yes, that's what -make all will do (it checks timestamps to see what needs to be rerun)

On Mon, 15 Feb 2010, Alessandro D. Gagliardi wrote:

I wanted to avoid using recon-all because it generally takes so much time, but from your message it sounds like it will only redo the tasks that need redoing. Is that correct?

Thanks, -Alessandro

On Sat, Feb 13, 2010 at 4:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Alessandro,

usually that means that the smoothwm is out of date with the sphere.reg. You can run mris_euler_number on both to make sure they have the same number of vertices, faces and edges. Or you can just run

recon-all -s $subject -make all

which will rebuild things if it needs to

cheers Bruce

On Sat, 13 Feb 2010, Alessandro D. Gagliardi wrote:

...

Dear Freesurfers,

I just upgraded to the latest version of Freesurfer (leopard-i686-stable-pub-v4.5.0) and I want to rerun mris_ca_label to generate ?h.aparc.a2009s.annot files.  I figured I would just run the command described at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable, namely: mris_ca_label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot but when I do so, I get the following error: mris_ca_label: could not read surface file /Users/adfgagliardi/Documents/Lab/subjects/hj/surf/?h.smoothwm for hj No such file or directory surf/?h.smoothwm does exist for hj, so I don't know why it says "No such file".  I tried regenerating it using mris_smooth -n 3 -nw ?h.white ?h.smoothwm which completed without error, but mris_ca_label continues to say that it cannot read ?h.smoothwm Any help would be greatly appreciated.

Alessandro D. Gagliardi Ph.D. Candidate Integrative Neuroscience Program Rutgers University Mind Brain Analysis adfgagliardi@gmail.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer