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

[Morgan Hough]

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>*
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