Can you run FSL at all in your VB?
On 6/21/13 7:49 AM, Bianca van Kemenade wrote:
Dear Freesurfers,
I'm setting up freesurfer to do retinotopic mapping. I use a PC with
Windows XP, so I installed Freesurfer using the VirtualBox (with
Xubuntu). I managed to get through the initial steps for retinotopic
mapping, but I get stuck at the actual analysis.
The point where I get stuck is:
selxavg3-sess -a rtopy.self.lh -s P2_BK
It starts the analysis, but runs into problems at the stage "Using
FSL's BET to extract brain" and gives the following error output:
# ---------- Using FSL's BET to Extract Brain------------------ #
/home/virtualuser/freesurfer/
shared/P2_BK/bold
bet.fsl /tmp/mkbrainmask_4425/in.nii /tmp/mkbrainmask_4425/brain -m -f 0.1
/home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found
/home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found
[: 158: =: unexpected operator
/home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found
/bin/rm: cannot remove `_tmp*': Protocol error
ERROR: bet failed
I tried updating FSL in case that is the problem, but it is only
available for Ubuntu 10.04 and up, whereas the Ubuntu system that is
provided to install the Freesurfer virtual disk image is 9.04. If
anyone has an idea how to proceed let me know, any help is much
appreciated.
Thanks,
Bianca
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