Hi Freesurfers,
I've downloaded and installed Freesurfer on in VirtualBox running Ubuntu 12.04 (on a Windows 7 host machine). In my shell, though, it's installed with CentOS4 (see below)
I've been working through the page on testing the installation. Everything works nicely, until I get to the recon-all commands. When I try having it just run the -autorecon1 stage on its own, I get this error:
-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni
arose@HarryCallahan:/usr/local/freesurfer/subjects/buckner_data/tutorial_subjs$ recon-all -s bert -autorecon1
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer rm: cannot remove `/usr/local/freesurfer/subjects/bert/scripts/recon-all.cmd': Permission denied mv: cannot move `/usr/local/freesurfer/subjects/bert/scripts/recon-all.env' to `/usr/local/freesurfer/subjects/bert/scripts/recon-all.env.bak': Permission denied -rw-rw-rw- 1 root root 805935 May 21 16:53 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log Linux HarryCallahan 3.11.0-20-generic #35~precise1-Ubuntu SMP Fri May 2 21:32:55 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux rm: cannot remove `/usr/local/freesurfer/subjects/bert/scripts/recon-all.done': Permission denied /usr/local/freesurfer/subjects/bert/scripts/IsRunning.lh+rh: Permission denied. arose@HarryCallahan:/usr/local/freesurfer/subjects/buckner_data/tutorial_subjs$
Is there something simple that I do so that the files it creates are automatically allowed to be moved/removed etc? The sudo command doesn't help, unfortunately.
Thanks in advance, Ashley