[Pkg-exppsy-pynifti] Converting NiftiImage to ndarray gives "ValueError: dimensions too large"

[Nicholas Dowson]

Michael: Thank you for your speed of response and apologies for taking so long to reply.

Here is another (small) file of a 4x4x4 cube.  The same code causes a segmentation fault (repeated for ease of copy-paste)
from nifti import *
from numpy import *
mynifti = NiftiImage('test4x4x4.nii')
myarray = mynifti.getDataArray()
myarray

Thanks, Nick


> Date: Fri, 7 Aug 2009 07:27:27 -0400
> From: michael.hanke at gmail.com
> To: nick314 at hotmail.com
> CC: pkg-exppsy-pynifti at lists.alioth.debian.org
> Subject: Re: [Pkg-exppsy-pynifti] Converting NiftiImage to ndarray gives "ValueError: dimensions too large"
> 
> Hi Nicholas,
> 
> do you mind sharing the image, so I can check what is going on?
> 
> 
> Michael
> 
> 
> On Fri, Aug 07, 2009 at 05:29:26AM +0000, Nicholas Dowson wrote:
> > 
> > Hello,
> > 
> > The following code using pynifti gives me an error (ValueError: dimensions too large):
> > from nifti import *
> > from numpy import *
> > mynifti = NiftiImage('T1noise3bias0.nii')
> > myarray = mynifti.getDataArray()
> > 
> > This is very strange because the number of voxels is low:
> > In [11]: mynifti.nvox
> > Out[11]: 7109137
> > In [12]: mynifti.extent
> > Out[12]: (181, 217, 181)
> > 
> > Other information:
> > I am running Ubuntu 8.10, with the standard packages for python, numpy and scipy installed. I tried the above on ipython and python. Python just segfaults. I get the same error if I use getDataArray()
> > 
> > Here is the full output:
> > <BEGIN of output>
> > ERROR: An unexpected error occurred while tokenizing input
> > The following traceback may be corrupted or invalid
> > The error message is: ('EOF in multi-line statement', (60, 0))
> > 
> > ---------------------------------------------------------------------------
> > ValueError                                Traceback (most recent call last)
> > 
> > /home/dow178/extDownload/lib/VTKbuild/<ipython console> in <module>()
> > 
> > /var/lib/python-support/python2.5/nifti/niftiimage.pyc in asarray(self, copy)
> >     217         """
> >     218         # make sure data is accessible
> > --> 219         self.load()
> >     220 
> >     221         if copy:
> > 
> > /var/lib/python-support/python2.5/nifti/niftiimage.pyc in load(self)
> >     174             raise RuntimeError, "Unable to load image data."
> >     175 
> > --> 176         self._data = nifticlib.wrapImageDataWithArray(self.raw_nimg)
> >     177 
> >     178 
> > 
> > ValueError: dimensions too large.
> > 
> >  <END of Output>
> > 
> > Does anyone know why this is occuring?
> > 
> > I tried installing the libnifti-dev package and searching for the wrapImageDataWithArray function to glean some information - but it doesn't live there. Any ideas where the c++ source code for wrapImageDataWithArray is?
> > 
> > Many thanks in advance,
> > Nick
> > 
> > 
> > 
> > 
> > 
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> GPG key:  1024D/3144BE0F Michael Hanke
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