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March 2015 TechTip

Neuralynx File Formats

All Neuralynx file types recorded by Cheetah have unique, but similar file structures. It is important to understand the overall structure to make writing of programs easier and their use more effective. The two main sections of each file type are the File Header and the File Data. The Header (16kByte fixed size text) contains the system settings and data attributes when the file’s data was originally recorded, and can be viewed using most text editors as well as Neuraview. The File Data section begins immediately following the Header, and is stored as a sequence of individual records in binary format. The size and data contained in each record varies based on the type of data being stored in the file, i.e.: Continuously Sampled Channel (CSC ), spike, event, video, and raw data.

The following example shows the Header and Data of a CSC file (.ncs extension) in the Neuraview application.

CSC File Header:

######## Neuralynx Data File Header

## File Name C:\CheetahData\2013-05-07_08-40-59\CSC1.ncs
## Time Opened (m/d/y): 5/7/2013 ( 8:41:5.841
## Time Closed (m/d/y): 5/7/2013 ( 8:42:40.832

-FileType CSC
-FileVersion 3.3.0
-RecordSize 1044

-CheetahRev 5.6.3

-HardwareSubSystemName AcqSystem1
-HardwareSubSystemType DigitalLynxSX
-SamplingFrequency 32000
-ADMaxValue 32767
-ADBitVolts 0.000000030518510385491027

-AcqEntName CSC1
-NumADChannels 1
-ADChannel 8
-InputRange 1000
-InputInverted True

-DSPLowCutFilterEnabled True
-DspLowCutFrequency 0.1
-DspLowCutNumTaps 0
-DspLowCutFilterType DCO
-DSPHighCutFilterEnabled True
-DspHighCutFrequency 9000
-DspHighCutNumTaps 32
-DspHighCutFilterType FIR
-DspDelayCompensation Enabled
-DspFilterDelay_µs 476

The Header includes useful information such as type of file, version of Cheetah and type of system used, sampling frequency, input range, filter settings, and ADBitVolts value. The ADBitVolts value is important when importing data into another analysis tool such as MATLAB®. The value indicated is the multiplier used in conjunction with the A/D value stored in each record from each sample. For example:

(Index 4: Sample4 value= 579) x (ADBitVolt value= 0.000000030518510385491027) = 0.000017670217513199304633 Volts or 17.67 µV

CSC File Data:The File Data of a CSC is broken into indices, starting at 0 (first record) and running continuously until the recording is paused or ended. Each Index is equal to one record. Each record contains the following information: Timestamp, acquisition channel number, sampling frequency, number of valid samples in the record, and the 512 individual samples of that record (example image below). The Timestamp is a 64-bit unsigned integer (quad-word) in units of microseconds. In the example below, records have a Timestamp difference of 15,728 microseconds - the record size (512) divided by the sampling rate (32,556 Hz). If recording is paused during an experiment, there will a large gap between records’ Timestamps. For example, if recording was stopped for 30 seconds, there will be a 30 million microsecond difference in Timestamp values around the gap.

File Header and record data must be used together while performing data analysis.For more information on file structures, please refer to Cheetah Reference Guide, Neuralynx File Formats, and Neuraview Quick Start Guide, or contact MATLAB is a registered trademark of The MathWorks, Inc.