Hello,

A clarification about this (based on my understanding/reading of the recon-all code) to help avoid any potential confusion about how the - clean-bm flag operates more generally:

If you rerun the skull stripping without the -clean-bm flag, recon-all will preserve any edits previously made to brainmask.mgz as part of the new brainmask.mgz. However, the brainmask.auto.mgz is not simply "copied" (i.e., Linux 'cp' command) to brainmask.mgz (as is the case the first time an analysis is run, or if the -clean-bm flag is specified).

This distinction is necessary to interpret the following output to the recon-all.log file (which Gabi might have noticed in her output):

INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz.

cheers, -Mike H.

On Tue, 2008-12-02 at 10:32 -0500, Allison Stevens wrote:

recon-all will copy the brainmask.auto.mgz to the brainmask.mgz so they should be the same. Allison

On Tue, 2 Dec 2008, Barkay, Gavriel wrote:

...

Hi, I ran recon-all -all crashed for reasons unrelated to FreeSurfer. I re-ran the analysis without -clean. Is the new skull stripped volume stored in brainmask.auto.mgz instead of brainmask.mgz? Thanks, Gabi

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