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Open a terminal… cat >> $HOME/.bash_profile <<EOF FSLDIR=/usr/local/fsl PATH=$FSLDIR/bin:$PATH export FSLDIR PATH . $FSLDIR/etc/fslconf/fsl.sh EOF (assuming FSL was installed to /usr/local) Open a new terminal and try running the commands from there. Duncan On 17 Jun 2014, at 16:17, Robert Bromley <[log in to unmask]> wrote: > Sorry - I thought I had this cracked. It turns out the GUI isn't working though. Typing 'fsl' into terminal just brings up 'Command not found' regardless of the directory I run it in. If I double click on fsl_gui then I get the message 'You need to set the FSLDIR environment variable to point to the FSL installation directory before you can run anything.' > > I don't suppose you know what I should do? > > Thanks > Rob > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Duncan Mortimer > Sent: 05 June 2014 11:17 > To: [log in to unmask] > Subject: Re: [FSL] Problem installing FSL > > > On 5 Jun 2014, at 11:07, Robert Bromley <[log in to unmask]> wrote: > >> Hi Duncan, >> >> Thanks a lot for getting back to me about this. I managed to get the script running, although, I used Wifi instead of Ethernet, downloaded the newest installer and used the -D switch, so I'm not sure which bit made it work. >> > I wonder if there is some restriction in place on your ethernet network. > >> Unfortunately, I'm still having problems. The script ran as below and I can see fslview in Applications but when I click on it I just get a dialogue box which says The alias "fslview" can't be opened because the original item can't be found. The button options are to delete or fix the alias. I don't suppose you've got any idea of what I can try next? >> > Check that the fslview alias points at the correct location: > > ls -l /Applications/fslview.app > > this should report /usr/local/fsl/bin/fslview.app. If not: > > sudo rm /Applications/fslview.app > sudo ln -s /usr/local/fsl/bin/fslview.app /Applications/ > > and try again. > > Duncan > >> Thanks >> Rob >> >> Last login: Thu Jun 5 09:47:17 on console campus-10-41-252-244:~ >> root# cd ~/Downloads campus-10-41-252-244:Downloads root# python >> fslinstaller.py >> --- FSL Installer - Version 2.0.14 --- [OK] Installer is current Where >> would you like to install FSL? [/usr/local]: FSL Install location doesn't exist, should I create it? [yes]: Yes Downloading FSL version 5.0.6 (this may take some time) >> Checking download... >> [OK] Download is good. >> Installing FSL software... >> [OK] FSL software installed. >> Creating Application links... >> Checking for X11 windowing system (required for FSL GUIs). >> [OK] X11 software (required for FSL GUIs) is installed. >> campus-10-41-252-244:Downloads root# >> >> >> -----Original Message----- >> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On >> Behalf Of Duncan Mortimer >> Sent: 03 June 2014 13:41 >> To: [log in to unmask] >> Subject: Re: [FSL] Problem installing FSL >> >> Hi, >> >> Could you try re-downloading the installer, there was a bug in the error reporting on older versions of Python (as available on OS X) - there has been an issue with determining the download settings but the bug is preventing the error message from being displayed. This has been fixed in version 2.0.14. >> >> Once you have this try running it with the '-D' option and we'll see if there is any useful information as to why you are getting a download failure. >> >> Duncan >> On 29 May 2014, at 14:05, Rob Bromley <[log in to unmask]> wrote: >> >>> Hi everyone, >>> >>> I'm having a bit of trouble installing FSL and I'm hoping someone might be able to help! >>> >>> I've downloaded fslinstaller.py for OSX and followed the instructions to run it from the Downloads directory with the commands: >>> >>> cd ~/Downloads >>> >>> python fslinstaller.py >>> >>> When I do though, I'm just getting the following error: >>> >>> Last login: Thu May 29 11:27:54 on console psc-pc120:~ root# cd >>> ~/Downloads psc-pc120:Downloads root# python fslinstaller.py >>> --- FSL Installer - Version 2.0.13 --- Traceback (most recent call >>> last): >>> File "fslinstaller.py", line 1975, in <module> >>> installer(options,args) >>> File "fslinstaller.py", line 1720, in installer >>> a_result = fastest_mirror() >>> File "fslinstaller.py", line 901, in fastest_mirror >>> MsgUser.debug(e.reason.strerror) >>> AttributeError: 'error' object has no attribute 'strerror' >>> psc-pc120:Downloads root# >>> >>> I'm running OSX 10.6 with the most recent updates and I've tried logging in as the root user. >>> >>> Any ideas? >>> >>> Thanks >>> >>> Rob >> >> -- >> Duncan A B Mortimer DPhil MChem >> Computing Officer, FMRIB Centre, University of Oxford, >> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. >> Tel: (0)1865 222713 email: [log in to unmask] >> Personal email (not for IT support): [log in to unmask] > > -- > Duncan A B Mortimer DPhil MChem > Computing Officer, FMRIB Centre, University of Oxford, > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. > Tel: (0)1865 222713 email: [log in to unmask] > Personal email (not for IT support): [log in to unmask] -- Duncan Mortimer Computing Officer, FMRIB Centre, University of Oxford John Radcliffe Hospital, Oxford, UK