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