[Mrtrix-discussion] Update and version checking / orientation plot

[Donald Tournier]

Hi Markus,

Good to hear everything works as expected. As far as I can tell, the locale
and xlib messages are nothing to worry about. The locale warning means that
it probably won't know how to handle non-ascii filenames and other
region-specific differences. RANDR refers to an X11 extension for Resize
and Rotate (to allow on-the-fly screen configuration changes on X11-based
systems), which is probably handled just fine by MacOSX's Quartz backend.
So as long as it all works OK, I wouldn't worry about it.

Cheers,

Donald.


On 2 March 2012 07:20, Markus Gschwind <markus.gschwind at gmail.com> wrote:

> Dear Donald!
>
> Thank you, brilliant, exactly as you said!
> I  run down the list of all mrtrix functions and deleted them out of the
> /usr/local/bin folder.
>
> And now I also can script mrtrix functions (which did not work with my
> previous installation), great!
>
> And also the mrview orientation plot overlay works, thank you!!
>
> One last question:
>
> When opening mrview it gives me always the following error:
>
> (process:2135): Gtk-WARNING **: Locale not supported by C library.
> Using the fallback 'C' locale.
> Xlib:  extension "RANDR" missing on display "/tmp/launch-KsUFRz/org.x:0".
>
> Is this a problem?
>
>
> Thank you so much!
> Best wishes,
> Markus
>
> 2012/3/1 Donald Tournier <d.tournier at brain.org.au>
>
>> Hi Markus,
>>
>> The problem you're having is probably something I should have documented
>> for this new release - the previous installation does indeed need to be
>> removed. Essentially, the problem is that the "./build install" command
>> will copy the executables into a different folder than where the
>> documentation of the previous installations would have suggested. So you'll
>> end up having a copy of each executable in two different locations, and it
>> will then depend on which the system finds first (i.e. which location is
>> listed first in your PATH). This should only be a problem for those
>> upgrading to the new version via the "./build install" command - new or
>> subsequent installs using this command will overwrite the previous version.
>>
>> To remove the previous installation, the simplest thing to do is to ask
>> the system which executables it's running, and then remove them. So chose
>> one of the commands from the old version:
>>
>> $ mrconvert -version
>> (should return 0.2.9)
>>
>> ask the system which it's using:
>> $ which mrconvert
>> (should return something like /opt/mrtrix/bin/mrconvert)
>>
>> and delete all MRtrix executables in that folder (or the whole folder if
>> you know that it contains only MRtrix commands). So you could for instance
>> delete the whole /opt/mrtrix folder (assuming that's where the old
>> installation is located). Command for that is (use this with extreme
>> caution - this is a permanent delete):
>> $ sudo rm -rf /opt/mrtrix
>>
>> Hope this sort out the problem!
>> Cheers,
>>
>> Donald.
>>
>>
>> On 29 February 2012 22:33, Markus Gschwind <markus.gschwind at gmail.com>wrote:
>>
>>> Dear Donald,
>>>
>>> Thank you very much for the hint.
>>>
>>> Although I run
>>>
>>> sudo  ./build install
>>>
>>> indeed for all fonctions of mrtrix the -version option gives 0.2.9, only
>>> for three new fonctions (e.g.tracks2vtk) it gives 0.2.10.
>>> I understand that the old version is not overwritten and that the two
>>> versions are now coexisting.
>>>
>>> What can I do in order to overwrite the former version clearly?
>>>
>>> Thank you so much!
>>>
>>> Markus
>>>
>>>
>>>
>>>
>>> 2012/2/28 Donald Tournier <d.tournier at brain.org.au>
>>>
>>>> Hi Markus,
>>>>
>>>> To check the running version, run any MRtrix command with the -version
>>>> option. e.g.:
>>>> $ mrview -version
>>>>
>>>> Or in MRView, click on Help->About.
>>>>
>>>>  Otherwise, the orientation plot overlay was a tricky one to get
>>>> working on Mac, so may well have issues. That said, I just checked it on a
>>>> Snow Leopard system, and it works fine there.
>>>>
>>>> On the other hand, there are a couple of other reasons why it might not
>>>> work. One is that it will not work when the "Image->Lock to image axes"
>>>> option is unticked - it's hard to figure out how to regrid the FODs when
>>>> off-axis, so I've simply disabled it. The other reason could be that the
>>>> 'progressive' option of the orientation plot overlay does not work on the
>>>> Mac version, so make sure it is unticked. If neither of these is the
>>>> culprit, then I'll have to investigate further, but it'll be a while before
>>>> I get round to it.
>>>>
>>>> Cheers,
>>>>
>>>> Donald.
>>>>
>>>>
>>>> On 28 February 2012 08:21, Markus Gschwind <markus.gschwind at gmail.com>wrote:
>>>>
>>>>> Dear Experts,
>>>>>
>>>>> I just have updated the mrtrix installation from 0.2.9 to 0.2.10 on my
>>>>> Mac (Snow Leopard).
>>>>> I am not sure I am now running the new version or the old one.
>>>>>
>>>>> Is there any control function to evaluate if the installation is
>>>>> really working and what version is running?
>>>>>
>>>>> And my second question: The orientation plot in mrview is not running
>>>>> in the overlay modus (I do not see anything). Is this to be expecte in Mac
>>>>> installations?
>>>>>
>>>>> Thanks for the great tool!
>>>>> Best
>>>>> Markus
>>>>>
>>>>> _______________________________________________
>>>>> Mrtrix-discussion mailing list
>>>>> Mrtrix-discussion at www.nitrc.org
>>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Jacques-Donald Tournier (PhD)
>>>> Brain Research Institute, Melbourne, Australia
>>>> Tel: +61 (0)3 9035 7033
>>>>
>>>
>>>
>>>
>>> --
>>>
>>
>>
>>
>> --
>> Jacques-Donald Tournier (PhD)
>> Brain Research Institute, Melbourne, Australia
>> Tel: +61 (0)3 9035 7033
>>
>
>
>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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