4D data reading

Mon Oct 6 16:54:57 CEST 2008

Dear Andrej, dear Gopa,

Sorry to bother you again, but I tried to make a point in my last
mail that it is not necessary to intermediately convert your raw
epoched or continuous 4D-data into another format, prior to be able
to read it into Fieldtrip. Of course you are free to do so, but the
most natural way to me would seem to work on the raw datafiles
directly. Fieldtrip should support this and it has reading routines
for the raw data-file (beginning with e, or c,), the config-file, and
the file containing the digitized head-surface positions.
You should be able to obtain the header information directly by
calling: hdr = read_header('e,thenameofyourrawdatafile') (give or
take an accidental 'keyboard'-statement in the low-level function
read_4d_hdr, this will be fixed in tonight's release version: if it
occurs now, just type dbcont on the command line when it prompts:
K>>) As far as I know hdr contains a structure grad, which specifies
the sensor-positions. At least it works on our Glaswegian 248-sensor
system.

Yours,

Jan-Mathijs

On Oct 6, 2008, at 3:31 PM, Gopakumar Venugopalan wrote:

> Sure will send you those files. Please remember in my files there are
> only 146 channel locations as we turned off two channels.I also have a
> matlab file from Don Rojas for the 148 channel layout and a file which
> he created for the 146 channel layout. Please give some time today, as
> I run those programs on a different machine.
> 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.