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
<fis...@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usually that means that the smoothwm is out of date with the sphere.reg.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
adfgaglia...@gmail.com
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