[MINC-users] mincaverage error

[Simon Eskildsen]

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
>