[Mrtrix-discussion] Fwd: MRtrix mrconvert in windows
Jesse Ross-Jones
jesse.rj at gmail.com
Tue Jun 11 07:08:14 PDT 2013
Dear MRtrix community,
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: *The
application was unable to start correctly (0xc0000142). *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
*-system=X specify the architecture to build
*. Could this be used to compile the executable for use on another system?
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.
thank you,
Jesse
---------- Forwarded message ----------
From: Jesse Ross-Jones <jesse.rj at gmail.com>
Date: Mon, Jun 3, 2013 at 9:21 AM
Subject: Re: MRtrix mrconvert in windows
To: Jeurissen Ben <Ben.Jeurissen at ua.ac.be>
Dear Ben,
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:
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.
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?
Thank you very much
Jesse
On Wed, Apr 10, 2013 at 10:56 AM, Jeurissen Ben <Ben.Jeurissen at ua.ac.be>wrote:
> Dear Jesse,
>
> I have no experience with building mrtrix using an IDE. Best place to
> ask is on the mailinglist. If there's no answer, it probably means no-one
> has tried or succeeded before.
>
> 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.
>
> 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.
>
> Cheers,
> Ben
>
> Ben Jeurissen, Ph.D.
> Post-doctoral researcher
> Vision Lab, Dept. of Physics
> University of Antwerp
> Universiteitsplein 1, N.1.18
> B-2610 Wilrijk, Belgium
> Phone: +32 3 265 24 77
> Email: ben.jeurissen at ua.ac.be
> Url: http://visielab.ua.ac.be/people/ben-jeurissen
> ------------------------------
> *From:* Jesse Ross-Jones [jesse.rj at gmail.com]
> *Sent:* 08 April 2013 08:37
>
> *To:* Jeurissen Ben
> *Subject:* Re: MRtrix mrconvert in windows
>
> Hi Ben,
> Thank you once again for your previous help.
> 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.
> Much appreciated and Best Regards,
> Jesse
>
>
> On Thu, Mar 21, 2013 at 2:54 PM, Jesse Ross-Jones <jesse.rj at gmail.com>wrote:
>
>> Hi Ben,
>> 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?
>> Best Regards,
>> Jesse
>>
>>
>> On Thu, Mar 21, 2013 at 10:34 AM, Jesse Ross-Jones <jesse.rj at gmail.com>wrote:
>>
>>> Thanks very much!
>>> Following the build procedure i run the build but I run into the
>>> following even though gsl is included in my path..
>>>
>>>
>>> failed with output:
>>> In file included from lib/ptr.h:26:0,
>>> from lib/file/dicom/image.h:33,
>>> from lib\file\dicom\image.cpp:44:
>>> lib/mrtrix.h:69:29: fatal error: gsl/gsl_version.h: No such file or
>>> directory
>>> compilation terminated.
>>>
>>> Is there another path python is using?
>>>
>>> Much appreciated,
>>> Jesse
>>>
>>>
>>> On Thu, Mar 21, 2013 at 9:25 AM, Jeurissen Ben <Ben.Jeurissen at ua.ac.be>wrote:
>>>
>>>> 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.
>>>>
>>>> Cheers,
>>>> Ben
>>>>
>>>> Ben Jeurissen, Ph.D.
>>>> Post-doctoral researcher
>>>> Vision Lab, Dept. of Physics
>>>> University of Antwerp
>>>> Universiteitsplein 1, N.1.18
>>>> B-2610 Wilrijk, Belgium
>>>> Phone: +32 3 265 24 77
>>>> Email: ben.jeurissen at ua.ac.be
>>>> Url: http://visielab.ua.ac.be/people/ben-jeurissen
>>>> ------------------------------
>>>> *From:* Jesse Ross-Jones [jesse.rj at gmail.com]
>>>> *Sent:* 21 March 2013 09:10
>>>> *To:* Jeurissen Ben
>>>> *Subject:* Re: MRtrix mrconvert in windows
>>>>
>>>> Hi Ben,
>>>> 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?
>>>>
>>>> Much appreciated!
>>>> Jesse
>>>>
>>>>
>>>> On Wed, Mar 20, 2013 at 1:11 PM, Jeurissen Ben <Ben.Jeurissen at ua.ac.be>wrote:
>>>>
>>>>> Dear Jesse,
>>>>>
>>>>> I don't have any recent experience with eclipse.
>>>>>
>>>>> If you encounter linking issues this probably means you are missing
>>>>> library flags in your link commmand.
>>>>>
>>>>> You need to add the library paths with the -L switch and link the
>>>>> specific libraries with the -l switch.
>>>>>
>>>>> What link related switches do you currently have?
>>>>>
>>>>> Cheers,
>>>>> Ben
>>>>>
>>>>>
>>>>>
>>>>> Ben Jeurissen, Ph.D.
>>>>> Post-doctoral researcher
>>>>> Vision Lab, Dept. of Physics
>>>>> University of Antwerp
>>>>> Universiteitsplein 1, N.1.18
>>>>> B-2610 Wilrijk, Belgium
>>>>> Phone: +32 3 265 24 77
>>>>> Email: ben.jeurissen at ua.ac.be
>>>>> Url: http://visielab.ua.ac.be/people/ben-jeurissen
>>>>> ------------------------------
>>>>> *From:* Jesse Ross-Jones [jesse.rj at gmail.com]
>>>>> *Sent:* 19 March 2013 16:19
>>>>> *To:* Jeurissen Ben
>>>>> *Subject:* MRtrix mrconvert in windows
>>>>>
>>>>> Hi Dr. Jeurissen,
>>>>>
>>>>> First of all, thank you very much for your work on the MRtrix
>>>>> project.
>>>>>
>>>>> I am sending you this email in hopes that you might be able to help me
>>>>> to compile mrconvert (part of MRtrix) in windows.
>>>>>
>>>>> Following the instructions:
>>>>> http://www.brain.org.au/software/mrtrix/install/windows.html
>>>>> I have downloaded the dependencies and source.
>>>>>
>>>>> 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.
>>>>> The errors I am receiving are all "undefined reference" for example:
>>>>>
>>>>> undefined reference to `Glib::Timer::elapsed() const' mrconvert
>>>>> line 453,
>>>>>
>>>>> undefined reference to `gsl_isnan' mrconvert line 453
>>>>>
>>>>> undefined reference to `gsl_matrix_alloc' mrconvert line 153
>>>>>
>>>>> I would very much appreciate your insight into compiling MRtrix in
>>>>> windows and help to compile mrconvert.
>>>>>
>>>>> Best Regards,
>>>>> Jesse
>>>>>
>>>>
>>>>
>>>
>>
>
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