Hi Joao,
Sorry for the late response, but I've been away for two weeks ...
When recon-all is first run (and there is not talairach.xfm), it will
create talairach.auto.xfm and copy that to talairach.xfm. In subsequent
runs, recon-all will create a new talairach.auto.xfm. Immediately prior
to this, it will check to see whether talairach.auto.xfm is the same as
talairach.xfm. If they are the same, it assumes that you have not made
any manual edits to it and it will copy the newly generated
talariach.auto.xfm to talairach.xfm. If there are differences, it
generates the new talairach.auto.xfm but does not copy it. This is
overridden when you add -clean-talairach. It is done this way to help
protect the user from accidentally overwriting manual changes. This
strategy is also used with brainmask.mgz.
doug
Joao Pereira wrote:
Hi,
I have just realized I made a mistake when I ran recon-all -s
subj -notalairach -autorecon1 -autorecon2, as the -notalairach option is
overridden by autorecon1. Nevertheless, when I look at the dates of the
files, I see that talairach.xfm is the one I edited, although talairach.log
has a posterior date. Moreover, when I look at the transforms with
tkregister2, they seem just as I have left them. What am I missing here?
Thanks!
Joao
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