[MINC-users] conflicting HDF libraries

[Vladimir S. FONOV]

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