2008-06-19
eva
large platform exploration (choc. pellets) - 60min
good beh and explor., no cable problems
16
102
20000
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1000
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1250
lfp
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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_concatenate
spotsSamplingRate
Optional
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_extractchannels
nChannels
Mandatory
channels
Mandatory
Extract channels from .dat file (i.e. remove those channels that are not listed).
PARAMETERS
# nChannels
Number of channels in the initial .dat file (before extraction)
# channels
Space-separated list of channels to extract, numbered from 0
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
2.2
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
1250
Mandatory
Downsample a .dat file to create the corresponding LFP file.
PARAMETERS
# samplingRate
Target sampling rate (default = 1250Hz)
ndm_mergedat
suffixes
Mandatory
nChannels
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
Mandatory
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 of the directories where the NCS files are located
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.
# gap
A data record is considered to match an 'acquisition restart' event if it is close in time and follows a sampling gap exceeding this threshold (in seconds, default = 1).
# ignoreEvents
In newer versions of Neuralynx, NEV files may not correctly list 'acquisition start/stop' events, which results in incorrect conversion; if this happens, set ignoreEvents to 'true' and reprocess to fix this issue (default = false).
ndm_nev2evt
suffixes
Mandatory
Convert from .nev (Neuralynx files) to .evt format.
PARAMETERS
# suffixes
List of suffixes of the directories where the NEV files to convert are located
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.
# gap
A data record is considered to match an 'acquisition restart' event if it is close in time and follows a sampling gap exceeding this threshold (in seconds, default = 1).
ndm_nvt2spots
suffix
Mandatory
Extract spots from .nvt (Neuralynx files).
PARAMETERS
# suffix
Suffix of the directory where the NVT file is located
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.
# gap
A data record is considered to match an 'acquisition restart' event if it is close in time and follows a sampling gap exceeding this threshold (in seconds, default = 1).
ndm_pca
before
8
Optional
after
11
Optional
extra
true
Optional
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_reorderchannels
channels
Mandatory
Reorder channels in .dat file.
PARAMETERS
# channels
List of reordered channels, numbered from 0
ndm_resample
suffixes
Mandatory
samplingRates
Mandatory
nChannels
Mandatory
Resample individual .dat files from their original sampling rates to the common sampling rate of the final .dat file.
PARAMETERS
# suffixes
List of suffixes for the individual files to resample
# samplingRate
List of original sampling rates (in the same order as the suffixes)
# nChannels
List of numbers of channels in the individual data files (in the same order as the suffixes)
ndm_smi2sts
suffix
Mandatory
Extract spots timestamps from .smi (Neuralynx files).
WARNING: In the absence of a useable NVT file, you may wish to extract spots from the MPEG file(s) and timestamps from the SMI file(s), and then match them. This is what ndm_smi2sts is for, and spots2pos will try its best to help you do this, but the results are *not* reliable. This is because Neuralynx systems do not control MPEG video streams. Instead, they leave the task to the operating system, which does a very poor job as far as timing accuracy is concerned. As a result, the video gets started after a random delay following acquisition start, and video frames are shifted by an unpredictable amount (up to hundreds of milliseconds). Again, in the absence of a useable NVT file, this may be your only solution, but please keep these limitations in mind when analyzing your data.
PARAMETERS
# suffix
Suffix of the directory where the SMI file is located
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.
# gap
A data record is considered to match an 'acquisition restart' event if it is close in time and follows a sampling gap exceeding this threshold (in seconds, default = 1).
ndm_smr2dat
reverse
true
Mandatory
suffixes
Mandatory
channelsExcluded
Mandatory
Convert from .smr (CED files) to .dat format.
PARAMETERS
# reverse
Whether the signals should be reversed (e.g. to compensate for NeuraLynx amplifiers which reverse all signals - this sets them back to normal)
# suffixes
List of suffixes for the individual files to convert
# channelsExcluded
List of channels to exclude for each individual file to convert (type - for none)
ndm_smr2evt
suffixes
Optional
rename
Optional
Convert from .smr (CED files) to .evt format.
PARAMETERS
# suffixes
List of suffixes for the individual files to convert
# rename
Optional name of a script used to automatically rename events and event files
ndm_start
suffixes
002
Mandatory
wideband
false
Mandatory
video
false
Mandatory
events
false
Mandatory
concatenation
false
Mandatory
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)
# 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 = false)
ndm_transcodevideo
suffix
Mandatory
extension
avi
Mandatory
codec
Optional
Transcode video file (convert to a different codec).
PARAMETERS
# suffix
Suffix of the directory where the video files to transcode are located
# extension
Extension of the original video file (e.g. avi, mpg, etc.)
# codec
Output file codec - possible choices include:
* x264 (MPEG-4 AVC)
* m1v (video-only MPEG-1)
Leave empty if no transcoding is required