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Hi Molly, (Thanks for your help Christina!) It will probably be easier to create a link to FSLeyes, instead of editing your search path. Type the following commands into a terminal: cd /usr/local/fsl/bin sudo mv FSLeyes.app FSLeyes.app_old sudo cp /path/to/where/you/have/unzipped/FSLeyes.app . If you are using FSL 5.0.10, then fsleyes should now start working. However, if you are using an older version of FSL, you will need to do a little more work: cd /usr/local/fsl/bin sudo ln -s FSLeyes.app/Contents/MacOS/fsleyes ./fsleyes Cheers, Paul On 9 August 2017 at 14:04, Chr. Rossmanith <[log in to unmask]> wrote: > Well, you've just added the lines to your .bashrc. But this has no effect > for the moment unless you log out and log in again (which executes > ~/.bashrc) or enter the following in the terminal (only effective for THAT > single shell!): source ~/.bashrc > > This executes all command in your .bashrc including the new ones and > modifies your current shell. > > Christina > > > On 09.08.2017 14:59, Molly Pepper wrote: > > Hi Christina, > > Thank you - makes sense. I have extended the path variable and tried to > add the lines you suggest. > I am not sure I am adding the lines correctly. I have typed the following > into the terminal (and they return no error): > > echo 'export PATH=/Users/Molly/Desktop/softwares/FSLeyes' >> ~/.bashrc > > echo 'export PATH' >> ~/.bashrc > > I still get the 'fsleyes: command not found' error. > > Am I doing something obviously wrong? > > Molly. > > > > > On Wed, Aug 9, 2017 at 12:55 PM, Chr. Rossmanith < > [log in to unmask]> wrote: > >> Search path is the list of directories where your shell is looking for >> executables/programs. I don't know, where you've unzipped the archive, >> let's say it was /opt/Software/FSLeyes. In the terminal you could either >> call /opt/Software/FSLeyes/fsleyes (calling with the full path) or you >> could extend you PATH variable: export PATH=/opt/Software/FSLeyes:$PATH >> Now your shell is prepared to find fsleyes like it finds fslview. If you >> add the following two lines to your ~/.bashrc file you don't have to >> prepare your shell everytime you want to work with fsleyes: >> >> PATH=/opt/Software/FSLeyes >> export PATH >> >> Of course you always have to replace "/opt/Software/FSLeyes" with the >> directory where your fsleyes has been extracted to. >> >> Christina >> >> >> >> On 09.08.2017 13:43, Molly Pepper wrote: >> >> Thanks. Sorry but I am not sure what you mean by search path? >> I am working via the terminal. I cannot open using the full path because >> it reads as a directory and so will not open. >> >> Should I not be able to call it by typing 'fsleyes' similar to fslview >> without having to move to it directory location? >> >> Thanks. >> >> M. >> >> >> >> On Wed, Aug 9, 2017 at 12:33 PM, Chr. Rossmanith < >> [log in to unmask]> wrote: >> >>> Hi, >>> >>> sounds like fsleyes isn't in your search path. Try calling it with the >>> full path or add the location where you've unpacked it to your search path. >>> >>> Regards, >>> Christina Rossmanith >>> >>> >>> On 09.08.2017 12:16, Molly Pepper wrote: >>> >>> Hi, >>> >>> I have downloaded fsleyes and unzipped in my location of choice (fsl >>> directory). >>> >>> Fsleyes will open when I double click the icon but I cannot get it to >>> open in the command line as I previously done with fslview e.g: >>> >>> $ fsleyes /usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz >>> caudate_individual.nii.gz >>> >>> However, I get the following message: >>> >>> -bash: fsleyes: command not found >>> >>> I am using a macbook air with Sierra OS. >>> >>> Any ideas? >>> >>> Thanks. >>> >>> >>> >>> >>> >>> >> >> > >