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getting_started:neuralynx_fcdc [2010/04/07 12:02]
timeng ft_prefix
getting_started:neuralynx_fcdc [2017/08/17 11:21] (current)
127.0.0.1 external edit
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 {{tag>​neuralynx lfp dataformat}} {{tag>​neuralynx lfp dataformat}}
  
-====== Getting started with the Neuralynx data recorded at the FCDC  ​======+====== Getting started with the Neuralynx data recorded at the Donders Institute ​ ​======
  
 ===== Introduction ===== ===== Introduction =====
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 ===== Background ===== ===== Background =====
  
-At the FCDC, we record brain activity using an ECoG electrode grid with 252 electrodes. The signal is amplified by a factor of 20 using a headstage amplifier (Headstage 32V-G20, Plexon Inc., Dallas, TX, USA), and subsequently low-pass filtered at 8 kHz and digitized at ~32 kHz sampling frequency using a Neuralynx amplifier (Digital Lynx, 256 channels, Neuralynx Tucson, AZ, USA). +At the Donders Institute, we record brain activity using an ECoG electrode grid with 252 electrodes. The signal is amplified by a factor of 20 using a headstage amplifier (Headstage 32V-G20, Plexon Inc., Dallas, TX, USA), and subsequently low-pass filtered at 8 kHz and digitized at ~32 kHz sampling frequency using a Neuralynx amplifier (Digital Lynx, 256 channels, Neuralynx Tucson, AZ, USA). 
  
 To deal with the tremendous amounts of data recorded each session (approximately 1.5 Gb/min), we develop a recording procedure that allows us to: To deal with the tremendous amounts of data recorded each session (approximately 1.5 Gb/min), we develop a recording procedure that allows us to:
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     cfg = ft_spikedownsample(cfg); ​   ​     cfg = ft_spikedownsample(cfg); ​   ​
  
-By using the option **format** in the configuration structure, we can choose the file format to which the downsampled LFP data will be written. FieldTrip can write the file dataset in several formats (see **[[reference:​write_data]]**). We use the Plexon *.nex format which provides us the best compromise between data read/write speed and storage capacity. To get more details about the  Plexon dataformats,​ please see the [[getting_started:​plexon|getting started with Plexon data]] section. The output dataset directory for the LFP data uses the suffix //_ds//.+By using the option **format** in the configuration structure, we can choose the file format to which the downsampled LFP data will be written. FieldTrip can write the file dataset in several formats (see **[[reference:​ft_write_data]]**). We use the Plexon *.nex format which provides us the best compromise between data read/write speed and storage capacity. To get more details about the  Plexon dataformats,​ please see the [[getting_started:​plexon|getting started with Plexon data]] section. The output dataset directory for the LFP data uses the suffix //_ds//.
  
 The raw *.nrd file and the split DMA files contains AD values that are not scaled in uV and require an additional factor of 64x. In addition, our acquisition system includes a Plexon headstage with an additional amplification of 20x. Thus, in our case the calibration should be specified as 1/(64*20). The raw *.nrd file and the split DMA files contains AD values that are not scaled in uV and require an additional factor of 64x. In addition, our acquisition system includes a Plexon headstage with an additional amplification of 20x. Thus, in our case the calibration should be specified as 1/(64*20).
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 In contrast, the timestamp clock in the Plexon acquisition hardware ticks at the native sampling frequency of 40kHz, meaning that subsequent samples in a Plexon file are 40000/​Fsample timestamps apart. In a channel that is sampled at 40kHz subsequent samples are one clocktick apart, in a channel that is sampled at 1kHz the subsequent samples are 40 clockticks apart. In contrast, the timestamp clock in the Plexon acquisition hardware ticks at the native sampling frequency of 40kHz, meaning that subsequent samples in a Plexon file are 40000/​Fsample timestamps apart. In a channel that is sampled at 40kHz subsequent samples are one clocktick apart, in a channel that is sampled at 1kHz the subsequent samples are 40 clockticks apart.
  
-In FieldTrip the relation between the timestamps and the samples is represented in the header. If you call **[[reference:​read_header|read_header]]** on your datafile, you'll see something like this+In FieldTrip the relation between the timestamps and the samples is represented in the header. If you call **[[reference:​ft_read_header|ft_read_header]]** on your datafile, you'll see something like this
  
-  >> hdr = read_header('​256_noev_DigitaLynx_DMA.nrd'​)+  >> hdr = ft_read_header('​256_noev_DigitaLynx_DMA.nrd'​)
   hdr =    hdr = 
               Fs: 32556               Fs: 32556
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 or this or this
  
-  >> hdr = read_header('​p021parall.nex'​)+  >> hdr = ft_read_header('​p021parall.nex'​)
   hdr =    hdr = 
                 nChans: 15                 nChans: 15
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        time: {[1x3001 double] ​ [1x3001 double] ​ [1x3001 double]}        time: {[1x3001 double] ​ [1x3001 double] ​ [1x3001 double]}
     fsample: 1000     fsample: 1000
 +
         cfg: [1x1 struct]         cfg: [1x1 struct]
 </​code>​ </​code>​