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| Once the conversion is complete, a single .bst file will be created that contains all the acquisition events, the spiking events and the LFP signals (saved in the dataset’s folder in brainstorm_db). This file will automatically be imported in the database with the suffix _''LFP''''. ''''''''The channels file will be copied to the new entry. Users can now just use this file for the entire analysis. This makes it very practical for exchange reasons with other researchers since a 30KHz raw file would be converted to a 30 times smaller LFP file. ''' | |
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Once the conversion is complete, a single .bst file will be created that contains all the acquisition events, the spiking events and the LFP signals (saved in the dataset’s folder in brainstorm_db). This file will automatically be imported in the database with the suffix _''LFP''''. ''The channels file will be copied to the new entry. Users can now just use this file for the entire analysis. This makes it very practical for exchange reasons with other researchers since a 30KHz raw file would be converted to a 30 times smaller LFP file. {{attachment:convertedLFPOutput.png}} |
''' {{attachment:convertedLFPOutput.png}} ''' |
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| If the Bayesian spike removal box is not selected, the conventional LFP conversion will be applied. LFP is considered to [[file:///C:/Users/McGill/Dropbox/Basic%20Electrophysiology%20analysis%20in%20Brainstorm.docx#_msocom_1|[MOU1]]] , therefore the signals are filtered to [0.5-150] Hz, and then sequentially downsampled to 1000Hz. |
If the Bayesian spike removal box is not selected, the conventional LFP conversion will be applied. LFP is considered to, therefore the signals are filtered to [0.5-150] Hz, and then sequentially downsampled to 1000Hz. |
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| * Zanos, T. P., Mineault, P. J. & Pack, C. C. Removal of spurious correlations between spikes and local field potentials. J. Neurophysiol. 105, 474–486 (2011). | |
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· Zanos, T. P., Mineault, P. J. & Pack, C. C. Removal of spurious correlations between spikes and local field potentials. J. Neurophysiol. 105, 474–486 (2011). |
Deriving LFP signals from Raw signals
Author: Konstantinos Nasiotis
Contents
The toolbox features a convenient signal converter that produces local field potential time series from raw signals. The converter jointly processes the recorded raw data and the events generated by the spike sorter. The fast-sampled raw signals are downsampled to a new sampling rate (1000 Hz), with an anti-aliasing bandpass filter (e.g., [0.5, 150] Hz) applied. The event latencies are also adjusted to the new sampling rate before both the new event file and the LFP time series are automatically featured in the Brainstorm database as new data files.
Everything needed for the electrophysiology analysis will be incorporated into a single .bst file (Brainstorm binary file format), located in the brainstorm_db folder.
In order to get the LFP from the raw file after spike sorting, users need to drag and drop the link to raw file into the processing box, and then click Run->Electrophysiology->Convert Raw to LFP.
Note: Following the spike sorting steps is not needed in order to Derive the LFP from the RAW signal. Users can go straight to this step if needed.
Once the conversion function is selected, a new window appears with the following options:
- Despike LFP: Apply Bayesian Spike Removal (See next section).
- Parallel Processing: Activate the parallel toolbox and run processes in parallel. Greatly improves the speed of the process (requires Matlab’s parallel toolbox).
Memory to use for demultiplexing: There is a demultiplexing process that separates the electrodes into separate files in the background. The larger the RAM selected is, the faster this process will be performed. Make sure a high portion of the Computer’s RAM is selected. Demultiplexing should have already been performed on the spike-sorting step. In case the temp folder emptied (Brainstorm restarted), or users went straight to LFP conversion, only then demultiplexing would be performed again.
Once the conversion is complete, a single .bst file will be created that contains all the acquisition events, the spiking events and the LFP signals (saved in the dataset’s folder in brainstorm_db). This file will automatically be imported in the database with the suffix _LFP'. The channels file will be copied to the new entry. Users can now just use this file for the entire analysis. This makes it very practical for exchange reasons with other researchers since a 30KHz raw file would be converted to a 30 times smaller LFP file.
Conversion to LFP without Bayesian Spike Removal
If the Bayesian spike removal box is not selected, the conventional LFP conversion will be applied. LFP is considered to, therefore the signals are filtered to [0.5-150] Hz, and then sequentially downsampled to 1000Hz.
Conversion to LFP with Bayesian Spike Removal
Although traditionally the spike waveforms are considered to contain spectral power on the higher frequencies, it has been shown that there are low frequency components that could affect the computations in functions that rely on spiking activity. This function applies a prior on the activity on the entire electrode, for removing the spiking spectral features on the lower frequencies, following a Bayesian framework.
Therefore, if spiking analysis (spike field coherence, spike triggered average etc.) is required in the study, it is highly recommended that users enable this option.
Zanos, T. P., Mineault, P. J. & Pack, C. C. Removal of spurious correlations between spikes and local field potentials. J. Neurophysiol. 105, 474–486 (2011).