I have not done any manual interventions. I would like to re-run 
recon-all with different  expert options in mri_normalize, and 
-skullstrip, and -mprage, and wanted be sure that my changes would be 
reflected in the downstream output.<div><font color="#999999">-<br></font></div><br>
<br><br><div class="gmail_quote">On Fri, Apr 20, 2012 at 12:52 PM, Joshua Lee <span dir="ltr">&lt;<a href="mailto:jkilee@ucdavis.edu">jkilee@ucdavis.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

If I were to want to re-run a recon-all completely fresh on a subject, what do I need to do aside from creating a new subject directory?<br><br>I had previously thought that by adding the -all flag, all old files would be over written (i.e. overwrite with a new brainmask.mgz). I want everything fresh.<br>


Does the -clean flag do it all?<br>Thanks<br>Josh<br>
</blockquote></div><br>