retinotopic mapping selxavg3-sess error - Freesurfer

21 Jun 2013


      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