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Hi Paul and Christina,

I am using the latest version of fsl and I have done exactly as you have
suggested but I get the following error (!):

Mollys-MacBook-Air:bin Molly$ cd /usr/local/fsl/bin

Mollys-MacBook-Air:bin Molly$ sudo mv FSLeyes.app FSLeyes.app_old

mv: rename FSLeyes.app to FSLeyes.app_old/FSLeyes.app: No such file or
directory


Since attempting to change the search path and editing the ~/.bashrc file,
I am now also unable to open fsl.. Really not sure what I have done wrong!

Any ideas would be appreciated!


Thanks,


Molly

On Wed, Aug 9, 2017 at 3:30 PM, paul mccarthy <[log in to unmask]>
wrote:

> 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.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>