:23PM

Re: Grid mismatch problem

Daniel Glen December 21, 2009 03:29PM