2015-10-08
david
16
67
20000
20
1000
0
1250
lfp
1250
0
2
4
6
1
3
5
7
9
11
13
15
16
18
20
22
8
10
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14
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62
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63
2
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32
16
6
1
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5
7
32
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15
32
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6
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22
32
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32
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32
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1
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1
23
--
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6
9
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8
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9
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14
12
21
11
9
11
24
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--
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36
14
55
--
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75
10
2
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14
9
10
9
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17
9
57
----
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9
61
--------
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9
62
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63
9
65
--------
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7
18
7
23
--
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--
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0.2
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0
ndm_clean
Clean intermediate files after pre-processing is complete.
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
Delete single-session wideband data files (default = true).
# xml
Delete single-session xml files (default = true).
# spots
Delete single-session spots files (default = false).
# pos
Delete single-session pos files (default = false).
# hipass
Delete the high-pass filtered data file (default = true).
ndm_extractspikes
thresholdFactor
1.3
Mandatory
refractoryPeriod
16
Mandatory
peakSearchLength
32
Mandatory
start
240
Mandatory
duration
240
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)