Hi Denis,
I have tested with single_trial_power() but I obtain exactly the same
results that my use with _time_frequency(). Here is my code:
https://gist.github.com/arnaudferre/11215335. I don?t understand what the
problem is. With a sinusoid, I must have a band of high power around the
fundamental frequency of the sinusoid, right?
For the GUI, I don?t find documentation on the use with Windows. But ok, I
must compile the sources with the makefile. It?s been a long time that I
didn?t play with C! But I will try (I believe that I must download the
software Make to begin). But in fact, I don?t know why I spoke of GUI,
sorry. I think that I thought at a possibility to play with data directly
with a GUI in the way that I want.
I?m not sure to understand what you name ?Raw object?. Is it the name of an
existing object from MNE? But, with the knowledge of this object, I can
write a function which return this directly. My problem is that I?m not an
expert on the data and her format. But if it?s substantially a problem of
parsing, I can step in the discussion.
I read your link on the S-transform. Yes, it could be very interesting to
test my data with this method. But I must already test older results from a
study with Fourier Transform. In literature, the wavelet transform with
morlet wavelet seems to be adequate to my project (Phase-Amplitude coupling
then cross-frequency coupling). So, I want finish with this method to have
my first result. But thank you, I keep it in a corner for later.
Best,
Arnaud
2014-04-23 11:22 GMT+02:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:
Hi Arnaud,
Hi Denis,
Thanks for the fast reply.
Yes I can share my test. Here:
https://gist.github.com/arnaudferre/11206945.
Thanks, will have a look later.
Ok, I will try to use single_trial_power() function now.
For the GUI, unfortunately, I must develop a ?biologists-friendly?
software. In consequence (and with others constraints), I must develop on
Windows and the GUI doesn?t work on Windows if I have correctly understood.
Which GUI? The MNE C GUI indeed compile on Windows. However,
`mne.gui.coregistration` in Python is supposed to work on Windows.
For my file format, I have already develop my own functions to parse
the original data (my goal: adapt raw signal to can use just the useful
data). This format can be ?CED Spike2 SMR files? or an alternative in TXT
from Local Field Potential acquisition. So, I store the data of a single
trial in a dictionary, then in a pickle file (maybe not a good idea?).
I agree. I would strongly encourage you to write a custom constructor
function that returns a Raw object from your data. We're happy assist you
with that Also it would be a great test case for new tools we're about to
develop that aim at making exactly this task easier. In fact I need to
write a couple of functions very soon that allow me to read in data stored
in Mat files. Sounds like that would follow the same logic.
I do this certainly with my personal way. For these reasons, I tried to
adapt the MNE-Python script to read my data. It seems not far yet! But I
don?t know if I can really add idea in your conversation due to these
specific data.
I think you can. See above. Also we're happy to add support to additional
EEG / electrophysiology formats.
Anyway, it seems that MNE contains all the tools what we need here. It?s
very encouraging yeah. But, I think we need time to know to use these tools.
Arnaud
FYI something I'm working on at the moment that might also be of interest
to you:
https://github.com/mne-tools/mne-python/pull/1233
Best,
Denis
2014-04-19 12:34 GMT+02:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:
Hi Arno,
let my reply inline,
Hi all,
I work on EEG data in behavioral field. I understand the basics of
signal processing and I?m not so bad in Python. But for a beginner like me,
MNE-Python is pretty huge. I was advised to use MNE knowing my constraints,
but I?m starting to think that it?s maybe too evolved for a non-expert
scientist in this field like me.
I?m just trying to draw a time-frequency PSD from a single trial with a
CWT (with morlet wavelets). I thought to have found what functions used,
but in testing my script, I don?t obtain correct result.
In fact, I tested with a simple sinusoid function with a frequency of
10Hz on 1sec (1000points). I expected to see a lot of "red blobs" aligned
on the 10Hz in y-axis but not. I have a continuous and very thin band
around 1.5 Hz and a residual band around the 90Hz. I looked the wavelets
and it seems fine. What is strange is that I see the correct number of
blob, so I think it?s not so far of correct result. In first, I thought of
a problem in adjusting my display, but it seems not.
Could you share an example script, e.g. using https://gist.github.com/
That would be very helpful.
I use mainly the function _time_frequency(data, Ws), one of the
functions in tfr.py in mne.time_frequency where data is a 2D-array
containing only my signal in data[0].
I read this link:
http://martinos.org/mne/stable/auto_examples/stats/plot_cluster_1samp_test_time_frequency.html,
but as I don?t use data with the standard format, it seemed to me
complicated. Moreover, I think that _time_frequency(data, Ws) is just
needed to do what I want. And yet, maybe that the specificities of the
function single_trial_power in tfr.py is the solution?
In fact `single_trial_power` would be the way to go. (
http://martinos.org/mne/dev/generated/mne.time_frequency.single_trial_power.html#mne.time_frequency.single_trial_power
)
In general it's not recommended not use functions starting with
underscores unless you know exactly what you do. Things are much easier
once you use the top-level API. Is your file format that prevents you from
doing this? What kind of EEG data do you use? We're currently working on
improving support for custom data:
https://github.com/mne-tools/mne-python/issues/1229
Please feel free to participate in the discussion on Github and tell us
more about your use case.
Thanks in advance
Arnaud
I hope we can encourage you to keep exploring the new terrain 
Denis
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