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Oops, those instructions should be:

cd $FSLDIR/bin
sudo rm -rf FSLeyes*app*
sudo rm -f fsleyes
sudo unzip /Users/molly/Downloads/FSLeyes-macos-latest.zip

On 9 August 2017 at 19:31, paul mccarthy <[log in to unmask]> wrote:

> Hi Molly,
>
> Start from scratch again. Don't run any other commands, or follow any
> other instructions.
>
> 1. Download FSLeyes from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes
> 2. Open a terminal
> 3. Type the following:
>
> cd $FSLDIR/bin
> rm -rf FSLeyes*.ap*
> rm -f fsleyes
> unzip /Users/molly/Downloads/FSLeyes-macos-latest.zip
> ln -s FSLeyes.app/Contents/MacOS/fsleyes ./fsleyes
>
> Cheers,
>
> Paul
>
>
>
>
>
> On 9 August 2017 at 19:17, Molly Pepper <[log in to unmask]> wrote:
>
>> Hi Paul,
>>
>> Sorry, it still does not work..
>>
>> I have removed everything and started the download from scratch but still
>> fail:
>>
>> Mollys-MacBook-Air:bin Molly$ sudo cp -r /usr/local/fsl/bin/FSLeyes.app .
>>
>> cp: /usr/local/fsl/bin/FSLeyes.app: No such file or directory
>>
>> Mollys-MacBook-Air:bin Molly$ fsleyes
>>
>> -bash: fsleyes: command not found
>>
>>
>> Do you have idea what might be wrong?
>>
>>
>> Thank you.
>>
>>
>> Molly.
>>
>> On Wed, Aug 9, 2017 at 6:13 PM, paul mccarthy <[log in to unmask]>
>> wrote:
>>
>>> Hi Molly,
>>>
>>> The finder view is probably showing FSLeyes.app_old (it is hiding the
>>> .app_old extension from you).
>>>
>>> If the FSLeyes-latest-macos.zip file in that directory is the one that
>>> you downloaded, just do this (from within /usr/local/fsl/bin):
>>>
>>> sudo unzip FSLeyes-latest-macos.zip
>>> sudo ln -s FSLeyes.app/Contents/MacOS/fsleyes ./fsleyes
>>>
>>> Cheers,
>>>
>>> Paul
>>>
>>> On 9 August 2017 at 18:00, Molly Pepper <[log in to unmask]> wrote:
>>>
>>>> Hi Paul,
>>>>
>>>> Thanks! The bash profile issue is resolved. But, tI just cannot get
>>>> FSLeyes to work.
>>>>
>>>> I have done exactly as you have said as well as ignoring the orectory
>>>> error and it still does not work:
>>>>
>>>> Mollys-MacBook-Air:bin Molly$ pwd
>>>>
>>>> /usr/local/fsl/bin
>>>>
>>>> Mollys-MacBook-Air:bin Molly $ sudo mv FSLeyes.app FSLeyes.app_old
>>>>
>>>> Password:
>>>>
>>>> mv: rename FSLeyes.app to FSLeyes.app_old/FSLeyes.app: No such file or
>>>> directory
>>>>
>>>> Mollys-MacBook-Air:bin Molly $ sudo cp -r
>>>> /usr/local/fsl/bin/FSLeyes.app .
>>>>
>>>> cp: /usr/local/fsl/bin/FSLeyes.app: No such file or directory
>>>>
>>>> Mollys-MacBook-Air:bin Molly $
>>>>
>>>>
>>>> One thing I have noticed is that when I 'ls' the FSLeyes.app is not
>>>> listed even though it is present in the finder window (see screenshots) and
>>>> FSLeyes.app_old is not visiable in the finder.
>>>>
>>>>
>>>> I am completely confused..
>>>>
>>>>
>>>> Molly.
>>>>
>>>>
>>>> [image: Inline image 1][image: Inline image 2]
>>>>
>>>> On Wed, Aug 9, 2017 at 5:39 PM, paul mccarthy <[log in to unmask]>
>>>> wrote:
>>>>
>>>>> Hi Molly,
>>>>>
>>>>> For the first issue, just ignore that error, and run the third command
>>>>> (sudo cp -r ...)
>>>>>
>>>>> As for the second issue, it looks like you have corrupted your PATH
>>>>> variable (you didn't add :$PATH at the end, whcih is very important).
>>>>>
>>>>> You will need to open ~/.bashrc in a text editor, and remove the
>>>>> lines that you added previously. Type this into a terminal:
>>>>>
>>>>> /usr/bin/open -a TextEdit ~/.bash_profile
>>>>>
>>>>> Remove the lines that you added, then save the file. You will then
>>>>> need to open a new terminal, or possiblty log out and log back in.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Paul
>>>>>
>>>>> On 9 August 2017 at 17:24, Molly Pepper <[log in to unmask]>
>>>>> wrote:
>>>>>
>>>>>> Hi Paul and Christina,
>>>>>>
>>>>>> I am using the latest version of fsl and I have done exactly as you
>>>>>> have suggested but I get the following error (!):
>>>>>>
>>>>>> Mollys-MacBook-Air:bin Molly$ 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.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>