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/binsudo mv FSLeyes.app FSLeyes.app_oldsudo 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/binsudo ln -s FSLeyes.app/Contents/MacOS/ fsleyes ./fsleyesCheers,PaulOn 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.
On 09.08.2017 14:59, Molly Pepper wrote:
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/soft
wares/FSLeyes' >> ~/.bashrc
echo 'export PATH' >> ~/.bashrc
I still get the 'fsleyes: command not found' error.
Am I doing something obviously wrong?
On Wed, Aug 9, 2017 at 12:55 PM, Chr. Rossmanith <[log in to unmask]
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:$PA
TH 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:
Of course you always have to replace "/opt/Software/FSLeyes" with the directory where your fsleyes has been extracted to.
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?
On Wed, Aug 9, 2017 at 12:33 PM, Chr. Rossmanith <[log in to unmask]
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.
On 09.08.2017 12:16, Molly Pepper wrote:
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/M
However, I get the following message:
-bash: fsleyes: command not found
I am using a macbook air with Sierra OS.