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Hi Paul,

Thanks! I am almost there. I now though get the following error when trying
to open fsleyes:

Mollys-MacBook-Air:bin Molly$ fsleyes

2017-08-09 20:02:03.505 fsleyes[1050:44762] The Info.plist file must have a
PyRuntimeLocations array containing string values for preferred Python
runtime locations.  These strings should be "otool -L" style mach ids;
"@executable_stub" and "~" prefixes will be translated accordingly.




On Wed, Aug 9, 2017 at 7:42 PM, paul mccarthy <[log in to unmask]>
wrote:

> Sorry again. I have a suspicion that gmail has been clipping the last
> command in that block. The full set of commands (including the last one,
> which I think you might have been missing) is:
>
> cd $FSLDIR/bin
> sudo rm -rf FSLeyes*.ap*
> sudo rm -f fsleyes
> sudo unzip /Users/Molly/Downloads/FSLeyes-latest-macos.zip
> sudo ln -s FSLeyes.app/Contents/MacOS/fsleyes ./fsleyes
>
> This is all you should need to do
>
> Paul
>
> On 9 August 2017 at 19:33, paul mccarthy <[log in to unmask]> wrote:
>
>> 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.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>