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/
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