From sorench at gmail.com  Mon Jan  7 22:28:21 2013
From: sorench at gmail.com (Soren Christensen)
Date: Tue, 8 Jan 2013 04:28:21 +0100
Subject: [MINC-users] Fedora 17 issue with mouse modifiers in glut callbacks
Message-ID: <CAHfsrRZHZpP5C0fKwjE8h1J+KZgi7Q4=PUX+Uv7iWD+rCspEpw@mail.gmail.com>

Hi,
 I unable to use any of the mouse modifier functionality (shift left
drag to erase ROI etc - crtl alt and shift do not modify the mouse
click). It seems this is a fedora 17 thing. I tried a proposed fix to
set the mouse modifier to empty but this seems not to work with the
newest updates. I have tried gnome, xcfe and kde with the same result
on two different fedora 17 machines..
There seems to be others with the issue too:
http://forums.fedoraforum.org/showthread.php?p=1624213#post1624213

If anyone has any suggestions please let me know. I guess it is a
Fedora-only issue since no one seems to notice this in Ubuntu?

Thanks
Soren

From sorench at gmail.com  Thu Jan 31 01:40:12 2013
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 30 Jan 2013 22:40:12 -0800
Subject: [MINC-users] conflicting HDF libraries
Message-ID: <CAHfsrRZCiDR0mKStdwi4EjQZ3v7Xt3GeJ8oZv4bpkPiF4J4yuQ@mail.gmail.com>

Hi,
 I am having trouble building a program on Linux that links to minc2.a and the
ITK libraries (admitted I included all of them in cmake with the
${ITK_LIBRARIES} variables).
The problem seems to be a conflict between the hdf.a that is linked to by
minc2.a and then the hdf.a in the ITK library folder.

 I know a lot of people here seem to use ITK with MINC so what is the best
way around this HDF issue?  Build against the same (which?) HDF or is there
a way to link HDF statically into minc2.a so that minc2 calls resolve to
that HDF version and other calls to the one on the link line?

Thanks
Soren

From a.janke at gmail.com  Thu Jan 31 01:43:14 2013
From: a.janke at gmail.com (Andrew Janke)
Date: Thu, 31 Jan 2013 16:43:14 +1000
Subject: [MINC-users] conflicting HDF libraries
In-Reply-To: <CAHfsrRZCiDR0mKStdwi4EjQZ3v7Xt3GeJ8oZv4bpkPiF4J4yuQ@mail.gmail.com>
References: <CAHfsrRZCiDR0mKStdwi4EjQZ3v7Xt3GeJ8oZv4bpkPiF4J4yuQ@mail.gmail.com>
Message-ID: <CAG0CB22Pw6fg=xQLup2JbTp9Y1q5sK6RJh5pMG1iNjBuGNMP0w@mail.gmail.com>

Hi Soren,

Vladimir has put a lot of effort into this as of late with minc_lite:

   https://github.com/BIC-MNI/libminc/tree/minc_lite

Primarily for the same reasons you are currently having with ITK. In
short it was a world of pain for him so he embarked upon the project
above.

I'd suggest you build against this if you plan to use ITK + MINC in the future.


a


On 31 January 2013 16:40, Soren Christensen <sorench at gmail.com> wrote:
> Hi,
>  I am having trouble building a program on Linux that links to minc2.a and the
> ITK libraries (admitted I included all of them in cmake with the
> ${ITK_LIBRARIES} variables).
> The problem seems to be a conflict between the hdf.a that is linked to by
> minc2.a and then the hdf.a in the ITK library folder.
>
>  I know a lot of people here seem to use ITK with MINC so what is the best
> way around this HDF issue?  Build against the same (which?) HDF or is there
> a way to link HDF statically into minc2.a so that minc2 calls resolve to
> that HDF version and other calls to the one on the link line?
>
> Thanks
> Soren
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users

From sorench at gmail.com  Thu Jan 31 02:44:18 2013
From: sorench at gmail.com (Soren Christensen)
Date: Wed, 30 Jan 2013 23:44:18 -0800
Subject: [MINC-users] conflicting HDF libraries
In-Reply-To: <CAG0CB22Pw6fg=xQLup2JbTp9Y1q5sK6RJh5pMG1iNjBuGNMP0w@mail.gmail.com>
References: <CAHfsrRZCiDR0mKStdwi4EjQZ3v7Xt3GeJ8oZv4bpkPiF4J4yuQ@mail.gmail.com>
	<CAG0CB22Pw6fg=xQLup2JbTp9Y1q5sK6RJh5pMG1iNjBuGNMP0w@mail.gmail.com>
Message-ID: <CAHfsrRYM+HWFCbXYU7RS7=n6zE7KjK_5j=8D-igUhKQDRKDVRw@mail.gmail.com>

Thanks that sounds like a great effort!
So do I install the indicated (in libminc) versions?  I tried this but have
trouble getting cmake to pick up my custom hdf folder even when specifying
it in the cmake interface.
I can see in the cmake file there is some reference to ITK_FOUND (but I
cannot see where the ITK search module is run?).
What is the best way to use and build this lib with ITK?

Thanks
Soren


On Wed, Jan 30, 2013 at 10:43 PM, Andrew Janke <a.janke at gmail.com> wrote:

> Hi Soren,
>
> Vladimir has put a lot of effort into this as of late with minc_lite:
>
>    https://github.com/BIC-MNI/libminc/tree/minc_lite
>
> Primarily for the same reasons you are currently having with ITK. In
> short it was a world of pain for him so he embarked upon the project
> above.
>
> I'd suggest you build against this if you plan to use ITK + MINC in the
> future.
>
>
> a
>
>
> On 31 January 2013 16:40, Soren Christensen <sorench at gmail.com> wrote:
> > Hi,
> >  I am having trouble building a program on Linux that links to minc2.a
> and the
> > ITK libraries (admitted I included all of them in cmake with the
> > ${ITK_LIBRARIES} variables).
> > The problem seems to be a conflict between the hdf.a that is linked to by
> > minc2.a and then the hdf.a in the ITK library folder.
> >
> >  I know a lot of people here seem to use ITK with MINC so what is the
> best
> > way around this HDF issue?  Build against the same (which?) HDF or is
> there
> > a way to link HDF statically into minc2.a so that minc2 calls resolve to
> > that HDF version and other calls to the one on the link line?
> >
> > Thanks
> > Soren
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>

From vladimir.fonov at gmail.com  Thu Jan 31 08:58:08 2013
From: vladimir.fonov at gmail.com (Vladimir S. FONOV)
Date: Thu, 31 Jan 2013 08:58:08 -0500
Subject: [MINC-users] conflicting HDF libraries
In-Reply-To: <CAHfsrRYM+HWFCbXYU7RS7=n6zE7KjK_5j=8D-igUhKQDRKDVRw@mail.gmail.com>
References: <CAHfsrRZCiDR0mKStdwi4EjQZ3v7Xt3GeJ8oZv4bpkPiF4J4yuQ@mail.gmail.com>
	<CAG0CB22Pw6fg=xQLup2JbTp9Y1q5sK6RJh5pMG1iNjBuGNMP0w@mail.gmail.com>
	<CAHfsrRYM+HWFCbXYU7RS7=n6zE7KjK_5j=8D-igUhKQDRKDVRw@mail.gmail.com>
Message-ID: <CAMCwi7M7F_7Eb5fZ5kmbh+7ioSrjQnyXjDF-5jDrMxgyXOkHJA@mail.gmail.com>

Hello ,

there are two possibilities:

1. re-compile minc or libminc using HDF5 which comes with ITK (there
are confuguration options in cmake configuration script for that)

2. If you are using ITKv4  there is work in progress of integrating
libminc inside of it (the one Andrew have mentioned). In short you
have to checkout current ITKv4 source code from github, and then apply
patch from here: http://review.source.kitware.com/#/c/9033/ - it is
under review withing ITK and is expected to become part of mainline
ITK source code sometime soon - this code will download and compile
it's own version of libminc. Unfortunately, this reader/writer only
supports MINC2 file format (but works much faster then the old one).

On Thu, Jan 31, 2013 at 2:44 AM, Soren Christensen <sorench at gmail.com> wrote:
> Thanks that sounds like a great effort!
> So do I install the indicated (in libminc) versions?  I tried this but have
> trouble getting cmake to pick up my custom hdf folder even when specifying
> it in the cmake interface.
> I can see in the cmake file there is some reference to ITK_FOUND (but I
> cannot see where the ITK search module is run?).
> What is the best way to use and build this lib with ITK?
>
> Thanks
> Soren
>
>
> On Wed, Jan 30, 2013 at 10:43 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Hi Soren,
>>
>> Vladimir has put a lot of effort into this as of late with minc_lite:
>>
>>    https://github.com/BIC-MNI/libminc/tree/minc_lite
>>
>> Primarily for the same reasons you are currently having with ITK. In
>> short it was a world of pain for him so he embarked upon the project
>> above.
>>
>> I'd suggest you build against this if you plan to use ITK + MINC in the
>> future.
>>
>>
>> a
>>
>>
>> On 31 January 2013 16:40, Soren Christensen <sorench at gmail.com> wrote:
>> > Hi,
>> >  I am having trouble building a program on Linux that links to minc2.a
>> and the
>> > ITK libraries (admitted I included all of them in cmake with the
>> > ${ITK_LIBRARIES} variables).
>> > The problem seems to be a conflict between the hdf.a that is linked to by
>> > minc2.a and then the hdf.a in the ITK library folder.
>> >
>> >  I know a lot of people here seem to use ITK with MINC so what is the
>> best
>> > way around this HDF issue?  Build against the same (which?) HDF or is
>> there
>> > a way to link HDF statically into minc2.a so that minc2 calls resolve to
>> > that HDF version and other calls to the one on the link line?
>> >
>> > Thanks
>> > Soren
>> > _______________________________________________
>> > MINC-users at bic.mni.mcgill.ca
>> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users



-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com

From sorench at gmail.com  Thu Jan 31 18:02:10 2013
From: sorench at gmail.com (Soren Christensen)
Date: Thu, 31 Jan 2013 15:02:10 -0800
Subject: [MINC-users] conflicting HDF libraries
In-Reply-To: <CAMCwi7M7F_7Eb5fZ5kmbh+7ioSrjQnyXjDF-5jDrMxgyXOkHJA@mail.gmail.com>
References: <CAHfsrRZCiDR0mKStdwi4EjQZ3v7Xt3GeJ8oZv4bpkPiF4J4yuQ@mail.gmail.com>
	<CAG0CB22Pw6fg=xQLup2JbTp9Y1q5sK6RJh5pMG1iNjBuGNMP0w@mail.gmail.com>
	<CAHfsrRYM+HWFCbXYU7RS7=n6zE7KjK_5j=8D-igUhKQDRKDVRw@mail.gmail.com>
	<CAMCwi7M7F_7Eb5fZ5kmbh+7ioSrjQnyXjDF-5jDrMxgyXOkHJA@mail.gmail.com>
Message-ID: <CAHfsrRYeHE35+8DMrCsTacYxp_vBHVjf=bcZXjnoyY=fPMRy_A@mail.gmail.com>

Thanks a lot to both of you (again)!
I went for option 2 and after a ~5 hour build of ITK 4 this seems to work!

Cheers
Soren



On Thu, Jan 31, 2013 at 5:58 AM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Hello ,
>
> there are two possibilities:
>
> 1. re-compile minc or libminc using HDF5 which comes with ITK (there
> are confuguration options in cmake configuration script for that)
>
> 2. If you are using ITKv4  there is work in progress of integrating
> libminc inside of it (the one Andrew have mentioned). In short you
> have to checkout current ITKv4 source code from github, and then apply
> patch from here: http://review.source.kitware.com/#/c/9033/ - it is
> under review withing ITK and is expected to become part of mainline
> ITK source code sometime soon - this code will download and compile
> it's own version of libminc. Unfortunately, this reader/writer only
> supports MINC2 file format (but works much faster then the old one).
>
> On Thu, Jan 31, 2013 at 2:44 AM, Soren Christensen <sorench at gmail.com>
> wrote:
> > Thanks that sounds like a great effort!
> > So do I install the indicated (in libminc) versions?  I tried this but
> have
> > trouble getting cmake to pick up my custom hdf folder even when
> specifying
> > it in the cmake interface.
> > I can see in the cmake file there is some reference to ITK_FOUND (but I
> > cannot see where the ITK search module is run?).
> > What is the best way to use and build this lib with ITK?
> >
> > Thanks
> > Soren
> >
> >
> > On Wed, Jan 30, 2013 at 10:43 PM, Andrew Janke <a.janke at gmail.com>
> wrote:
> >
> >> Hi Soren,
> >>
> >> Vladimir has put a lot of effort into this as of late with minc_lite:
> >>
> >>    https://github.com/BIC-MNI/libminc/tree/minc_lite
> >>
> >> Primarily for the same reasons you are currently having with ITK. In
> >> short it was a world of pain for him so he embarked upon the project
> >> above.
> >>
> >> I'd suggest you build against this if you plan to use ITK + MINC in the
> >> future.
> >>
> >>
> >> a
> >>
> >>
> >> On 31 January 2013 16:40, Soren Christensen <sorench at gmail.com> wrote:
> >> > Hi,
> >> >  I am having trouble building a program on Linux that links to minc2.a
> >> and the
> >> > ITK libraries (admitted I included all of them in cmake with the
> >> > ${ITK_LIBRARIES} variables).
> >> > The problem seems to be a conflict between the hdf.a that is linked
> to by
> >> > minc2.a and then the hdf.a in the ITK library folder.
> >> >
> >> >  I know a lot of people here seem to use ITK with MINC so what is the
> >> best
> >> > way around this HDF issue?  Build against the same (which?) HDF or is
> >> there
> >> > a way to link HDF statically into minc2.a so that minc2 calls resolve
> to
> >> > that HDF version and other calls to the one on the link line?
> >> >
> >> > Thanks
> >> > Soren
> >> > _______________________________________________
> >> > MINC-users at bic.mni.mcgill.ca
> >> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>