[Mne_analysis] ICA with mne_python v0.8

Wed Aug 13 09:49:29 EDT 2014

Hello MNE users,

I started to use mne_python version 0.8 (great tool btw), and I have a
question related to ICA within the script plot_ica_from_raw.py

(http://martinos.org/mne/stable/auto_examples/preprocessing/plot_ica_from_ra
w.html#example-preprocessing-plot-ica-from-raw-py)

My question is related to the command ica.find_bads_eog that will return
'eog_inds' and 'scores'

In the example on the website the scores is a np.array with one dimension.

Whereas when I run it, I have a 2 dimension array

eog_inds, scores =ica.find_bads_eog(raw)

In[356]: scores

Out[356]: 

[array([-0.00048168, -0.42372344, -0.0140817 ,  0.02141039,  0.01795695,

       -0.06170853, -0.01864879, -0.00278151, -0.04799586, -0.02081424,

       -0.04495371, -0.00866799,  0.01401663,  0.0052837 ,  0.00837509,

        0.0635164 ,  0.01747246, -0.00974186,  0.19293349,  0.03663461,

       -0.03982205, -0.00588006, -0.04194552,  0.0367501 , -0.0095143 ,

        0.00641498, -0.00223432, -0.00572408,  0.01120724, -0.00707822,

        0.03354455, -0.01167412, -0.01716788,  0.0521022 ,  0.01204061,

       -0.01250779, -0.02080896, -0.02087199, -0.06090518,  0.01263185,

        0.0617042 , -0.01924968,  0.07025745]),

array([ -6.90115011e-04,   2.01336477e-02,  -1.94085728e-02,

         5.54494463e-03,   1.85259423e-02,  -6.44562593e-02,

         9.22072187e-03,   2.48208247e-02,   6.48755505e-03,

         2.96724141e-02,  -2.95860189e-02,  -1.32707432e-02,

         2.55635523e-02,   8.35349233e-03,  -1.40756479e-02,

        -7.64950200e-02,  -1.91362435e-02,  -5.59807386e-02,

        -5.37760229e-01,  -1.44527756e-03,   2.62353032e-02,

         3.55718290e-03,   4.53971390e-03,  -3.73325017e-02,

        -4.44052114e-02,   2.42345592e-02,   5.23123704e-02,

         6.99711147e-03,   4.66395629e-02,   1.14460067e-02,

        -1.71193294e-02,   8.64111157e-03,   2.42794389e-02,

        -1.02563756e-02,   2.66764223e-02,  -1.22480541e-03,

        -6.26583675e-04,   7.31585385e-02,   3.24236294e-04,

        -3.61010677e-02,  -2.74582253e-02,   1.88243641e-02,

        -5.08565452e-02])]

Now I compared with the command used in a previous version of mne_pyhton

eog_scores = ica.find_sources_raw(raw, target='EOG062',
score_func='pearson')

In [368]: eog_scores

Out[368]: 

array([  1.66649505e-02,   2.16342706e-02,   4.83022984e-03,

        -4.35487020e-04,  -1.20631032e-02,  -2.35856136e-02,

         1.23689301e-02,   8.71059801e-03,  -1.01489847e-02,

         1.03843218e-03,  -5.75965904e-03,   1.23044678e-05,

        -6.77430607e-03,  -1.14913804e-02,  -1.94694511e-03,

        -4.53459854e-02,  -2.64928079e-03,  -9.15942420e-03,

        -3.69825806e-01,   7.58370880e-03,  -6.07496046e-03,

         2.34470256e-02,  -1.30305829e-03,   2.84655600e-03,

        -2.25454800e-02,   8.44810084e-03,   1.41810585e-02,

         9.74897473e-04,   2.38848977e-02,  -8.01684853e-03,

         1.35224050e-03,  -1.48211516e-03,   9.42452704e-04,

        -6.67442395e-04,  -3.01227394e-03,  -7.98317803e-03,

         2.84740542e-03,  -5.71626494e-03,  -5.39340114e-03,

        -5.48041671e-03,  -7.14136517e-03,   8.17430479e-03,

        -1.31954753e-02])

Here are my questions

1)      I assume that with the new command I should specify scores[1] to use
accordingly for plotting and ranking?

Is the 2 arrays output an error in programming or are both values usefull?
If so can you explain what are the differences between both?

2)      Why both commands do not return the same scores values? Is it
because the new command filtered the data & eog, which is not the case for
the oldest one?

Thanks in advance

Elisabeth

__________________________________________________________

Dr Elisabeth Fonteneau

Neurolex Group

Department of Psychology

University of Cambridge

Downing Street, Cambridge CB2 3EB, UK

Phone: +44 1223 333 548

Email:  <mailto:ef309 at cam.ac.uk> ef309 at cam.ac.uk

Web:  <http://www.neurolex.psychol.cam.ac.uk/directory/ef309@cam.ac.uk>
www.neurolex.psychol.cam.ac.uk/directory/ef309 at cam.ac.uk

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