[Mne_analysis] "Value too large to be stored in data type" when running mne_mark_bad_channels in tcsh

Stephen Politzer-Ahles spa268 at nyu.edu
Mon Nov 25 08:08:27 EST 2013
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Hi Alexandre (et al),

I uploaded one of my .fifs and the corresponding bad channel to Google
Drive, if it helps you for figuring out the issue.  The command I issued
that caused the error was:

set subject=A0007
mne_mark_bad_channels --bad $SAMPLE/$subject/badch
$SAMPLE/$subject/$subject.fif

Best,
Steve
​
 A0007.fif<https://docs.google.com/file/d/0B6-m45Jvl3ZmOFR4WUxadUVZZ00/edit?usp=drive_web>
​​
 badch<https://docs.google.com/file/d/0B6-m45Jvl3ZmdmxvZTlJcnMtRDA/edit?usp=drive_web>
​



Stephen Politzer-Ahles
New York University, Abu Dhabi
Neuroscience of Language Lab
http://www.nyu.edu/projects/politzer-ahles/


On Mon, Nov 25, 2013 at 12:34 PM, Stephen Politzer-Ahles <spa268 at nyu.edu>wrote:

> Hi Alexandre,
>
> It started as Yokogawa .con data, I wrote it to fif using mne.gui.kit2fiff
> in the mne-python tools.
>
> Best,
> Steve
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
>
> On Mon, Nov 25, 2013 at 12:32 PM, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
>
>> Steve,
>>
>> how did you write this file?
>>
>> standard .fif file should not exceed 2GB.
>>
>> Alex
>>
>>
>> On Mon, Nov 25, 2013 at 7:34 AM, Stephen Politzer-Ahles <spa268 at nyu.edu>
>> wrote:
>> > Hi Eric,
>> >
>> > Thanks, I will keep trying various things out in the meantime. I was
>> also
>> > concerned about file size limits, but it seems weird that other
>> functions
>> > like mne_process_raw still work on my big files.
>> >
>> > If I don't find a solution, is it possible instead to just run
>> > mne_mark_bad_channels on the averaged data (and make sure to use the
>> > averaged, rather than the raw, as the --meas file in later steps of the
>> > pipeline)?
>> >
>> > Best,
>> > Steve
>> >
>> >
>> >
>> > Stephen Politzer-Ahles
>> > New York University, Abu Dhabi
>> > Neuroscience of Language Lab
>> > http://www.nyu.edu/projects/politzer-ahles/
>> >
>> >
>> > On Mon, Nov 25, 2013 at 5:20 AM, Eric Larson <larson.eric.d at gmail.com>
>> > wrote:
>> >>
>> >> Hey Steve,
>> >>
>> >> It is possible that this has to do with file locations being stored
>> using
>> >> 32-bit integers. I thought FIFF had an effective file-size limit of
>> 2GB for
>> >> that reason (using 32-bit signed integers would make this the limit),
>> but
>> >> I'm not 100% sure. If nobody beats me to a more definitive answer and
>> you
>> >> can't find anything about this issue yourself by tomorrow or Tuesday,
>> I can
>> >> look into it more then.
>> >>
>> >> Cheers,
>> >> Eric
>> >>
>> >>
>> >> On Sun, Nov 24, 2013 at 12:33 PM, Stephen Politzer-Ahles <
>> spa268 at nyu.edu>
>> >> wrote:
>> >>>
>> >>> To whom it may concern:
>> >>>
>> >>> When I try to run mne_mark_bad_channels in tcsh on a raw .fif file
>> (about
>> >>> 3.25 GB), I get an error like the following:
>> >>>
>> >>> "/Volumes/data/....../A0007.fif ... [failed] fseek : Value too large
>> to
>> >>> be stored in data type"
>> >>>
>> >>> As far as I can tell this seems to be some kind of Unix error, not
>> >>> something specific to MNE...but this happens regardless of which
>> drive I
>> >>> happen to be trying to modify data on, and also other functions that
>> also
>> >>> need to open the data (such as mne_process_raw) work fine, so I don't
>> think
>> >>> it's necessarily a permission or filesystem issue. Does anyone have
>> any idea
>> >>> what might be causing this?
>> >>>
>> >>> Thanks for your input,
>> >>> Steve
>> >>>
>> >>>
>> >>> Stephen Politzer-Ahles
>> >>> New York University, Abu Dhabi
>> >>> Neuroscience of Language Lab
>> >>> http://www.nyu.edu/projects/politzer-ahles/
>> >>>
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