Sorry - the first block of commands in my previous email should look like this:

cd /usr/local/fsl/bin

sudo mv FSLeyes.app FSLeyes.app_old

sudo cp -r /path/to/where/you/have/unzipped/FSLeyes.app .

On 9 August 2017 at 15:24, paul mccarthy <[log in to unmask]> wrote:

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.