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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Brad Buchsbaum
March 03, 2010 12:24PM

Hi,

using align_epi_anat.py with an input file ending with .nii.gz leads to an putput that adds "suffix.nii.gz" to the input filename.

e.g. inputfile.nii.gz.suffix.nii.gz


just a minor annoyance.

Also having a heck of a time with anatomical alignment to 1.5T epi scans with a fair amount of frontal dropout (see e.g. "Milwaukee" NITRC dataset). I'd be curious, if you guys are also working with that data set, what parameters you're using to get good epi->anat alignment.

"lpc" works very well when it works but when it fails it seems to fail catastrophically. I wonder if an option to initialize (lpc) registration with a transformation derived from e.g. "nmi" would help in that regard. Does such an option exist?

thanks,

Brad Buchsbaum
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Subject Author Posted

align_epi_anat.py (some issues)

Brad Buchsbaum March 03, 2010 12:24PM

Re: align_epi_anat.py (some issues)

Daniel Glen March 03, 2010 12:38PM