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 < biancavankemen...@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 > <gr...@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 >> >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > 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/ > -- 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/
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