[Mne_analysis] continuation (from Fieldtrip list) of writing fifs
Matti Hamalainen
msh at nmr.mgh.harvard.edu
Thu Jan 31 00:31:50 EST 2013
Hey!
The reason why, e.g., mne_browse_raw (and Matlab writing routines) write raw files as 32-bit floats is that there might have been some intervening operations and precision might be lost if the data are written back as 16-bit integers.
MNE-Matlab does not write 64-bit (double precision floats) and I do not think MNE-Python does either. This data type is not supported by the fif raw data reading routines in MNE C code.
- Matti
On Jan 30, 2013, at 9:50 PM, Eric Larson wrote:
> Hey Andy,
>
> Yes, it should be possible to implement a precision argument in mne-python. I should be able to get to it this week.
>
> Cheers,
> Eric
>
>
>
> On Wed, Jan 30, 2013 at 6:38 AM, Dykstra, Andrew <Andrew.Dykstra at med.uni-heidelberg.de> wrote:
> Hi Alexandre, Peter,
>
> While it's not nearly as problematic as going from 2 to 18 Gb, I also
> experience file size increases (usually exact doubling minus the last
> small buffer) when rewriting fif files, not only in MATLAB but also with
> the Python tools. In my case, I've always wondered whether it's just a
> difference in the default writing precisions between the modern MNE
> package and our system (Neuromag 122), in which case I'm content with
> storing the data in the higher precision. In any case, would it be
> possible to include a precision argument in the Python writing tool?
>
> Cheers,
> Andy
>
> --
> Andrew R. Dykstra, PhD
> Auditory Cognition Lab
> Neurologie und Poliklinik
> Universitätsklinikum Heidelberg
> Im Neuenheimer Feld 400
> 69120 Heidelberg
>
> "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov
>
>
>
> "hi Peter,
>
> > The size of the input file is ~2gb but when
> > writing, the output is approx ~18gb. I suspect I'm writing a WHOLE bunch of
> > redundant data, but am unable to open the new file, even on a machine
> > running 16gb RAM.
>
> what is likely to happen is that the matlab code writes data as double precision
> while the original neuromag data were in float 16. Note that a single fif file
> cannot exceed 2Go due to internal pointer arithmetic otherwise it will
> be broken.
> What you can do is hack the fif writing to make sure it's written back
> in float16.
>
> Best,
> Alex
>
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---------
Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
msh at nmr.mgh.harvard.edu
mhamalainen at partners.org
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