[FieldTrip] creating new dataset

[Rojas, Don]

Hi Jessie,

If you wish to take a FieldTrip dataset back to the native 4D format, then it will not be trivial, but if you have the original data in 4D format, there is a potential solution in Eugene Kronberg's pdf4D matlab object code:

http://biomag.wikidot.com/msi-matlab

If you do not have the native 4D data, this will not work. Look at the duplicate and write_data_block methods. However, note that if you do duplicate the dataset, it will expect there to be as many channels in the new dataset as in the original. You would then have to delete those channels in the 4D MSI software using the deleter command. Or, alternatively, if you have a working copy of the MSI software, you can delete the channels in the original dataset within 4D, then use the duplicate method on that file, then write your data back to it using the write_data_block method.

Feel free to contact me off list if you have questions.

Best,

Don

On Sep 26, 2011, at 8:26 AM, jan-mathijs schoffelen wrote:

Hi Jessie,

FieldTrip is not able to write back into the native 4D neuroimaging format. If you want to create a new dataset, you need to have a look at the software which is provided by the 4D neuroimaging company. Your requested functionality may either be a feature of one of the applications, or may be implemented in one of the command line utilities. You may want to look in the software documentation for this.

Best wishes,

Jan-Mathijs

On Sep 26, 2011, at 4:11 PM, Luo, Jessie (NIH/NIMH) [V] wrote:

Thanks for your answer Jörn  . Yes I can use those functions to 'exlucde', but these definitions cannot be read by other software. What is why I intended to create a new dataset. Looks like fieldtrip does not allow that...

Jessie
________________________________________
From: "Jörn M. Horschig" [jm.horschig at donders.ru.nl<mailto:jm.horschig at donders.ru.nl>]
Sent: Sunday, September 25, 2011 4:09 AM
To: Email discussion list for the FieldTrip project
Subject: Re: [FieldTrip] creating new dataset

Hi Jessie,

not quite sure what you are up to by saying that you do not want to use ft_ functions for that (maybe I misunderstood that part). Of course you could write your own loop, but the easier option would be to call ft_channelselection on your data and then call ft_preprocessing (this will return a new data-structure). See the help of these ft_channelselection:

You can also exclude channels or channel groups using the following syntax
   {'all', '-POz', '-Fp1', -EOG'}




>From ft_preprocessing:

If you are calling FT_PREPROCESSING<http://fieldtrip.fcdonders.nl/reference/ft_preprocessing> with also the second input argument
 "data", then that should contain data that was already read from file in
 a previous call to FT_PREPROCESSING<http://fieldtrip.fcdonders.nl/reference/ft_preprocessing>. In that case only the configuration
 options below apply.

 The channels that will be read and/or preprocessed are specified with
   cfg.channel      = Nx1 cell-array with selection of channels (default = 'all'),
                      see FT_CHANNELSELECTION<http://fieldtrip.fcdonders.nl/reference/ft_channelselection> for details


You could also use ft_selectdata instead of ft_preprocessing in case you are handling already processed data (e.g. tfr-data ). Alternatively, you can check ft_channelrepair for interpolating the bad channels.

Hope this all helps to what you are up to!
Best,
Jörn

On 9/24/2011 10:12 PM, Luo, Jessie (NIH/NIMH) [V] wrote:

Hi,

If there are bad channels (e.g. for a 4D system) in a dataset, Is it possible to create a new dataset by excluding them? I meant creating a NEW dataset  without those channels (not by defining them using the ft_... in fieldtrip).

Thanks,

Jessie
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--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl<mailto:jm.horschig at donders.ru.nl><mailto:jm.horschig at donders.ru.nl>
Tel:    +31-(0)24-36-68493
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Visiting address:
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NL-6525 EN Nijmegen
The Netherlands


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Jan-Mathijs Schoffelen, MD PhD
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl<mailto:J.Schoffelen at donders.ru.nl>
Telephone: +31-24-3614793

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-----------------------
Don Rojas, Ph.D.
Associate Professor of Psychiatry
U. of Colorado Denver Anschutz Medical Campus
Director, UCD Magnetoencephalography Lab
13001 E. 17th Pl F546
Aurora, CO 80045
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