Sorry for the delay. I'm new to FSL, Freesurfer, and VB, so maybe I'm doing it wrong, but I have the impression I cannot run FSL from the VB:
- Typing 'fsl' yields 'fsl: Command not found'.
- Checking the environment with 'echo $FSLDIR' yields 'FSLDIR: undefined variable'

- Checking the path with 'flirt -version' yields 'flirt: Command not found'

However, typing 'fsl' + tab shows the following available commands:

- fsl2par

- fsl_label2voxel

- fslmaths.fsl

- fslorient.fsl

- fslregister

- fslregister -sess

- fsl_rigid_register

- fslsfonts

- fsl_sub_seychelles

- fslswapdim.fsl

So it seems there are some FSL-related files installed, but apparently not all. I did download the virtual disk image for Freesurfer, so I assumed a complete FSL version would be included? I'm sorry if there's an obvious solution, but I can't seem to find it...

Thanks again,
Bianca

On Fri, Jun 21, 2013 at 6:16 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

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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Bianca van Kemenade, MSc
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Klinik für Psychiatrie und Psychotherapie
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--
Bianca van Kemenade, MSc
Doctoral Candidate, Berlin School of Mind and Brain

Klinik für Psychiatrie und Psychotherapie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
http://www.mind-and-brain.de/