[Eeglablist] .set to EGI.raw format

Mon Jun 27 20:17:02 PDT 2011

Giovanni et al,

in the process of doing the same with EEGLAB and ERPLAB. Overall there is
currenlty low interoperability of meta-data (event-data) across software
packages, especially for beginning users.

Several quick thoughts and options below in this email, let me know if any
of this helps, or if I was unclear/mistaken somewhere.
Also,  when and if you find a solution path, please share with us and the
list! Happy EEG!

1. considering doing the averaging and analyses in eeglab and/or erplab.

2.1. If one is an expert eeglab user and mid to high level matlab
programmer, one can deal with all the issues described below.
However, as a novice who is also working on transferring metadata across
eeglab, NS, and EPtoolkit, these problems
still seem important.

2.2. An issue to keep in mind is that in order to get good ICA
decompositions, you should do some cleaning (removing of
continuous or epoched time periods) before feeding the data to ICA. Thus,
these "missing" time periods need to be taken
into account when considering some of the options below. Anyway, the crucial
bit is that your arrays of events and times
are correct and match up across the various imports/exports described below.

2.3. Another issue to keep in mind ACROSS IMPORTS/EXPORTS ACROSS SOFTWARE
PACKAGES
(I want to put it in the foreground) is timing issues (for examples, event
times may shift or be distorted slightly),
data quality issues (for example, channel amplitude or channel locations may
get mixed up slightly distorted),
and event time matchup issues.
I would suggest that, untill we are sure, let's assume that back and
forthing between software packages is not very safe,
 and may be affecting the data in undocumented ways.  This suggests it's
better to stay native, or only migrate once across
software packages (rather than two or more times, across two or more
packages)

3. AN EXISTING PATH TO HELP YOUR IMMEDIATE PROBLEM. If you look over the
recent postings on this topic (see below), you will note Dr. Dominguez's (
l.garcia.d at gmail.com) note that he has developed a working path (using
Joseph Dien's EP toolkit, search for it on Google) that works pretty well.
He basically exported the events from Netstation, and then ran the
netstation file through eeglab, then imported to EPToolkit, then exported to
Netstation, and then read in the events via the Netstation markup tool. This
should be one way to solve your issue. But read on...

4. An option for EXPORTING EEGLAB EVENTS AND IMPORTING INTO NETSTATION
a. exporting eeglab events with at least time and event name [either with
existing functions, or via matlab script]
b. formatting the exported file so it is readable by Netstation [by
examining/practicing with Markup chapter in NS manuals]
c. Making sure that the times in the exported file matches the times in the
Netstation file [that the event time and relative location transfers
correctly between the eeglab file and the destination netstation  file

5. An option for GETTING  EVENTS FROM NETSTATION TO EEGLAB
These general points in Point #4 should also work in reverse,
when one wants to export events from netstation, and get them loaded into
eeglab.
One could either import the event file (that was exported from NS)
by using eeglab event updating functions, or by writing a little matlab
script to do the same,
essentially populate event fileds in eeglab with the event fields (TRSPs)
from Netstation.
One needs to be careful here (AGAIN) about being sure that timing is matched
up, and that nothing is lost in translation.

6. GETTING RICH EVENTS FROM NETSTATION TO EEGLAB
Exporting events from NS to eeglab is especially helpful when dealing with
rich "TRSPs" or "event-fields' that may have 5 to 100 subfields. One way to
bypass (some of ) these problems is to put is to develop a series of epochs
in Netstation
via the epoch markup tool ? (when you are in a segmenting tool, there is the
option to NOT segment but rather to create NEW events
that represent the zero point of the segment in question. This allows you to
create all the extra events you need
that may better reflect your "rich" events in Netstation. From there you can
directly export and import into eeglab,
and you should see all these new events. See elesewhere in this email
regarding options for marking up this file once you reimport it
Netstation after having worked on it in eeglab.

5. If anybody has Netstation events into EEGLAB events experience, or vice
versa, please let us know.
Eventually we can setup a webpage for the Netstation-EEGLAB gang.
If any of the options described above can be bettered, we would be glad to
hear of it !

6. Eventually, the new Netstation format will help things go more smoothly
for inter-operability between software packages.
Also, for now, remember that you have the option of using EGI's toolbox for
generating
Netstation files from within matlab, possibly skipping the EP step.

On Mon, Jun 27, 2011 at 5:05 AM, Giovanni Mento <giovanni.mento at unipd.it>wrote:

>  Dear all,
> I have read the messages about saving back files .set (after for example
> ICA on eeglab) in formats readable by Net Station.
> I have imported a .raw continous eeg recorded with net station, segmented
> with EEGLAB epoching tool in 300 epochs (3 conditions), run ICA, removed
> artifactual components and saved as ICA_pruned.set file. So far so good.
> Then, I have opened the .set with EP toolkit and simply saved the file as
> both .egis and binary file. Net station is now able to open the epoched and
> pruned .egis file but there is not the event-list (it only distinguishes
> cell 1 and cell2), therefore I'm not able to run additional analyses like
> averaging.
>
> How can I save in .raw format?
>
> Is there any way to export or save the .egis file with the event list?Or
> simply to import an event-list on a continuous or segmented .raw file in Net
> station?
>
> Maybe is better to segment before with net station and to run ICA on
> already segmented files instead of epoching with eeglab?
>
> I realized that ICA is a beautiful tool for rejecting artifacts (i.e., eye
> blink, 50 Hz noise, etc), but it is not very simple to re-import files in
> net station.
>
> Could anyone help me please?
>
> Many thanks
>
>
>
> Giovanni Mento, PhD
> Department od General Psychology
> University of Padua
> Via Venezia, 8.
> 35131, Padova (PD)
> tel. +39 (0)49 827 6149
> fax. +39 (0)49 827 6600
>
>  Il giorno 07/mag/11, alle ore 03:19, Joseph Dien ha scritto:
>
>  There have been some further developments on this front.  EGI has been
> developing a new file format and been working with other software developers
> to get it supported.  The problem with the NetStation native format is that
> it utilized some third-party software, which kept them from being able to
> have it be directly supported by others.  This new MFF format has now been
> added to FieldTrip's fileio module by Ingrid Nieuwenhuis (who I am cc'ing
> on this).  FieldTrip's Fileio module is used by other open source Matlab
> packages like EEGlab, SPM, and my own EP Toolkit to support other file
> formats so it should take very little effort to make use of it.  I haven't
> had a chance to try it out myself yet but it sounds like it is ready to use.
>  I think it is necessary to have the new 4.5 release of NetStation to try it
> out though.  Perhaps Ingrid can give us more information.
>
> Cheers!
>
> Joe
>
>
>
>  On May 4, 2011, at 8:32 PM, Tarik S Bel-Bahar wrote:
>
>   Hi Stephanie, Another user had a similar question recently. here is the
> response from me further below. Let me know if you got this email.
> *Please do let me know via email if you find a solution that works for
> you.
> Please also let the eeglab list know.
> Also don't forget solutions like ERPlab which allow you to forget about NS.
> *
>
>
> Greetings,
> If you look over the most recent postings on this topic (see below), you
> will note Dr. Dominguez's (l.garcia.d at gmail.com) note that he has
> developed a working path (using Joseph Dien's EP toolkit, search for it on
> Google) that works pretty well. Thus far, EEGLAB itself has not been
> extended for writing data that is readable back into Netstation. EGI
> support ( "Support Team" <supportteam at egi.com> ) also has a matlab file
> that can help you write RAW files from matlab that are readable into
> Netstation. This file from EGI (as well as looking at the EP Toolkit
> code-which exports files readable by both EGI and EEGLAB), and a better
> understanding of the EGI file structure (by looking at their File Manual)
> may help you develop your own plugin. As there is a general interest in
> streamlining this process (see EEGLAB list archive and below), please let
> the EEGLAB list know if you make any further progress in this area, and
> perhaps we can add an EGI file exporter plugin to EEGLAB in the future. One
> related area that could also use some examination is maintaining the
> consistency of events codes and rich event sub-fields between Netstation and
> EGI, although this issue is generally resolved by saving out time stamped
> events from or into Netstation. If there are other users out there who have
> other working solutions in this general "Netstation to EEGLAB and back"
> area, please also let the list know, and perhaps we can collate all the
> current solutions onto a singular webpage for future reference.
> Respectfully. tb
>
>
>
> [Eeglablist] from Netstation to EEGLab and back*Michiel Spape* Michiel.Spape
> at nottingham.ac.uk <eeglablist%40sccn.ucsd.edu?Subject=Re:%20%5BEeglablist%5D%20from%20Netstation%20to%20EEGLab%20and%20back&In-Reply-To=%3C09DAEA8BC192C94EB62C8E71FC35A5D92DD78EA4FE%40EXCHANGE3.ad.nottingham.ac.uk%3E>
> *Mon Mar 14 02:54:35 PDT 2011*
>
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> ------------------------------
>
> Hi,
> Sorry - are you talking about reading in Netstation 'session files' rather than exported "raw" Netstation files? In that case, I, and probably most people using Netstation and EEGLab would be most interested. Any chance this could be added to the standard import/export plugins of EEGLab?
>
> Best,
> Michiel
>
> Michiel Spapé
> Research Fellow
> Perception & Action group
> University of Nottingham
> School of Psychology
> www.cognitology.eu
>
>
> -----Original Message-----
> From: eeglablist-bounces at sccn.ucsd.edu <http://sccn.ucsd.edu/mailman/listinfo/eeglablist> [mailto:eeglablist-bounces at sccn.ucsd.edu <http://sccn.ucsd.edu/mailman/listinfo/eeglablist>] On Behalf Of Luis Garcia Dominguez
>
> Sent: 09 March 2011 13:49
> To: eeglablist at sccn.ucsd.edu <http://sccn.ucsd.edu/mailman/listinfo/eeglablist>
> Subject: [Eeglablist] from Netstation to EEGLab and back
>
> In case some of you have problems exporting and importing segmented
>
> files between Netstation and eeglab (ERP Toolkit) I can help. I have
> been able to export files from NS to eeglab (with help from EGI), do
> some transformation to the data and, save the files back in NS format
> keeping all the necessary events. I know some of you have been
>
> interested on this issue in the past.
> Many thanks to Tarik Bel Bahar, Joseph Dien, and Gaynor Foster (EGI)
> for helping me.
>
> --
> Luis García Domínguez
>
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>
> On Tue, May 3, 2011 at 12:20 AM, Stephanie C <s.connell at psy.gla.ac.uk>wrote:
>
>> Hi,
>>
>> I am looking for guidance on how to export the data and associated
>> metaddata from an EEGLAB .set file format back to a EGI.raw file format?
>>
>> Any help would be greatly appreciated!
>>
>> Cheers,
>> Stephanie
>>
>>
>> Stephanie Connell
>> Ph.D Student
>> School of Psychology
>> University of Glasgow
>>
>>
>>
>>
>>
>>
>>
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