Hi,
I just wanted to let you know that I solved the problem by creating a new virtual machine on which I installed the newest version of Ubuntu (13.04), FSL, and Freesurfer manually. I guess there could have been a solution with the virtual machine running Xubuntu via the Freesurfer virtual disk image, but I didn't manage to figure it out so I decided to take this longer route. Anyway it seems to run well now!
Best, Bianca
On Mon, Jun 24, 2013 at 11:36 AM, Bianca van Kemenade < biancavankemenade@gmail.com> wrote:
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.eduwrote:
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 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/
-- 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/
freesurfer@nmr.mgh.harvard.edu
-
Bianca van Kemenade