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

[J-Donald Tournier]

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*
*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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