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

[Donald Tournier]

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
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