[FieldTrip] processing ANT cnt files with FieldTrip

Thu Jan 10 09:40:06 CET 2013

If you don't use the seg file, how do you know where the data is segmented?
it is important when filtering raw data for example, where you have traces
which and at certain y value and continue at a very different one the next
sample. reading the data with fieldtrip currently doesn't let you know
where the data is segmented which can sometime develop into a
serious headache. If anyone have overcome this issue before please share
with us.

On 10 January 2013 09:42, Arnaud Delorme <arno at cerco.ups-tlse.fr> wrote:

> I think the .seg file should not be used (it is internal to the ASA
> software).
> Only the .trg file should be used.
> If you modify the .trg file though (move events), you need to remove the
> .seg file or ASA will use the .seg file to set the events in its graphic
> interface.
> All based on memory so I could be wrong.
>
> Arno
>
> On 9 Jan 2013, at 23:33, Yuval Harpaz wrote:
>
> by the way, did anyone decode the .seg file?
> it has the beginning time of segments but it is in seconds since 1900 or
> so.
> thanks, yuval
>
> On 10 January 2013 09:08, Arnaud Delorme <arno at cerco.ups-tlse.fr> wrote:
>
>> Hi Dave and Robert,
>>
>> By the way, after much research, we figured out there was a bug for the
>> 32 bit version of the software when importing events (scaling of time was
>> in second instead of milliseconds)
>> The issue is that the Windows 32 bit version uses
>>
>> read_eep_trg.dll
>>
>> to read triggers and that the 64 bit version uses
>>
>> read_eep_trg.m
>>
>> (programmed by Robert)
>> now I would suggest to *delete read_eep_trg.dll*, which does not bring
>> much speed anyway.
>> Just so you know,
>>
>> Arno
>>
>> On 21 Dec 2012, at 23:22, Robert Oostenveld wrote:
>>
>> Hi Dave,
>>
>> Raquels reply pointed me to the (now fully open source) version of
>> libeep. Previous versions of the libraries and mex files were hard to
>> compile, but I have just given it another try and after a few attempts I
>> ended up with
>>
>> make distclean
>> ./configure --enable-matlab  --enable-shared=no
>> make
>>
>> which compiled the mex files in a format that did not require the shared
>> libraries. This is the best way for having them, because then you don't
>> have to bother with the shared library path. I guess that this would also
>> work on your 64-bit linux computer.
>>
>> It would be nice to have the latest version of the mex files working out
>> of the box again, so I will file this as bug (see
>> http://bugzilla.fcdonders.nl/show_bug.cgi?id=1913). Getting it on all
>> three common (win/linux/.osx) platforms and in 32 and 64 bit versions will
>> take some time though.
>>
>> best regards,
>> Robert
>>
>>
>> On 18 Dec 2012, at 20:18, Dave Britton wrote:
>>
>> Thanks, Arno,
>>
>> I've installed the ant-eep import files into the EEGLAB plugin directory,
>> but EEGLAB gives me the same error message as I got with FieldTrip:
>>
>>
>> EEGLAB error in function loadeep() at line 75
>>
>> Invalid MEX-file
>> '/home/dave/eeglab11_0_4_3b/plugins/anteeimport1.08/read_eep_cnt.mexa64':
>> libeep.so.3:cannot open shared object file:No such file or directory
>>
>>
>> The libeep.so.3 file is copied into the same directory as the
>> read_eep_cnt.mexa64 file.
>>
>>
>> Do you have any suggestions?
>>
>> -Dave
>>
>>
>>
>> On 12/18/2012 12:38 PM, Arnaud Delorme wrote:
>>
>> Dear Dave,
>>
>>
>> last time I have checked FileIO (the Fieldtrip data importer) will not
>> read ANT trigger files by default (it should read the raw data though -
>> Robert Oostenveld one of the main developer of Fieldtrip was interning at
>> ANT about 10 years ago and wrote the Matlab import function for them).
>>
>> The anteepimport1.09 is a plugin for the EEGLAB software. It can import
>> events (and then you can save the data in EEGLAB format and reload it in
>> Fieldtrip). You cannot recompile the ANT project (their source files are
>> proprietary and not included).
>>
>>
>> Hope this helps.
>>
>> Best wishes,
>>
>>
>> Arno
>>
>>
>> On 18 Dec 2012, at 08:59, Dave Britton wrote:
>>
>>
>> I am trying to process EEG data in .cnt files obtained from the ANT
>> system. I am using a Linux Xubuntu 12.04 amd64 operating system. I have
>> installed the Linux 64 bit version of FieldTrip.
>>
>>
>> What is required to successfully process ANT eeg .cnt and .trg files? The
>> libraries that came with the FieldTrip download did not work as it came
>> from the download, and my investigations led me to what should be the
>> latest version of the ANT import library. I have downloaded the latest ANT
>> eep library, anteepimport1.09/libeep-3.3.167, and run config, make and make
>> install, successfully, but MATLAB cannot find the shared object file it
>> should generate, even when I link the .so.3 file into the same directory as
>> the MATLAB m-file and the MATLAB current directory.
>>
>>
>> Initially the system was unable to read the cnt files, which is why I
>> attempted to reinstall the anteepimort library. Is there more to this
>> installation than the standard" configure, make, make install" process? Any
>> clues would be appreciated!
>>
>>
>> Dave Britton
>>
>> City College of New York
>>
>> Psychology Dept.
>>
>>
>> Here is the error message I get:
>>
>>
>> cfg.headerfile = '/home/dave/semanticflanker/data/ANT/20121114_1013.cnt';
>>
>> cfg.hdr = ft_read_header(cfg.headerfile);
>>
>> Invalid MEX-file
>>
>>
>> '/home/dave/fieldtrip-20121102/anteepimport1.09/libeep-3.3.167/mex/matlab/read_eep_cnt.mexa64':
>>
>> libeep.so.3: cannot open shared object file: No such file or directory
>>
>>
>> Error in ft_read_header (line 627)
>>
>> hdr = read_eep_cnt(filename, 1, 1);
>>
>>
>>
>>
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>
>
>
> --
> Yuval
>
>
>
>
> Dr .Harpaz
>
> BIU MEG lab <http://faculty.biu.ac.il/~goldsa/index.html>
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-- 
Yuval

Dr .Harpaz

BIU MEG lab <http://faculty.biu.ac.il/~goldsa/index.html>
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