<div dir="ltr"><div><div><div>Dear MRtrix community, <br></div><br></div><div>I have compiled MRtrix in windows after a lot of work installing the gtk libraries. Now however, when I try to run mrconvert on another computer running the same operating system (Win8 32 bit) I get the error: <b>The application was unable to start correctly (0xc0000142). </b>At first I thought this was an error with DLLs, however using dependancy walker I have found this is not the case. I am wondering now if the error is perhaps there is a flag I must use during the compilation in order to use the exes on another machine. Looking at the build script I see the following option <b> -system=X specify the architecture to build</b>. Could this be used to compile the executable for use on another system? <br>
</div>Once I am able to compile and run MRconvert in windows, I would be happy to contribute the process for others in the future to follow. I have already made a list of all the dependencies and the required versions needed to compile. <br>
<br></div>thank you,<br>Jesse<br><div><div><div><div><div><div><div><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Jesse Ross-Jones</b> <span dir="ltr"><<a href="mailto:jesse.rj@gmail.com">jesse.rj@gmail.com</a>></span><br>
Date: Mon, Jun 3, 2013 at 9:21 AM<br>Subject: Re: MRtrix mrconvert in windows<br>To: Jeurissen Ben <<a href="mailto:Ben.Jeurissen@ua.ac.be">Ben.Jeurissen@ua.ac.be</a>><br><br><br><div dir="ltr"><div><div><div><div>
Dear Ben,<br>
<br></div>After much work I have finally succeed in compiling MRtrix in windows. It is quite a bit of work to find the correct versions of the dependencies. Now however when I try to run the compiled exe on another windows (same OS ) machine I get an error: <br>
</div>The application was unable to start correctly (0xc0000142). And when I dig a bit further I find this is likely related to problems with 64 bit and 32bit libraries. However when I try with another 32 bit machine it also doesnt work. <br>
<br></div>I was wondering if you would know either how to compile MRtrix such that the executables can be run on other machines, or perhaps there is a way to package the exes with the required libraries? <br><br></div>Thank you very much<span class=""><font color="#888888"><br>
Jesse<br></font></span></div><div class=""><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Apr 10, 2013 at 10:56 AM, Jeurissen Ben <span dir="ltr"><<a href="mailto:Ben.Jeurissen@ua.ac.be" target="_blank">Ben.Jeurissen@ua.ac.be</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div>Dear Jesse,</div>
<div><br>
</div>
I have no experience with building mrtrix using an IDE. <font>Best place to ask is on the mailinglist. If there's no answer, it probably means no-one has tried or </font>succeeded<font> before.</font>
<div>
<div><br>
</div>
<div><span style="font-size:10pt">I'm pretty sure it's possible to make a debug build with the mrtrix build environment and then do the debugging of the binary with your debugger/IDE of choice.</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">If you insist on doing everything in the IDE, then you will have to look into how the IDE handles dependencies and convert the dependency resolving mechanism of mrtrix to something your IDE can handle.</span><br>
<div>
<div><br>
</div>
<div>Cheers,</div>
<div>Ben</div>
<div><br>
<div>
<div>
<div><font size="1"></font></div>
</div>
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<div><span style="font-size:x-small">Ben Jeurissen, Ph.D.</span><br>
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div style="text-transform:none;text-indent:0px;letter-spacing:normal;font-style:normal;font-variant:normal;font-size:13px;line-height:normal;font-family:Tahoma;white-space:normal;word-spacing:0px">
<div style="font-weight:normal"><font size="1">Post-doctoral researcher</font></div>
<div style="font-weight:normal"><font size="1">Vision Lab, Dept. of Physics</font></div>
<div style="font-weight:normal"><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1, N.1.18</font></div>
<div style="font-weight:normal"><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: <a href="tel:%2B32%203%20265%2024%2077" value="+3232652477" target="_blank">+32 3 265 24 77</a></font></div>
<div style="font-weight:normal"><font size="1">Email: <a href="mailto:ben.jeurissen@ua.ac.be" target="_blank">ben.jeurissen@ua.ac.be</a></font></div>
<div style="font-weight:normal"><font size="1">Url: <a href="http://visielab.ua.ac.be/people/ben-jeurissen" target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
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<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Jesse Ross-Jones [<a href="mailto:jesse.rj@gmail.com" target="_blank">jesse.rj@gmail.com</a>]<br>
<b>Sent:</b> 08 April 2013 08:37<div><div><br>
<b>To:</b> Jeurissen Ben<br>
<b>Subject:</b> Re: MRtrix mrconvert in windows<br>
</div></div></font><br>
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<div dir="ltr">
<div>Hi Ben,<br>
Thank you once again for your previous help. <br>
I was wondering if you might be able to help me get in contact with someone who knows how to compile MRtrix in a debugging environment? I posted a message on the mailing list last week but did not receive a response.
<br>
</div>
Much appreciated and Best Regards,<br>
Jesse<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Mar 21, 2013 at 2:54 PM, Jesse Ross-Jones <span dir="ltr">
<<a href="mailto:jesse.rj@gmail.com" target="_blank">jesse.rj@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>Hi Ben,<br>
</div>
Being unable to run the build in windows, i've started to compile the source in linux and try to extract the necesarry libraries from there, however, i see over a hundred .o libraries .... Do you think you would be able to provide an example of the -l switch
you are using to compile? Would having a successful build in linux be of any help when compiling in windows?<br>
</div>
Best Regards,<br>
</div>
Jesse<br>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Mar 21, 2013 at 10:34 AM, Jesse Ross-Jones <span dir="ltr">
<<a href="mailto:jesse.rj@gmail.com" target="_blank">jesse.rj@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Thanks very much! <br>
Following the build procedure i run the build but I run into the following even though gsl is included in my path..
<br>
<br>
<br>
<div>
<div>
<div>
<div class="gmail_extra">failed with output:<br>
In file included from lib/ptr.h:26:0,<br>
from lib/file/dicom/image.h:33,<br>
from lib\file\dicom\image.cpp:44:<br>
lib/mrtrix.h:69:29: fatal error: gsl/gsl_version.h: No such file or directory<br>
compilation terminated.<br>
<br>
</div>
<div class="gmail_extra">Is there another path python is using?<br>
<br>
</div>
<div class="gmail_extra">Much appreciated,<br>
Jesse<br>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Thu, Mar 21, 2013 at 9:25 AM, Jeurissen Ben <span dir="ltr">
<<a href="mailto:Ben.Jeurissen@ua.ac.be" target="_blank">Ben.Jeurissen@ua.ac.be</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">
<div><span style="font-size:10pt">This list is generated by the python build script as part of the build procedure. The easiest way would be to run this script and see what libraries it wants to link. Alternatively you can look through the build script and
find the relevant libraries yourself. However, they are not in there hardcoded but I think they are obtained through the pkg-config package.</span></div>
<div>
<div><br>
Cheers,</div>
<div>
<div>Ben<br>
<div><br>
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
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<div style="text-indent:0px;letter-spacing:normal;font:13px Tahoma;text-transform:none;white-space:normal;word-spacing:0px">
<div><font size="1"></font></div>
<font size="1">Ben Jeurissen, Ph.D.</font></div>
<div style="text-transform:none;text-indent:0px;letter-spacing:normal;font-style:normal;font-variant:normal;font-size:13px;line-height:normal;font-family:Tahoma;white-space:normal;word-spacing:0px">
<div style="font-weight:normal"><font size="1">Post-doctoral researcher</font></div>
<div style="font-weight:normal"><font size="1">Vision Lab, Dept. of Physics</font></div>
<div style="font-weight:normal"><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1, N.1.18</font></div>
<div style="font-weight:normal"><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: <a href="tel:%2B32%203%20265%2024%2077" value="+3232652477" target="_blank">
+32 3 265 24 77</a></font></div>
<div style="font-weight:normal"><font size="1">Email: <a href="mailto:ben.jeurissen@ua.ac.be" target="_blank">
ben.jeurissen@ua.ac.be</a></font></div>
<div style="font-weight:normal"><font size="1">Url: <a title="http://visielab.ua.ac.be/people/ben-jeurissen
Ctrl+Click to follow link" href="http://visielab.ua.ac.be/people/ben-jeurissen" target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
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<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Jesse Ross-Jones [<a href="mailto:jesse.rj@gmail.com" target="_blank">jesse.rj@gmail.com</a>]<br>
<b>Sent:</b> 21 March 2013 09:10<br>
<b>To:</b> Jeurissen Ben<br>
<b>Subject:</b> Re: MRtrix mrconvert in windows<br>
</font><br>
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<div>
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<div>
<div dir="ltr">Hi Ben,<br>
Thank you for the quick reply. I am a little at a loss as to how to identify exactly which libraries i need to link to with -l. Currently none are linked and that would be why I am getting those errors. Is there a way generate some sort of list, or manual searching
that needs to be done?<br>
<br>
Much appreciated!<br>
Jesse<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Mar 20, 2013 at 1:11 PM, Jeurissen Ben <span dir="ltr">
<<a href="mailto:Ben.Jeurissen@ua.ac.be" target="_blank">Ben.Jeurissen@ua.ac.be</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Dear Jesse,
<div><br>
</div>
<div>I don't have any recent experience with eclipse.</div>
<div><br>
</div>
<div>If you encounter linking issues this probably means you are missing library flags in your link commmand.</div>
<div><br>
</div>
<div>You need to add the library paths with the -L switch and link the specific libraries with the -l switch.</div>
<div><br>
What link related switches do you currently have?</div>
<div><br>
</div>
<div><span style="font-size:10pt">Cheers,</span></div>
<div>Ben</div>
<div><br>
</div>
<div><br>
<div><br>
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div style="text-indent:0px;letter-spacing:normal;font:13px Tahoma;text-transform:none;white-space:normal;word-spacing:0px">
<div><font size="1"></font></div>
<font size="1">Ben Jeurissen, Ph.D.</font></div>
<div style="text-transform:none;text-indent:0px;letter-spacing:normal;font-style:normal;font-variant:normal;font-size:13px;line-height:normal;font-family:Tahoma;white-space:normal;word-spacing:0px">
<div style="font-weight:normal"><font size="1">Post-doctoral researcher</font></div>
<div style="font-weight:normal"><font size="1">Vision Lab, Dept. of Physics</font></div>
<div style="font-weight:normal"><font size="1">University of Antwerp</font></div>
<div><font size="1">Universiteitsplein 1, N.1.18</font></div>
<div style="font-weight:normal"><font size="1">B-2610 Wilrijk, Belgium</font></div>
<div><font size="1">Phone: <a href="tel:%2B32%203%20265%2024%2077" value="+3232652477" target="_blank">
+32 3 265 24 77</a></font></div>
<div style="font-weight:normal"><font size="1">Email: <a href="mailto:ben.jeurissen@ua.ac.be" target="_blank">
ben.jeurissen@ua.ac.be</a></font></div>
<div style="font-weight:normal"><font size="1">Url: <a href="http://visielab.ua.ac.be/people/ben-jeurissen" target="_blank">http://visielab.ua.ac.be/people/ben-jeurissen</a></font></div>
</div>
</div>
</div>
</div>
</div>
<div style="font-size:16px;font-family:Times New Roman">
<hr>
<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> Jesse Ross-Jones [<a href="mailto:jesse.rj@gmail.com" target="_blank">jesse.rj@gmail.com</a>]<br>
<b>Sent:</b> 19 March 2013 16:19<br>
<b>To:</b> Jeurissen Ben<br>
<b>Subject:</b> MRtrix mrconvert in windows<br>
</font><br>
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<div>Hi Dr. Jeurissen,<br>
<br>
</div>
First of all, thank you very much for your work on the MRtrix project. <br>
<br>
I am sending you this email in hopes that you might be able to help me to compile mrconvert (part of MRtrix) in windows.
<br>
<br>
</div>
<div>Following the instructions: <a href="http://www.brain.org.au/software/mrtrix/install/windows.html" target="_blank">
http://www.brain.org.au/software/mrtrix/install/windows.html</a><br>
</div>
<div>I have downloaded the dependencies and source. <br>
<br>
</div>
<div>I have set up a project in eclipse using the mingw compiler and I have copied the mrconvert.cpp into a new project and added paths to eclipse pointing to all the header files required by mrconvert and its includes. However.... I am running into linking
issues. <br>
</div>
<div>The errors I am receiving are all "undefined reference" for example:<br>
<br>
undefined reference to `Glib::Timer::elapsed() const' mrconvert line 453,
<br>
<br>
undefined reference to `gsl_isnan' mrconvert line 453<br>
<br>
undefined reference to `gsl_matrix_alloc' mrconvert line 153<br>
<br>
</div>
<div>I would very much appreciate your insight into compiling MRtrix in windows and help to compile mrconvert.<br>
<br>
</div>
<div>Best Regards,<br>
</div>
<div>Jesse<br>
</div>
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