I see some reports of license failures, and seem to be having a similar problem. Our installations of 4.5 and 5.1 work normally, but with 5.3 I had a mysterious error in unpacksdcmdir that ultimately traced to a license error in mri_convert. I can reproduce the error like so:

mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz

mri_convert /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz T1.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz...
--------------------------------------------------------------------------
ERROR: Invalid FreeSurfer license key found in license file /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/.license
--------------------------------------------------------------------------

bugr

FREESURFER_HOME: /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full
Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
RedHat release: Red Hat Enterprise Linux Server release 5.9 (Tikanga)
Kernel info: Linux 2.6.18-308.4.1.el5 x86_64

cat $FREESURFER_HOME/.license

ppo...@mail.rockefeller.edu
9148
 *C7cx5HQ1V7ws

(This is the same license we use successfully with v4.5 and v5.1)

Thanks!  (Also, please advise and accept my apologies if I'm using the list wrong -- just getting started here.)

best,
stephen

stephen v. shepherd   phd
The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620