[FieldTrip] ft_redefinetrial problem

[jan-mathijs schoffelen]

Hi guys,

I agree with Nathan that some additional information would be helpful. The 'problem' Qi relates to (at least the issue with the hdr.grad) is a change in the way the sensor-array is defined in FT. A while ago we changed the .pnt/.ori naming scheme into .chanpos/.coilpos/.coilori to make the distinction between channels and coils more transparent. There is a thread on this mailing list about it and more documentation can be found on:

http://fieldtrip.fcdonders.nl/faq/how_are_electrodes_magnetometers_or_gradiometers_described

In general this change should not affect your analysis, unless you are relying on outdated code, or custom-written code which expects the .pnt/.ori fields still to be present.

If you want to chop up your data into short fixed length segment, you should use ft_redefinetrial with the options: cfg.length and cfg.overlap.

BW,

JM

On Jan 12, 2012, at 10:02 PM, Nathan Weisz wrote:

> Hi Qi, 
> 
> providing some code, including some output may actually help …
> 
> I am unaware of ft_redifinetrial altering the contents of your hdr field (i admit i have never paid attention to it), but even if it did how does this affect your subsequent analysis steps? e.g. at least to my knowledge, FT looks for data.grad (instead of data.hdr.grad) e.g. for plotting, source analysis etc. so if you add your grad info via ft_read_sens, then everything should be fine … 
> 
> otherwise, if the original hdr content is so important, then save it as a temporary variable and add it to your redefined trial later.
> 
> but perhaps i have totally misunderstood your problem. in that case see introductory remark on code.
> 
> good luck,
> n
> 
> On 12.01.2012, at 17:20, qi li wrote:
> 
>> Hi,
>> 
>> I have a fixed length experiment raw. I  apply ft_redefinetrial with cfg.trl to epoch it into many segments. When this step is done, the output.hdr.grad has different fields from the input field. More specifically the pnt and ori field are gone thus cause trouble for the later analysis.  I am using 12/23 version, is there a bug or it is suppose to be so.
>> 
>> If I only want to separate the long data into segments, which command can change only the time window while keeping all the other parameters unchanged?
>> 
>> Thanks!
>> 
>> Qi
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20120112/f5a047e6/attachment-0002.html>