4D data reading
Stancak, Andrej
A.Stancak at LIVERPOOL.AC.UK
Tue Oct 7 17:44:22 CEST 2008
Dear Gopakumar,
I followed your advice (pdf2set -u), and was almost successful in reading the 4d-148 data into FieldTrip.
I can read header all right with exception of one line that turns out to be decisive during reading data (read_data):
D=read_data ('d:\data\meg\windup\T1\2\c,rfdc','dataformat','4d');
??? Reference to non-existent field 'ChannelUnitsPerBit'.
Error in ==> read_data at 477
upb = hdr.orig.ChannelUnitsPerBit;
Clearly, we miss the field ChannelUnitsPerBit in hdr.orig structure. As read_event.m also calls read_data.m, this problem precludes reading events as well.
To test the rest of the code, I simply put upb = grad (grad is 1 line above in read_data) and then it works all very well (as grad is equal to 1 in all channel fields). So my hope is that if we can sort out the missing field in hdr.orig., we will be able to read all data very well.
I would be grateful for a hint here as have no idea how can we miss that field.
Best wishes
Andrej
Prof. Andrej Stancak, PhD.
The University of Liverpool
School of Psychology
The Eleanor Rathbone Building
Bedford Street South, Room 209
Liverpool
L69 7ZA
E:mail: a.stancak at liverpool.ac.uk (primary)
stancak at centrum.cz (secondary)
Phone: 0151 7946951
Office hours: Monday 10-12, Wednesday 10-12
-----Original Message-----
From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
Sent: Mon 06/10/2008 16:03
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] 4D data reading
Andrej, I see an error in my mail below. The three files
.xyz, .m4d and the acutal pdf is produced using the command:
pdf2set -u
You post the selection in the propreitary MSI environment, then type in
the command given above. It will put out the three files mentioned for
each data set.
I shall include only the .xyz and .m4d files from grand averaged files,
as they do not contain any identifiable information.
I believe that the .m4d file is also called the header file and
the .xyz is called the location or coordinate file.
Ken Velarde was immensely helpful with this, as were Christian
Weinbruch, and Don Rojas. Don Rojas's colleague Dr. Eugene Kronberg
also has created an interface that can read 4D data, and he was going
to create such a template as well--as per our last email exchange.
I also have a xls2matlab function that I used to create my own
template, as the sensor location file is usually a product of
individual MEG systems. If I may have mislead anyone it is
unintentional as I am constantly learning.
regards
gopa
Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> Dear Gopa and Almu,
>
> do I understand the procedure correctly: we should export data from
> 4D in FIF format (currently we export in native e,... (binary), and
> the text files for the header and the surface points), and then use a
> modified xyz file containing the layout of 148 sensors. I would be
> grateful for one sample xyz file to see whether we can read data this
> way. Naturally, the best would be to incorporate it into the reading
> procedures of FieldTrip.
>
> Best wishes
> Andrej
>
>
> Prof. Andrej Stancak, PhD.
> The University of Liverpool
> School of Psychology
> The Eleanor Rathbone Building
> Bedford Street South, Room 209
> Liverpool
> L69 7ZA
>
> E:mail: a.stancak at liverpool.ac.uk (primary)
> stancak at centrum.cz (secondary)
> Phone: 0151 7946951
> Office hours: Monday 10-12, Wednesday 10-12
>
>
>
> -----Original Message-----
> From: FieldTrip discussion list on behalf of Gopakumar Venugopalan
> Sent: Mon 06/10/2008 14:12
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] 4D data reading
>
> Dear Almu (that is a nice name!) thank you Rob Oostenveld, Christian
>
> Weinbruch and Arno (EEGLAB) may be the ones who can make it work for
>
> the other users. There was also a discussion about whether the
> systems
> were using third order gradiometers and/or magnetometers as the
> reference. There are mail postings in that thread.
> Everyone: I apologize for the typos in my hastily composed response
> earlier.
> regards
> gopa
>
>
> Quoting Almudena Capilla <a.capilla at PSY.GLA.AC.UK>:
>
> > Dear Gopa,
> >
> > I have got a template for the 4D - 148 channels system. I could
> give
> > it to
> > the Fieldtrip developers if this is helpful for other users of
> this
> > system.
> >
> > Best,
> > Almu
> >
> > -----Original Message-----
> > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL]
> On
> > Behalf
> > Of Gopakumar Venugopalan
> > Sent: 06 October 2008 13:22
> > To: FIELDTRIP at NIC.SURFNET.NL
> > Subject: Re: [FIELDTRIP] 4D data reading
> >
> > Hello everyone, I have been wrestling with these problems for a
> while
> >
> > too.
> > Here is what I found: Fieldtrip/EEGLAB will read neuroscan files
> > (.avg,
> > and .eeg), and will read raw data (e,..)from 4D.
> > I believe that EEGLAB/Fieldtrip may not have a template for the
> 148-
> > Channel system co-ordinates. Christian and Don Rojas created one
> for
> > me
> > in early April this year.
> > A FIF export from the 4D system may also solve this problem.
> Stephen
> >
> > Moratti helped me with this a while a ago. It puts out three
> > files .xyz, .4D and the original e,.. file. But, if the .xyz file
> > which
> > has coordinates for 148 channels does not match with the template,
> > then
> > the data will not load. I think for one may have to load a create
> a
> > 148
> > channel template for this purpose. This is my experience with
> EEGLAB,
> >
> > and I think that they underlying engine is the same for both
> EEGLAB
> > and
> > Fieldtrip
> > Then again, I may be completely wrong about everything except the
> > templates that were created for me.
> > regards
> > gopa
> >
> >
> > Quoting "Stancak, Andrej" <A.Stancak at LIVERPOOL.AC.UK>:
> >
> > > Dear all,
> > >
> > > we have some problems reading 4D Neuroimaging MEG data (148
> > > sensors). For now, we export original 4D data into BESA format,
> > and
> > > then read those into FieldTrip. This is not optimal, as e.g.
> > gradient
> > > coils information is not transferred into FieldTrip. We would be
> > > grateful for a plugin or a hint enabling us to read the 4D data
> > > directly into FieldTrip.
> > >
> > > Best wishes
> > > Andrej Stancak
> > >
> > >
> > > Prof. Andrej Stancak, PhD.
> > > The University of Liverpool
> > > School of Psychology
> > > The Eleanor Rathbone Building
> > > Bedford Street South, Room 209
> > > Liverpool
> > > L69 7ZA
> > >
> > > E:mail: a.stancak at liverpool.ac.uk (primary)
> > > stancak at centrum.cz (secondary)
> > > Phone: 0151 7946951
> > > Office hours: Monday 10-12, Wednesday 10-12
> > >
> > >
> > > ----------------------------------
> > > The aim of this list is to facilitate the discussion between
> users
> > of
> > > the FieldTrip toolbox, to share experiences and to discuss new
> > ideas
> > > for MEG and EEG analysis. See also
> > > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > > http://www.ru.nl/fcdonders/fieldtrip.
> > >
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the
> > FieldTrip toolbox, to share experiences and to discuss new ideas
> for
> > MEG
> > and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
> > ----------------------------------
> > The aim of this list is to facilitate the discussion between users
> of
> > the FieldTrip toolbox, to share experiences and to discuss new
> ideas
> > for MEG and EEG analysis. See also
> > http://listserv.surfnet.nl/archives/fieldtrip.html and
> > http://www.ru.nl/fcdonders/fieldtrip.
> >
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/fcdonders/fieldtrip.
>
----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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