Hi,
> Is the outcome of run_first_all supposed to be in standard mni space, or
> native subject space?
All the segmentations should be in native space. The FIRST takes the
transformation matrix inputed, inverts it, then applies it to the model
prior to fitting.
> Also, any suggestions as what to do when first_flirt fails to register
> even after masking out the neck?
Does the failure occur at the first stage (use -d option)?
Cheers,
Brian
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