001.mgz -> raw.mgz -> orig.mgz -> nu.mgz -> T1.mgz
If you only have one run, then 001 and raw are the same
orig.mgz is the first conformed volume
doug
> _______________________________________________
On 07/08/2013 12:38 PM, Tudor Popescu wrote:
> Thanks Bruce. I have looked at that part of the wiki but I was
> wondering whether the screenshots at all suggest that all artefacts
> are likely to be the result of the same problem, and that e.g.
> re-running recon for all subjects with a watershed>25 and with the
> -no-wsgcaatlas flag might be the thing to do in this case, rather than
> manually editing slices in tkmedit.
>
> So after making these corrections to all affected subjects, before
> proceeding to analyses, is a visual inspection in freeview of the
> brain.mgz of all subjects enough? It seems like some of these
> skull-stripping errors are quite subtle and can be easily missed (as I
> have, in fact, when I checked the output after my first recon-all).
>
> the T1.mgz is intensity corrected and conformed (the orig.mgz is
> just conformed).
>
> So are both derived from 001.mgz? Otherwise, what is the difference
> between 001.mgz and orig.mgz?
>
> Thanks!
> Tudor
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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