[MINC-users] mincaverage error

[Andrew Janke]

If it's memory, try mincbigaverage.  google knows where it is.

a
On 09/06/2015 5:15 PM, "Simon Eskildsen" <eskild at gmail.com> wrote:

> Hi Robert,
>
> I'm averaging 38 deformation fields. Here's the info on one of them:
>
> $ mincinfo 21/stx2_0004_20131113_091044_t1.mnc.21.i_grid_0.mnc
> file: 21/stx2_0004_20131113_091044_t1.mnc.21.i_grid_0.mnc
> image: signed__ float -10.166246414184570312 to 11.006509780883789062
> image dimensions: xspace yspace zspace vector_dimension
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     xspace                    388          0.5        -96.5
>     yspace                    460          0.5       -132.5
>     zspace                    388          0.5        -78.5
>     vector_dimension            3      unknown      unknown
>
> The files are quite big (~800 Mb each). Could this be a memory problem?
>
> I used mincaverage without any flags/options. Just a list of files in and a
> file out.
>
> Simon
>
> On Mon, Jun 8, 2015 at 3:46 PM, Robert D. Vincent <
> robert.d.vincent at mcgill.ca> wrote:
>
> > Hi Simon,
> >
> > It looks like HDF5 might be running out of resource ids, which seems
> > unlikely, but there could be a resource leak somewhere.
> >
> > Can you give me the details of the failing case (e.g. the files you're
> > using)?
> >
> >     -bert
> >
> >
> > On Mon, Jun 8, 2015 at 9:33 AM, Simon Eskildsen <eskild at gmail.com>
> wrote:
> >
> > > Hi all,
> > >
> > > Averaging a bunch of deformation fields using mincaverage, I got this
> > > error:
> > >
> > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
> > >   #000: /users/fristed/git/minc-toolkit/build/HDF5/src/H5A.c line 679
> in
> > > H5Aget_space(): can't get space ID of attribute
> > >     major: Invalid arguments to routine
> > >     minor: Can't get value
> > >   #001: /users/fristed/git/minc-toolkit/build/HDF5/src/H5Aint.c line
> 719
> > in
> > > H5A_get_space(): unable to register dataspace atom
> > >     major: Object atom
> > >     minor: Unable to register new atom
> > >   #002: /users/fristed/git/minc-toolkit/build/HDF5/src/H5I.c line 902
> in
> > > H5I_register(): no IDs available in type
> > >     major: Object atom
> > >     minor: Out of IDs for group
> > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0:
> > >   #000: /users/fristed/git/minc-toolkit/build/HDF5/src/H5S.c line 1383
> in
> > > H5Screate_simple(): unable to register dataspace ID
> > >     major: Object atom
> > >     minor: Unable to register new atom
> > >   #001: /users/fristed/git/minc-toolkit/build/HDF5/src/H5I.c line 902
> in
> > > H5I_register(): no IDs available in type
> > >     major: Object atom
> > >     minor: Out of IDs for group
> > > (from miicv_get): Should not happen!
> > >
> > > Setting -debug flag does not provide further information.
> > >
> > > Ideas for debugging this are very welcome.
> > >
> > > Simon
> > > _______________________________________________
> > > 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
> >
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