On 31.12.2013 14:13, Amira Chekir wrote:

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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.

Hi, Thanks for your answer. I use ubuntu 12.04 32 bits and python 2.7 I upgrade numpy to 1.8, but the error persists I think that the problem is in gzip.py : max_read_chunk = 10 * 1024 * 1024 # 10Mb What do you think? Best regards, AMIRA 2014/1/1 <[email protected]>

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Today's Topics:

1. Re: proposal: min, max of complex should give warning (Ralf Gommers) (David Goldsmith) 2. Re: NumPy-Discussion Digest, Vol 87, Issue 35 (Amira Chekir)

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Message: 1 Date: Tue, 31 Dec 2013 11:43:49 -0800 From: David Goldsmith <[email protected]> Subject: Re: [Numpy-discussion] proposal: min, max of complex should give warning (Ralf Gommers) To: [email protected] Message-ID: <CAFtPsZr9FN6wwr85ScDNhqdkWZhG7C+= [email protected]> Content-Type: text/plain; charset="iso-8859-1"

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As for your proposal, it would be good to know if adding a warning would actually catch any bugs. For the truncation warning it caught several in scipy and other libs IIRC.

Ralf

In light of this, perhaps the pertinent unit tests should be modified (even if the warning suggestion isn't adopted, about which I'm neutral...but I'm a little surprised that there isn't a generic way to globally turn off specific warnings).

DG