Dear Vina,
> Thanks that explains part of it. With the linear transformation
> there is part of the temporal cut-off (which appears to be
> appropriate). With the non-linear it appears the brain is
> stretched, there appear to be parts of the temporal lobe present
> that was not present before.
it is very hard to say what might have gone wrong without actually
seeing the data. Are you running fnirt from within feat (in which
case the correct config-file will automatically be used) or are you
running it at the command line (in which case you will have to
specify the config-file). The "default defaults" aren't really that
great, which is why we supply these configuration files.
If you want us to take a look at your data you can upload them to
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and then email me (off the mailbase) the reference number that you
get there.
Best regards Jesper
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