[Mne_analysis] Low pass filtering questions

Tue Mar 26 16:08:00 EDT 2013

hi Donald,

if you want to experiment with this you can run the PSD estimation on
raw data before
and after filtering as in :

http://martinos.org/mne/auto_examples/time_frequency/plot_compute_raw_data_spectrum.html#example-time-frequency-plot-compute-raw-data-spectrum-py

you'll see how many dB you loose at 42.5Hz.

Alex

On Tue, Mar 26, 2013 at 8:16 PM, Krieger, Donald N. <kriegerd at upmc.edu> wrote:
> Thank you for continuing to try to address this question.
>
> Please pardon my asking for clarification.
>
> My question boils down to this: If I use the standalone mne_process_raw and use the standard filter settings of 40 Hz with 5 Hz dropoff, is everything above 42.5 Hz cut to zero?
>
> Thanks,
>
> Don
>
> Don Krieger, Ph.D.
> Department of Neurological Surgery
> University of Pittsburgh
> (412)648-9654 Office
> (412)521-4431 Cell/Text
>
>
> -----Original Message-----
> From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Hari Bharadwaj
> Sent: Tuesday, March 26, 2013 2:31 PM
> To: Martin Luessi
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] Low pass filtering questions
> Importance: High
>
> Thanks! I should apologize for being too lazy to look at the C code.
>
> Regards,
> Hari
>
>
> On Tue, March 26, 2013 9:36 am, Martin Luessi wrote:
>> Hari,
>>
>> Please excuse the long silence. In the C code, method (1) is used, i.e.,
>> the filter is designed in the freq. domain with smooth transitions at
>> the corner frequencies (using a cosine). In MNE-Python on the other hand
>> method (2) is used. It can use both IIR or FIR filters, the FIR filters
>> are designed using
>>
>> http://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.firwin2.html
>>
>> the actual implementation uses an overlap-add FFT applied in forward and
>> backward direction to get zero phase (like filtfilt, as you mentioned).
>>
>> I hope this helps,
>>
>> Martin
>>
>> On 03/14/13 14:08, Hari Bharadwaj wrote:
>>> Hi Don, Alex and Matti,
>>>      Not to introduce any more confusion but I have a clarification
>>> question:
>>> Which of the following is true about the C-code?
>>> (1) The filter is realized in the frequency domain fully (i.e) the FFT
>>> coefficients for blocks of 2048 time samples are tapered to have a
>>> transition band of 5 Hz around the cutoff and then going back to time.
>>> In
>>> this case, the filter is a non-causal IIR filter with zero-group delay.
>>>
>>> (2) An FIR filter is designed first and then then implemented in the
>>> frequency domain using the overlap-add method with FFT blocks of 2048
>>> points each. In this case, the filter is FIR and non-causal with
>>> zero-group delay but there are (small) sidebands extending upto the
>>> Nyquist rate. This would be like MATLAB's fftfilt().
>>>
>>> Thanks,
>>> Hari
>>>
>>>
>>> On Thu, March 14, 2013 8:45 am, Matti Hamalainen wrote:
>>>>
>>>> On Mar 14, 2013, at 8:30 AM, Alexandre Gramfort wrote:
>>>>
>>>>> hi Don,
>>>>>
>>>>>> Please bear with a further question:
>>>>>> If the low-pass is set at 40 Hz, then the cos^2 drop off is applied
>>>>>> beginning at the 40 hz components and falling to zero at 45 ?  Or is
>>>>>> it
>>>>>> applied beginning at something like 38 hz so that the fourier
>>>>>> coefficients are attenuated by a fact of 2 at 40 ?
>>>>>
>>>>> I am not 100% about the C code but I bet for 40 to 45 with 0 at 45 Hz
>>>>>
>>>>>> And pardon this stupid question: Does this produce a gain of 0.0 for
>>>>>> all higher frequencies in the filtered signal above 45?  Or is there
>>>>>> some kind of ringing which occurs?
>>>>>
>>>>> it does remove all frequencies about 45Hz up to some numerical errors
>>>>> and if there is some ringing it will be in time. The less the stop
>>>>> band (here 5) the more ringing in time domain.
>>>>
>>>> Hi Don,
>>>>
>>>> In the C code the default width of the lowpass transition is 5 Hz. For
>>>> 40
>>>> Hz lowpass this means that the falloff starts at 37.5 Hz and ends at
>>>> 42.5
>>>> Hz. You can adjust this value in the mne_browse_raw or with the
>>>> --lowpassw
>>>> option in mne_process_raw and mne_browse_raw.
>>>>
>>>> The manual tells this in sections 4.5.1 and 4.2.1.
>>>>
>>>> - Matti
>>>>
>>>>
>>>>
>>>>
>>>> ---------
>>>>
>>>> Matti Hamalainen, Ph.D.
>>>> Athinoula A. Martinos Center for Biomedical Imaging
>>>> Massachusetts General Hospital
>>>>
>>>> msh at nmr.mgh.harvard.edu
>>>> mhamalainen at partners.org
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>> Mne_analysis at nmr.mgh.harvard.edu
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>>>
>>>
>>
>>
>> --
>> Martin Luessi, Ph.D.
>>
>> Research Fellow
>>
>> Department of Radiology
>> Athinoula A. Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> Harvard Medical School
>> 149 13th Street
>> Charlestown, MA 02129
>>
>> Fax: +1 617 726-7422
>>
>>
>>
>
>
> --
> Hari Bharadwaj
> PhD Candidate, Biomedical Engineering,
> Boston University
> 677 Beacon St.,
> Boston, MA 02215
>
> Martinos Center for Biomedical Imaging,
> Massachusetts General Hospital
> 149 Thirteenth Street,
> Charlestown, MA 02129
>
> hari at nmr.mgh.harvard.edu
> Ph: 734-883-5954
>
>
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