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

Thu Dec 4 01:55:38 PST 2014

Ahh. I see. That makes more sense. That must be why I didn’t have to set
anything as I already had /usr/local/include and /usr/local/lib set.

Cheers,

-M

On Thu, Dec 4, 2014 at 1:49 AM, J-Donald Tournier <jdtournier at gmail.com>
wrote:

> 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
>>> 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
> <%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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