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?
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. Does the -clean flag do it all? Thanks Josh
Hi Josh
if you specify a new directory that will certainly work. We try very hard to preserve any manual interventions you have taken so that is why -all doesn't start fresh - we don't want it to.
cheers Bruce
On Fri, 20 Apr 2012, Joshua Lee wrote:
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?
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. Does the -clean flag do it all? Thanks Josh
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. -
On Fri, Apr 20, 2012 at 12:52 PM, Joshua Lee jkilee@ucdavis.edu wrote:
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?
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. Does the -clean flag do it all? Thanks Josh
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Joshua Lee