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161 #ff0000 #ff0000 #0080ff 161 0 162 #ff0000 #ff0000 #0080ff 162 0 163 #ff0000 #0080ff #0080ff 163 0 164 #ff0000 #0080ff #0080ff 164 0 165 #ff0000 #0080ff #0080ff 165 0 ndm_concatenate spotsSamplingRate Mandatory Concatenate all session files (.dat, .pos and .evt) recorded on the same day. OPTIONAL PARAMETERS Note: To keep the interface simpler, optional parameters have default values and are not all listed in the 'Parameters' tab; to choose custom values, click the 'Add' button and manually add the required parameters (and custom values) to the list. # spotsSamplingRate Sampling rate for .spots files, i.e. original sampling rate for video or tracker data (this parameter does not have a default value; if no custom value is provided, time shifts between wideband and video signals will not be reported, although concatenation will be performed normally). # maxShift If the duration of wideband signals and position samples differ by more than this threshold (in s, default = 3), this triggers a warning message. ndm_extractspikes thresholdFactor 1 Mandatory refractoryPeriod 16 Mandatory peakSearchLength 32 Mandatory start 0 Mandatory duration 120 Mandatory Extract spikes from high-pass filtered .fil file (this creates .res and .spk files). First, the program automatically computes a baseline 'noise' level, using a subset of the data. Then, spikes are extracted whenever the signal crosses a threshold proportional to the baseline 'noise' level. To avoid spurious detections, the signal must have a local maximum (or minimum, depending on the sign of the signal) within a fixed search window starting at threshold crossing. Also, the duration between consecutive spikes must be greater than a fixed 'refractory' period. PARAMETERS # thresholdFactor Threshold = thresholdFactor * baseline 'noise' level # refractoryPeriod Number of samples to skip after a spike, before trying to detect a new spike # peakSearchLength Length of the peak search window (in number of samples) # start Starting point in the file (in s) for computation of baseline 'noise' level # duration Duration (in s) for computation of baseline 'noise' level ndm_hipass windowHalfLength 16 Mandatory High-pass filter a .dat file (required for spike extraction). The program uses a median-based (non-linear) filter to minimize spike waveform distortion. PARAMETERS # windowHalfWidth Determines the cutoff frequency ndm_lfp samplingRate 1250 Mandatory Downsample a .dat file to create the corresponding LFP file. PARAMETERS # samplingRate Target sampling rate (default = 1250Hz) ndm_pca before 4 Mandatory after 4 Mandatory extra false Mandatory Compute principal component analysis (PCA). PARAMETERS All mandatory parameters are defined in the 'Acquisition System' and 'Spike Groups' tab. OPTIONAL PARAMETERS # before Number of samples before the peak to use for the PCA. This can be either a space-separated list of numbers (one per electrode group), or a single common number for all groups. # after Number of samples after the peak to use for the PCA. This can be either a space-separated list of numbers (one per electrode group), or a single common number for all groups. # extra Whether extra features (spike peak value) should be included in the output files. ndm_start suffixes Mandatory wideband false Mandatory events false Mandatory video false Mandatory Perform all processing steps for a multiple sets of multiple-session recordings: format conversion, channel extraction and reordering, video transcoding and tracking, data concatenation, spike detection and extraction, etc. PARAMETERS # suffixes List of suffixes for the individual files to convert OPTIONAL PARAMETERS Note: To keep the interface simpler, optional parameters have default values and are not listed in the 'Parameters' tab; to choose custom values, click the 'Add' button and manually add the required parameters (and custom values) to the list. # wideband Process the wideband data files recorded by the acquisition system: convert to .dat format, resample, merge, extract and reorder channels (default = true) # video Process video files recorded by the acquisition system: transcode and extract LEDs (default = true) # events Process event files recorded by the acquisition system: convert to .evt format and rename events (default = true) # concatenation Concatenate subsession files (default = true) # spikes Process spikes: detect and extract spike waveforms, perform PCA (default = true) # lfp Downsample wideband signals to produce LFP files (default = true) # clean Remove intermediate files after pre-processing is complete (default = false) # log Save progress information to log files for later review (use 'cat' or 'less -R' for correct formatting) (default = true)