They are being run but do not need to be. It does not change the results, but it is not needed and wastes cycles.
On 04/10/2017 04:24 PM, Antonin Skoch wrote:
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I think the stages in the command line help are out of date On 04/08/2017 05:58 PM, Antonin Skoch wrote: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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