<div dir="ltr">Thanks Morgan, all good to hear.<div><br><div>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 <font face="monospace">#include <gsl/gsl_matrix.h></font>, 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 <font face="monospace">/usr/local/include/gsl</font>, then specifying <font face="monospace">-I/usr/local/include</font> should be enough.</div><div><br></div><div>Cheers,</div><div>Donald.</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 3 December 2014 at 22:20, Morgan Hough <span dir="ltr"><<a href="mailto:morgan.hough@gmail.com" target="_blank">morgan.hough@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">
<p><span>Hi Helen,</span></p>
<p><span></span><br></p>
<p><span>Following up on what Donald said, I see that the path for GSL includes an extra directory name (/gsl) after the include:</span></p>
<p><span></span><br></p>
<p><span>/usr/local/include/gsl/</span></p>
<p><span></span><br></p>
<p><span>or if you want to point to the Cellar directly</span></p>
<p><span></span><br></p>
<p><span>/usr/local/Cellar/gsl/1.16/include/gsl/</span></p><p><span></span></p>
<p><span></span><br></p>
<p><span>I am trying to figure out how I have this set because I don’t remember adding this include/lib path. </span></p>
<p><span></span><br></p>
<p><span>Cheers,</span></p>
<p><span></span><br></p>
<p><span>-Morgan</span></p><p><span><br></span></p><div class="gmail_extra">
<p><span>BTW Donald, all the building I have been doing has been on Yosemite too</span></p></div><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Dec 3, 2014 at 2:07 PM, J-Donald Tournier <span dir="ltr"><<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Helen,<div><br></div><div>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.</div><div><br></div><div>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:</div><div><br></div><div><div><font face="monospace"><font color="#999999">41</font><font color="#666666"> </font>cpp_flags_gsl = [ <font color="#ff0000">'-I/usr/local/Cellar/gsl/include'</font></font><span style="font-family:monospace"> ]</span></div><div><font face="monospace"><font color="#999999">42</font><font color="#666666"> </font># uncomment this line for default GSL BLAS implementation, or the next line for the optimised ATLAS libraries (recommended for performance):</font></div><div><font color="#999999" style="font-family:monospace">43</font><font color="#666666" style="font-family:monospace"> </font><font face="monospace">ld_flags_gsl = [ <font color="#ff0000">'-L/usr/local/Cellar/gsl/lib'</font></font><span style="font-family:monospace"><font color="#ff0000">,</font> '-lgsl', '-lgslcblas' ]</span></div></div><div><br></div><div>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. </div><div><br></div><div>Hope this helps!</div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><div><div><br><div class="gmail_quote">On 3 December 2014 at 17:57, Helen Carlson <span dir="ltr"><<a href="mailto:Helen.Carlson@albertahealthservices.ca" target="_blank">Helen.Carlson@albertahealthservices.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Hello MRTrix experts<br>
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.<br>
<br>
My $PATH contains: /Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin<br>
<br>
I then change directory to /Applications/mrtrix-0.2.12 and enter ./build. This is the first part of the error I get (it seems to be unable to find the GSL libraries).<br>
<br>
bash-3.2$ ./build<br>
[CC] lib/math/vector.o<br>
[CC] src/mrview/sidebar/roi_analysis.o<br>
[CC] cmd/dir2amp.o<br>
[CC] src/mrview/mode/base.o<br>
[CC] lib/file/dicom/quick_scan.o<br>
[CC] lib/image/format/list.o<br>
[CC] cmd/streamtrack.o<br>
[CC] src/mrview/window.o<br>
<br>
ERROR: [CC] lib/math/vector.o<br>
<br>
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<br>
<br>
failed with output:<br>
<br>
In file included from lib/math/vector.cpp:25:<br>
lib/math/vector.h:26:10: fatal error: 'gsl/gsl_vector.h' file not found<br>
#include <gsl/gsl_vector.h><br>
^<br>
1 error generated.<br>
<br>
Can someone please point me in the right direction so I can fix this?<br>
Thanks<br>
<br>
<br>
Helen<br>
<br>
This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you.<br>
_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
</blockquote></div><br><br clear="all"><div><br></div></div></div><span><font color="#888888">-- <br><div><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div><i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br></font></i></div><div><i><font color="#990000"><b>T:</b> <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">+44 (0)20 7188 7118 ext 53613</a></font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br></div></div></div>
</font></span></div>
<br>_______________________________________________<br>
Mrtrix-discussion mailing list<br>
<a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
<a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
<br></blockquote></div><br></div></div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div><i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br></font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br></div></div></div>
</div>