[Numpy-discussion] Loading large NIfTI file -> MemoryError

Julian Taylor jtaylor.debian at googlemail.com
Tue Dec 31 08:29:42 EST 2013


On 31.12.2013 14:13, Amira Chekir wrote:
> Hello together,
> 
> I try to load a (large)  NIfTI file (DMRI from Human Connectome Project,
> about 1 GB) with NiBabel.
> 
> import nibabel as nib
> img = nib.load("dmri.nii.gz")
> data = img.get_data()
> 
> The program crashes during "img.get_data()" with an "MemoryError"
> (having 4 GB of RAM in my machine).
> 
> Any suggestions?

are you using a 64 bit operating system?
which version of numpy?

assuming nibabel uses np.load under the hood you could try it with numpy
1.8 which reduces excess memory usage when loading compressed files.



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