2014-04-05
gabrielle
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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)