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