Hi Jeff,
> 1. how important is a good brain extraction to the TBSS
> process? BET does not work well with my dataset
It would definitely help to get this right. You can try different options, especially -f and the the robust option, to try to get a proper brain extraction. If this doesn't work, you can always try to edit the mask manually on one subject to see if this helps with the registration issues.
> 2. can I modify the TBSS registration to make it linear, or
> less-strenuous nonlinear?
Yes, you can... I really don't think that linear registration would be good enough though, but you can possibly try it to create a study-specific 7T template and check whether this helps the non-linear registration. The other possibility is indeed to modify the parameters in the config file of fnirt, but I'd leave this as a last resort (and Jesper would then be the right person to help you with this).
Cheers,
Gwenaëlle
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Gwenaëlle Douaud, PhD
FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington OX3 9DU Oxford UK
Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222 717
www.fmrib.ox.ac.uk/~douaud
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