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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Chris McNorgan
July 09, 2009 12:01PM
Hello all,

After running @auto_tlrc on a batch of 14 participants, when I look at the skull-stripped anatomical that gets generated, I find that the script does a good job at removing the skull for everybody, but that a decent chunk of non-brain material, in particular most of one or both eyeballs, is retained for about half of my participants. I was unclear, after a search through the message boards, as to what the best practice is here. For example, as in the following thread:
[afni.nimh.nih.gov]

This is the command that my script uses:
@auto_tlrc \
-base TT_N27+tlrc \
-input s${subj}_t1_mprage+orig

We're going to be doing a whole-brain analysis, so my instinct is that we're going to need an accurate description of the actual brain volume.

Thanks,
Chris
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Subject Author Posted

eyeballs and @auto_tlrc

Chris McNorgan July 09, 2009 12:01PM

Re: eyeballs and @auto_tlrc

ziad July 09, 2009 01:02PM