processRaw

PURPOSE

SYNOPSIS

DESCRIPTION

processes raw signal, extracts spikes. loads data directly from neuralynx
file.

filename: full path/name to neuralynx file
totNrSamples: nr of samples in this file
Hd: filter specification
howManyBlocks: >0 do only so many blocks
               0 : as many as there are
startWithBlock: 1=start with first block
                >1: dont process first x blocks
includeRange: from/to timestamps of periods to sort. if empty everything
is taken.

extractionThreshold: how many times the running std of the energy signal
to extract ?

prewhiten: yes/no

returns:
blockOffsets -> start of each processed block in absolute timestamps


urut/april04
updated urut/feb07

CROSS-REFERENCE INFORMATION

• computeNormalizedGround todo: note that this wont work if the gains are different on channels on the same ground.
• convertTimestamps converts from internal representation of timestamps to real timestamps
• determineBlocks determines the blocksize and how many of those are to be processed, based on the raw number of samples available in
• extractSpikes extracts spikes from raw signal
• getRawData reads raw continous data
• upsampleSpikes upsample spikes from raw sampling to 100kHz.
• posthocWhiten post-hoc whitening & upsampling of waveforms
• realigneSpikes realign spikes (after they were upsampled to 100KHz).

• StandaloneInit does detection standalone
• produceRawTraceFig produces a figure of the raw data traces and saves it in a file
• produceThresholdFig produces a figure showing the number spikes found as a function of different thresholds.