[Mrtrix-discussion] Difficulty installing MRtrix 0.2.12

Tue Mar 28 05:09:53 PDT 2017

(posted previous incomplete response by mistake, here's the complete
response!)

Hi,

This reply is based on a long back and forth that I had with Donald
Tournier, in which he helped me to install MRtrix 2.13. There are 2 main
issues that need to be addressed:

   1. *MRtrix version*: the latest release on NITRC (MRtrix 0.2.12) wasn't
   quite up to date, so Donald was kind enough to upload an updated version
   (0.2.13). Make sure you're using the latest version, which can be found
   here <https://www.nitrc.org/frs/?group_id=128&release_id=3487>.
   2. *GSL Version: *you need to downgrade GSL to a version prior to 2.0.
   This will depend on the channel through which it was installed. General
   instructions for this are available from here
   <https://trac.macports.org/wiki/howto/InstallingOlderPort>for Macports
   and here
   <http://effectif.com/mac-os-x/installing-specific-version-of-homebrew-formula>for
   Homebrew.

I also attached a text file with step-by-step instructions for installing
MRtrix 2.13 on a macOS Sierra using Macports. The instructions are quite
specific to what I had to do, so they might not be helpful to everybody,
but I thought I would share them anyway.

Thanks again, Donald! I hope I can make good use of your software.

Cheers,
Shereif

On Thu, Mar 23, 2017 at 9:20 AM, J-Donald Tournier <jdtournier at gmail.com>
wrote:

> Hi Shereif,
>
> I've already answered your question on the MRtrix3 forum, but if you need
> more advice, please carry on the conversation here, since this is about the
> old version of MRtrix.
>
> Just in case others are looking for my answer, it was:
>
> I think it's just that the instructions aren't quite up to date with the
> version you downloaded. Have you tried:
>
> $ cd mrtrix-0.2.12
>
> instead...?
>
> Cheers,
> Donald.
>
> On Wed, 22 Mar 2017 at 15:29 Luis Concha <lconcha at unam.mx> wrote:
>
>> Hi Shereif.
>>
>> Unless you have a very specific reason to stick to mrtrix version 2, I
>> strongly suggest you install mrtrix3 available here
>> <http://www.mrtrix.org/>. Installation instructions are very clear and
>> straightforward so you should not bump into any troubles.
>>
>> Make sure you subscribe to the new mailing list, as this one is merely
>> historical by now.
>>
>> Cheers.
>>
>> Dr. Luis Concha
>> Instituto de Neurobiología
>> Laboratorio C-13
>> UNAM, Campus Juriquilla
>> Boulervard Juriquilla 3001
>> Juriquilla, Querétaro.
>> C.P. 76230
>> México
>> Tel (442) 2 38 10 54
>> Fax (442) 2 38 10 46
>> http://personal.inb.unam.mx/lconcha/
>>
>> On Wed, Mar 22, 2017 at 8:34 AM, Haykal, S.A.M.M. <s.a.m.m.haykal at rug.nl>
>> wrote:
>>
>> Hello,
>>
>> I'm trying to install MRtrix 0.2.12 on a macOS Sierra 10.12.3, but for
>> some reason I can't manage to compile it. I installed both Xcode and
>> Xquartz (the X11 substitute), and I successfully installed the dependencies
>> using both Macports and Homebrew (on 2 separate occasions), but when try to
>> compile it using:
>>
>> $ cd mrtrix-0.2.10
>> $ ./build
>>
>>
>> I get the following error:
>>
>> -bash: cd: mrtrix-0.2.10: No such file or directory
>>
>> Same error with both methods. I can't even find a directory named
>> "mrtrix-0.2.10", so I completely understand the error message.
>>
>> What am I missing? I'm quite new to coding, so forgive me if my question
>> is more on the novice side of things. I feel like the solution to my
>> problem is really simple, but I just can't figure it out! I'd be very
>> grateful if someone can help me out. Thanks!
>>
>> Best,
>> Shereif
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
> --
> *Dr J-Donald Tournier (PhD)*
>
> *Senior Lecturer, **Biomedical Engineering*
>
> *Division of Imaging Sciences & Biomedical EngineeringKing's College
> London*
>
>
> *A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH*
> *T: +44 (0)20 7188 7118 ext 53613*
> *W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
> <http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
>
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MRtrix 2.12(2.13) installation on macOS Sierra (10.12.3)

- Download and extract “mrtrix-0.2.13_2017-03-25.tar.bz2” file from https://www.nitrc.org/projects/mrtrix/

- Install Xcode and XQuartz (X11 replacement)

- Install dependencies: Follow instructions on http://jdtournier.github.io/mrtrix-0.2/install/macosx.html to install dependencies. Different methods are available, but the rest of the instructions here assume the use of MacPorts. Make sure to uninstall Homebrew beforehand if previously used, since it somehow conflicts with Macports

- You may need to add /usr/local/bin folder to your PATH. In terminal:

	$ export PATH=$PATH:/usr/local/bin

- Your system will probably be using GSL version 2, which is not backward compatible with version 1 (which was current when MRtrix was originally being developed). To overcome this problem, you need to revert to using the older version of GSL. To do so, in terminal:

	$ git clone --single-branch https://github.com/macports/macports-ports.git
	$ cd macports-ports
	$ git checkout 1fa205ad58

	$ cd math/gsl
	$ sudo port install

This should get Macports to revert back to the last GSL version before it switched to GSL 2.0.

- If MRtrix was previously installed erroneously, use:

	$ ./build clean

If first attempt at installing, go directly to next step.

- Compile MRtrix: 

	$ cd mrtrix-0.2.13
	$ ./build
	$ sudo ./build install