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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Danny
July 02, 2014 10:23PM
Hi Daniel,

It looks like you use this instead of the default skull-stripping method? Then the final output is a Qwarped, skull-stripped brain aligned to a template that can later be used to align the EPI to?

I have a question regarding your script:

In your command "align_epi_anat.py -dset1 ${based}_un+orig -dset2 $template -giant_move -suffix _al2template \
-dset1_strip None -dset2_strip None -master_dset1 BASE", what does BASE refer to here, anatomy or the standard?

Thanks,

Danny
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Subject Author Posted

3dQwarp and skull-stripping issue

Danny June 30, 2014 02:48PM

Re: 3dQwarp and skull-stripping issue

Emperor Zhark July 01, 2014 09:07PM

Re: 3dQwarp and skull-stripping issue

Danny July 02, 2014 11:09AM

Re: 3dQwarp and skull-stripping issue

Daniel Glen July 02, 2014 04:36PM

Re: 3dQwarp and skull-stripping issue

Danny July 02, 2014 10:23PM

Re: 3dQwarp and skull-stripping issue

Daniel Glen July 03, 2014 11:07AM