[MINC-users] mincaverage error

[Simon Eskildsen]

Does it mean I can safely replace mincaverage in xfmavg with
mincbigaverage? Why hasn't already?

On Tue, Jun 9, 2015 at 10:37 AM, Andrew Janke <a.janke at gmail.com> wrote:

> supports most options yes. Will be identical apart from very small rounding
> errors.
>
> take note of the options for defining the number to average at once.
>
> a
> On 09/06/2015 6:25 PM, "Simon Eskildsen" <eskild at gmail.com> wrote:
>
> > Thanks. I'm trying this now. I assume same behaviour as mincaverage,
> right?
> >
> > On Tue, Jun 9, 2015 at 10:12 AM, Andrew Janke <a.janke at gmail.com> wrote:
> >
> > > 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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> > > >
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> > >
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