recon-all -s maryam -finalsurfs
Reza Rajimehr wrote:
Hi,
I have recently reconstructed a brain using "recon-all -autorecon" in dev environment. First I converted anatomicals to mgz format and then I ran the following commands sequentially:
recon-all -subjid subject -autorecon1 -legacy recon-all -subjid subject -autorecon2
The reconstruction has been done successfully without error. The inflated surface is almost fine (without topological defects) but the "curv" surfaces (curv.lh and curv.rh) do not look normal. They have only red boundaries (sulci); the green boundaries (gyri) are absent. The sulc surfaces look fine though.
on machine monkeylove
source /usr/local/freesurfer/nmr-dev-env
setenv SUBJECTS_DIR /space/ship/3/users/reza/mvp022106/3danat
which recon-all /usr/local/freesurfer/dev/bin//recon-all
cd /space/ship/3/users/reza/mvp022106/MYSTUDY
Thanks for any comments, Reza
Reza Rajimehr, MD
NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129
Email: reza@nmr.mgh.harvard.edu
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