You can ignore them or setenv NO_FSFAST 1 and it won't create the ~/matlab dir
doug
Peter J. Molfese wrote:
In the Mac version of Freesurfer, the FreeSurferEnv.sh script creates a matlab folder at ~/matlab. Can I change this location for running freesurfer on a grid (either Sun Grid Engine or Apple XGrid) where I won't always have access to a user folder? For instance, Xgrid runs jobs as an unprivileged user in a private directory (e.g. /private/var/xgrid/agent/tasks/TGSBflaF/working). Currently when I submit a job which sets up the freesurfer environment by calling the setup file and then a which to verify the environment is correct. The output shows that it executed the script and can now locate recon-all in /usr/local/freesurfer. But then I get a series of errors or warnings about matlab directory creation. Can I ignore these or silence them?
Script: #!/bin/bash
#setup Freesurfer export FREESURFER_HOME=/usr/local/freesurfer . $FREESURFER_HOME/SetUpFreeSurfer.sh
which recon-all
Output: INFO: /var/empty/matlab/startup.m does not exist ... creating /usr/local/freesurfer/bin/recon-all mkdir: /var/empty/matlab: Permission denied touch: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 213: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 214: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 215: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 216: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 217: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 218: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 219: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 220: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 221: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 222: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 223: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 224: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 225: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 226: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 227: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 228: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 229: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory
Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molfese@yale.edu
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