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Published 20 hours ago • verified publisher icon EtienneCmb

Automatic detection of sleep spindles issue.

Open Dolki opened this issue 4 years ago • 3 comments

Hello! -I have been trying to use the automatic detection of sleep spindles in python/Sleep modifying the settings but is does not seem to work properly. It seems that the number of spindles that are detected is the same no matter what frequency threshold I am using. Is there any explanation for that?

-In addition, many "spindle events" that are detected are not actual spindles, and some of the spindles that I can visually detect are missing form the automatic detection. Is there any suggestion for the proper use of this automatic detection tool ?

Screen Shot 2020-04-03 at 12 26 57 AM Screen Shot 2020-04-03 at 12 26 32 AM

Dolki avatar Apr 03 '20 04:04 Dolki

Hi @Dolki !

  1. Thanks for noting the issue with the frequency. In fact, what's happening under the hood is that Visbrain is automatically detecting the peak frequency in the 11 - 16 Hz power spectrum and then using a 1 Hz bandwidth around the peak. So, the Fmin and Fmax are not taken into account. I'll work on a PR to make this explicit.

  2. For a better and more accurate spindles detection, I highly recommend my command-line package YASA, specifically the yasa.spindles_detect function. As explained in the docs, you can also link YASA to Visbrain if you want to visualize the detected spindles.

Hope this helps, Raphael

raphaelvallat avatar Apr 03 '20 15:04 raphaelvallat

Hi @raphaelvallat !

Thank you so much for your response! I took a look at your suggestions and I have a couple of questions. -Is there a command line interface that I can use for YASA? (it seems to me that I have to create a new .py file, with yasa.spindles_detect in it and then run the .py file from the terminal).

-I gave it a shot and I saw that I have to give an array like argument as data. My data are .edf files. Do you have any suggestions?

Thanks a lot, Dolki

Dolki avatar Apr 04 '20 21:04 Dolki

Hi @Dolki !

  1. YASA is designed to be used with Jupyter notebook or Jupyter Lab

  2. To load EDF files into memory, please refer to the mne.io.read_raw_edf function

I would also recommend that you have a look at the tutorials to familiarize yourself with the functions.

Hope this helps! Raphael

raphaelvallat avatar Apr 04 '20 22:04 raphaelvallat