[FieldTrip] Using FieldTrip to analyse LFP recordings in rat
laetitia.lalla at inserm.fr
laetitia.lalla at inserm.fr
Fri Apr 8 10:27:58 CEST 2016
my name is Laetitia and I'm a Phd student in Marseille (France). I'm
doing in-vivo recording in freely-moving rats : I implant them with 2
electrodes deep into 2 different regions of the brain. I'm studying the
Local Field Potentials and I want to use FieldTrip to analyse the data.
To simplify :
- I have 2 rats.
- Each rat did 20 sessions of the task (on 20 different days).
- Each session consists of 20 trials of condition 1 and 20 trials of
I have 2 questions.
1) I have the feeling it would be meaningless to do "source
reconstruction" because my electrodes are already deep inside my
"source" and the LFP I am recording is very local. (My electrodes have
32 channels separated by 20-200 µm. The LFP is very very similar across
all the channels, so I averaged over the 32 channels to have one signal
for each region.)
However, I see that 2 different functions exist for the statistics :
FT_FREQSTATISTICS AND FT_SOURCESTATISTICS. So far, I've been using
ft_freqstatistics but I encounter some issues (for exemple, doing
monte-carlo permutation test to assess the imaginary coherence). I
thought of computing it manually, but I'm thinking that maybe more stuff
are implemented in ft_sourcestatisctics ?
→ Are these 2 functions fundamentally different or do they call the same
sub-fonctions (and my problem has actually nothing to do with that) ?
2) I'm a bit confused with the vocabulary from EEG and MEG studies (I'm
not used to it yet...). From what I understood, in human studies, you
can do comparison for a single subject (across trials) or across
subjects. But I have 3 levels of comparisons in my design :
- WITHIN A SESSION, I WANT TO COMPARE ACROSS TRIALS (the 20 trials of
condition 1 VS the 20 trials of condition 2).
- WITHIN A RAT, I WANT TO COMPARE ACROSS SESSIONS (between the 2
- then - in the very end - ACROSS RATS. But I have only 2 rats so far,
so I will deal with this later.
I'm a bit confused when reading the tutorials and the mailing list,
especially when it comes to the statistics... For example : this is from
an email from 2013 by Eric Maris about "Nonparametric statistical
testing of phase coherence"
"To compare coherence between conditions across subjects (instead of
trials), you need a different statfun: depsamplesT (for a
within-subjects design; subjects have participated in all conditions) or
indepsamplesT (for a between-subjects design; subjects have participated
in only one condition)."
→ If I want to compare across sessions (for a same rat), can I actually
consider that my different sessions are "subjects"? And then compare
coherence "across subjects" would be doing it "across sessions" ? And I
would be in a "within-subject design" since my sessions involve the 2
conditions every time ?
I realise that it may be very confusing... I hope you will understand my
And if anyone already applied fieldtrip functions to do statistics on a
different framework that the usual EEG/MEG, please let me know !
Thanks a lot,
PhD Student in Neuroscience
INMED, Marseille, France
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