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
January 22, 2009 04:52PM
You can try align_epi_anat.py with the various -partial_coverage options. If datasets are very close to start off, then you can use "-cmass nocmass" instead. If datasets are very far apart, try -giant_move. Output grids can be set for "-master_epi BASE" to give resolution and FOV of the full coverage T1 in this case. The cost function can be changed from the default of lpc to lpa as in the following example.

align_epi_anat.py -anat T1+orig -epi T1_2+orig -base_epi 0 -partial_coverage -master_epi BASE -prep_off -cost lpa -anat_has_skull no -epi_strip None -suffix _al2T1 -AddEdge

If datasets have little overlap at all, then @align_centers may be a useful preprocessing step. Viewing the final results can be done with the @AddEdge script, overlay/underlay features, edge enhancement and checkerboard features in the AFNI GUI.
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Subject Author Posted

Cropped FOV registration

Anastasia Ford January 22, 2009 02:08PM

Re: Cropped FOV registration

Daniel Glen January 22, 2009 04:52PM

Re: Cropped FOV registration

ziad January 23, 2009 08:40AM