[Mrtrix-discussion] Installation on Mac OS Yosemite ver 10.10.1

Thu Dec 4 01:49:11 PST 2014

Thanks Morgan, all good to hear.

By the way, the GSL includes are in the gsl folder, but are specified as
such in the code (i.e. the include directives take the form #include
<gsl/gsl_matrix.h>, etc.), so you shouldn't include that last 'gsl' part of
the path in the header search path. If the GSL headers are indeed in
/usr/local/include/gsl, then specifying -I/usr/local/include should be
enough.

Cheers,
Donald.

On 3 December 2014 at 22:20, Morgan Hough <morgan.hough at gmail.com> wrote:

> Hi Helen,
>
>
> Following up on what Donald said, I see that the path for GSL includes an
> extra directory name (/gsl) after the include:
>
>
> /usr/local/include/gsl/
>
>
> or if you want to point to the Cellar directly
>
>
> /usr/local/Cellar/gsl/1.16/include/gsl/
>
>
> I am trying to figure out how I have this set because I don’t remember
> adding this include/lib path.
>
>
> Cheers,
>
>
> -Morgan
>
>
> BTW Donald, all the building I have been doing has been on Yosemite too
>
> On Wed, Dec 3, 2014 at 2:07 PM, J-Donald Tournier <jdtournier at gmail.com>
> wrote:
>
>> Hi Helen,
>>
>> Really good to hear that MRtrix3 works on Yosemite - it's the first
>> report I've heard about it. And sorry about the lack of ROI editing on
>> MRtrix3, I'm working on this, hopefully I'll have something ready within
>> the next few weeks.
>>
>> Regarding your MRtrix 0.2 install, it sounds like the issue might that
>> your GSL libraries have ended up somewhere unexpected. If you can figure
>> out where the GSL headers got installed (most likely something like
>> /usr/local/Cellar/gsl/include, given the paths listed on that
>> command-line), then you can add them in by modifying the sysconf/darwin.py
>> file, like this:
>>
>> 41 cpp_flags_gsl = [ '-I/usr/local/Cellar/gsl/include' ]
>> 42 # uncomment this line for default GSL BLAS implementation, or the
>> next line for the optimised ATLAS libraries (recommended for performance):
>> 43 ld_flags_gsl = [ '-L/usr/local/Cellar/gsl/lib', '-lgsl', '-lgslcblas'
>> ]
>>
>> Note that line 43 modification assumes the GSL libraries themselves
>> (libgsl.so, libgslcblas.so) are installed in that location. You might want
>> to check that if it fails later at the linking stage.
>>
>> Hope this helps!
>> Cheers,
>>
>> Donald.
>>
>>
>> On 3 December 2014 at 17:57, Helen Carlson <
>> Helen.Carlson at albertahealthservices.ca> wrote:
>>
>>> Hello MRTrix experts
>>> I have upgraded to MRTrix 3 (which works fine) but would also like to
>>> run MRTrix 0.2.12 for editing ROIs and using some of the older functions
>>> and so I am attempting to install it and am getting stuck at the ./build
>>> stage (See below for the error message). My operating system is Mac OS
>>> Yosemite version 10.10.1. I have installed the dependencies using this
>>> command "brew install python glib gtk+ glibmm gtkmm gtkglext gsl". I have
>>> installed XCode 6.1, X11, QT 3.2.0.
>>>
>>> My $PATH contains:
>>> /Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
>>>
>>> I then change directory to /Applications/mrtrix-0.2.12 and enter
>>> ./build. This is the first part of the error I get (it seems to be unable
>>> to find the GSL libraries).
>>>
>>> bash-3.2$ ./build
>>> [CC] lib/math/vector.o
>>> [CC] src/mrview/sidebar/roi_analysis.o
>>> [CC] cmd/dir2amp.o
>>> [CC] src/mrview/mode/base.o
>>> [CC] lib/file/dicom/quick_scan.o
>>> [CC] lib/image/format/list.o
>>> [CC] cmd/streamtrack.o
>>> [CC] src/mrview/window.o
>>>
>>> ERROR: [CC] lib/math/vector.o
>>>
>>> clang++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing
>>> -DGL_GLEXT_PROTOTYPES -O2 -D_REENTRANT
>>> -I/usr/local/Cellar/glibmm/2.42.0/include/glibmm-2.4
>>> -I/usr/local/Cellar/glibmm/2.42.0/lib/glibmm-2.4/include
>>> -I/usr/local/Cellar/libsigc++/2.4.0/include/sigc++-2.0
>>> -I/usr/local/Cellar/libsigc++/2.4.0/lib/sigc++-2.0/include
>>> -I/usr/local/Cellar/glib/2.42.1/include/glib-2.0
>>> -I/usr/local/Cellar/glib/2.42.1/lib/glib-2.0/include
>>> -I/usr/local/opt/gettext/include -Ilib -Isrc lib/math/vector.cpp -o
>>> lib/math/vector.o
>>>
>>> failed with output:
>>>
>>> In file included from lib/math/vector.cpp:25:
>>> lib/math/vector.h:26:10: fatal error: 'gsl/gsl_vector.h' file not found
>>> #include <gsl/gsl_vector.h>
>>>          ^
>>> 1 error generated.
>>>
>>> Can someone please point me in the right direction so I can fix this?
>>> Thanks
>>>
>>>
>>> Helen
>>>
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>>
>>
>>
>> --
>> *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
>> <%2B44%20%280%2920%207188%207118%20ext%2053613>*
>> *W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>> <http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
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>>
>>
>

-- 
*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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