New FieldTrip User Questions

Eric Maris e.maris at DONDERS.RU.NL
Fri Apr 16 22:02:16 CEST 2010


Dear Allen,





1)      With regard to our frequency domain analysis, I've already used FFT
to look at general trends in the sample and delay periods but am interested
in plotting the evolution of those oscillations over trial time.  I believe
that the cluster analysis and MonteCarlo simulation are the best method to
adopt for quantifying difference between conditions, but please do correct
me if you have other suggestions.



The cluster-based permutation tests are for testing differences between
conditions, not for characterizing temporal evolution (unless you mean by
"temporal evolution" a mean power difference between the first part and the
second part of the trials).



2)      Another question is about the edge artifact of using multitapers at
ultralow frequencies on relatively short (57s) data segments.  Are
multitapers a good approach, and if so could padding help with the edge
artifact?



Do you call 57s short? With such a huge trial length, you definitely need
multitapers! I'm not aware of any edge artifact using dpss tapers.



3)      On a separate note, do you have any functions available/coming for
computing spike-field coherence?  Thank you again.



There are no special SFC-functions in FT, as far as I know. In my own
experience, running a coherence analysis on mixed LFP-spike data works fine.
But I have not studied this, and there may be room for improvement .





Best,



Eric









Best,

Allen





____________________________________________________________________________
______

Allen Ardestani    Email: aardesta at ucla.edu

Phone: (310) 825-5528

Medical Scientist Training Program

David Geffen School of Medicine at UCLA

Semel Institute for Neuroscience and Human Behavior

760 Westwood Plaza

Los Angeles, CA 90095-1759

USA



From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf
Of Eric Maris
Sent: Thursday, April 01, 2010 1:51 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] New FieldTrip User Questions



Hi Allen,



I just now came across the FieldTrip toolbox and have a few questions - I
apologize in advance if I am misusing this discussion forum or if my
questions are too obvious.  I am working with a very large dataset of
simultaneous LFP, unit, and NIRS signal from macaques for the purpose of
examining time and frequency dynamics of the signals in various cognitive
conditions.  I would like to implement the clustering/bootstrapping
methodology outlined in [Journal of Neuroscience Methods 164 (2007) 177-190]
to identify significant changes in synchronization and phase-locking.



The specific data in question are LFPs recorded while the monkeys perform a
working-memory task, which consists of a 2s visual sample, 20s delay, and
subsequent choice period.  A 20s baseline precedes the sample (t=0), which
is time-locked to the animal's foveation on the visual sample.  TF plots are
computed using Morlet wavelets for each trial, averaged across trials, and
then normalized with respect to the average baseline.  The first question
I'd like to address is: what time-frequency regions exhibit significant
difference between Correct (left plot) and Incorrect (right plot) trials.



cid:image002.jpg at 01CAA0E0.B7CEC3E0 cid:image003.jpg at 01CAA0E0.B7CEC3E0

I have a number of questions about the appropriateness of applying
bootstrapping to our specific dataset:

1)      Because we use wavelets for spectral decomposition (with
frequency-dependent changes in spectral and temporal resolution) is it valid
to simply cluster across different frequencies?



Yes it is. However, with your 20 sec. trials, I would not go for the high
temporal resolution that he wavelet transform gives you. I would do one
Fourier-based analyses for the first 2 seconds (encoding stage) and another
one for the rest of the trial (retention stage).



2)      We are interested in comparing different conditions, where each is
computed relative to its own baseline.  Is there anything wrong with using
the baselines of the same dataset for the null distribution as opposed to
using a different set of baseline data?



Do not baseline correct your data. Compare the raw power spectra for the
correct response trials with those of the incorrect response condition.



3)      The data have been recorded at 1KHz, and this oversampling results
in high spatial-frequency noise.  Do I need to do any downsampling/smoothing
before applying the statistics?





No. However, with such long trials, I would definitely smooth in the
frequency domain using multitapers (also available in Fieldtrip).





4)      For evaluating the relationship between channels, we compute the
phase-locking value (PLV), which has no meaningful single-trial
measuremetnt.  Is there any way to apply statistical analyses directly to
the average TF plots without resorting back to the individual trials?



Have look at the paper by Maris, Schoffelen, and Fries (2007, JNM) that
describes cluster-based permutation tests for coherence differences. This
may be what you need.







Best,

















____________________________________________________________________________
______

Allen Ardestani    Email: aardesta at ucla.edu

Phone: (310) 825-5528

Medical Scientist Training Program

David Geffen School of Medicine at UCLA

Semel Institute for Neuroscience and Human Behavior

760 Westwood Plaza

Los Angeles, CA 90095-1759

USA



----------------------------------

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.

http://listserv.surfnet.nl/archives/fieldtrip.html

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.

http://listserv.surfnet.nl/archives/fieldtrip.html

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.

http://listserv.surfnet.nl/archives/fieldtrip.html

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/neuroimaging/fieldtrip.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20100416/d1f2cf0e/attachment-0002.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 18296 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20100416/d1f2cf0e/attachment-0004.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 17871 bytes
Desc: not available
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20100416/d1f2cf0e/attachment-0005.jpg>


More information about the fieldtrip mailing list