2015-07-20
david
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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_extractleds
suffix
Mandatory
useTrackerData
true
Mandatory
threshold
90
Mandatory
extension
avi
Mandatory
show
false
Mandatory
Extract LEDs (= bright spots) from a video file.
For each video frame, all bright spots are detected and listed in a .spots file, one line per spot, listing on successive columns the frame number, number of pixels in the spot, x and y coordinates of the spot center, x and y sizes of the spot (defined as standard deviations of the distributions of x and y coordinates of all the pixels in the spot), and spot color (as a YCrCb triplet).
PARAMETERS
# suffix
Suffix of the directory where the video file is located
# useTrackerData
Depending on the acquisition systems, the successive positions of the LEDs across time can be extracted from either the video file, or the online tracking file if such a feature is available (e.g. Neuralynx systems). Because in some configurations both video and tracking files may be recorded in parallel, it is necessary to explicitly request one of the above two methods.
# threshold
Bright spots consist of pixels brighter than this threshold (from 0 to 255)
# extension
Extension of the video file (e.g. avi, mpg, etc.)
# show
Whether the video should be displayed during LED extraction
(hiding the video yields faster processing, especially over network connections)
ndm_extractspikes
thresholdFactor
1.3
Mandatory
refractoryPeriod
16
Mandatory
peakSearchLength
32
Mandatory
start
120
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
6
Mandatory
after
6
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
clean
true
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)