Dear Doug,
do you think that it is necessary/useful to rerun
-normalization2
-maskbfs
-segmentation
steps after wm.mgz have been edited (that is what the -autorecon2-wm is used
for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
In contrast, it seems to me that the documentation is more close to the optimum
(the three steps: normalization, mask and segmentation steps are run only when
it is needed - in -autorecon2-cp, not in -autorecon2-wm).
Antonin
I think the stages in the command line help are out of date
On 04/08/2017 05:58 PM, Antonin Skoch wrote:
> Dear experts,
>
> I noticed inconsistency between recon-all -help and actual code of
> recon-all in -autorecon2-wm option.
> According to the recon-all --help the -autorecon2-wm processes stages
> 15-23 (fill through make white surfaces) and -autorecon2-cp processes
> stages 12-23 (normalization2 throuhgh make white surfaces). But, in
> the code both -autorecon2-wm and -autorecon2-cp are equivalently
> processing stages 12-23.
>
> It seems to me that the stages 12-14 are not needed to process again
> in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
>
> Could you please comment on?
>
> Regards,
>
> Antonin Skoch
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