[MINC-users] conflicting HDF libraries

[Soren Christensen]

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
> _______________________________________________
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>