2011-04-28
lynn
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0.2
Z:/Buzsakilabspace/Datasets/RoyerS/RoyerS_som1/som1_2/som1_2.dat
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ndm_extractspikes
thresholdFactor
1.5
Mandatory
refractoryPeriod
16
Mandatory
peakSearchLength
32
Mandatory
start
0
Mandatory
duration
60
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
10
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
1252
Mandatory
Downsample a .dat file to create the corresponding LFP file.
PARAMETERS
# samplingRate
Target sampling rate (default = 1250Hz)
ndm_mergedat
suffixes
001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071
Mandatory
nChannels
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Mandatory
Merge multiple .dat files recorded simultaneously.
PARAMETERS
# suffixes
List of suffixes for the individual files to merge
# nChannels
List of number of channels in individual data files (in the same order as the suffixes)
ndm_ncs2dat
reverse
false
Mandatory
suffixes
001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071
Mandatory
split
Optional
Convert from .ncs (Neuralynx files) to .dat format.
PARAMETERS
# reverse
Whether the signals should be reversed (by default, NeuraLynx reverses all signals - this sets them back to normal)
# suffixes
List of suffixes for the individual files to convert
# split
If a value is provided, the output is split, creating a new file each time the difference between successive timestamps exceeds this gap (in ???s). In the Neuralynx recording system, each time acquisition is stopped/restarted, a new MPEG file is created for video output, but brain signals, events and video records are appended to their respective files. This option can be used to split the timestamp file to try and match MPEG files.
ndm_pca
beforePeak
4
Mandatory
afterPeak
4
Mandatory
nSamplesInPCA
16
Mandatory
THIS IS LEGACY CODE AND SHOULD BE REMOVED SOON.
Compute principal component analysis (PCA).
PARAMETERS
# beforePeak
Number of samples before the peak
# afterPeak
Number of samples after the peak
# nSamplesInPCA
Number of samples for PCA
Due to weird design decisions (back when the backend programs were coded), these parameters should be provided assuming an acquisition sampling rate of 10khz. The script will compensate for the actual sampling rate, i.e. multiply all values by 2 if the sampling rate is 20kHz.
ndm_session
convertBrainSignals
true
Mandatory
resample
false
Mandatory
extractChannels
false
Mandatory
reorderChannels
false
Mandatory
processSpikes
false
Mandatory
processVideo
false
Mandatory
processLFP
false
Mandatory
convertEvents
false
Mandatory
Perform all processing steps for a single session: format conversions, channel extraction and/or reordering, etc.
Although this script can be started manually, processing is normally done using 'ndm_start' instead, which repeatedly calls 'ndm_start_session' for each individual recording session in a given set (e.g. all sessions recorded on the same day, one after the other).
IMPORTANT NOTE
In the most common scenario, spike and LFP processing should be disabled at this stage. They should be performed by 'ndm_start'. See manual pages for 'ndm_start' and 'ndm_session' for details.
PARAMETERS
# convertBrainSignals
Whether the file(s) recorded by the acquisition system should be converted to .dat format
# convertEvents
Whether event files should be extracted from the file(s) recorded by the acquisition system
# resample
Whether individual .dat files should be resampled before merging (in cases where multiple files are recorded in parallel)
# merge
Whether individual .dat files should be merged (in cases where multiple files are recorded in parallel)
# extractChannels
Whether specific channels should be extracted (when multiple files recorded in parallel, this is done after the files have been merged)
# reorderChannels
Whether the channels should be reordered (this is done after channel extraction)
# processSpikes
Whether spikes should be detected/extracted (this is done after the .dat files were fully processed)
This should normally be DISABLED (see note above)
# processVideo
Whether video files should be processed (conversion + LED extraction)
# processLFP
Whether .dat files should be downsampled to produce LFP files
This should normally be DISABLED (see note above)
ndm_start
skipExisting
false
Mandatory
suffixes
001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071
Mandatory
processSessions
true
Mandatory
concatenate
false
Mandatory
processSpikes
true
Mandatory
processLFP
true
Mandatory
Start batch processing of multiple sets of session files.
This repeatedly calls 'ndm_session' to process each individual recording session in each set, optionally concatenating the resulting files within each set (see Help for 'ndm_session').
IMPORTANT NOTE
In the most common scenario, spike and LFP processing should be performed at this stage, but should be disabled for 'ndm_session'. See manual pages for 'ndm_start' and 'ndm_session' for details.
PARAMETERS
# skipExisting
Whether existing directories should be skipped
# suffixes
List of suffixes for the individual files to convert
# processSessions
Whether individual session files should be processed (this step can be skipped if it was already done previously)
# concatenate
Whether the .dat, .evt and .pos files should be concatenated
# processSpikes
Whether spikes should be detected/extracted (see note above)
# processLFP
Whether concatenated .dat files should be downsampled to produce LFP files (see note above)