2011-04-23 lynn 16 71 32552 20 1000 0 1252 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 46 47 56 57 58 59 60 61 62 0 45 48 49 50 51 52 53 54 55 63 64 65 66 67 68 69 70 1 2 3 4 5 6 7 52 26 3 8 9 10 11 12 13 14 15 52 26 3 16 17 18 19 20 21 22 23 52 26 3 24 25 26 27 28 29 30 31 52 26 3 32 33 34 35 36 37 38 39 52 26 3 40 41 42 43 44 46 47 52 26 3 56 57 58 59 60 61 62 52 26 3 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 1 11 1 12 -- -- -- -- -- 1 13 ---- ---- ---- ---- ---- 1 14 -- -- -- -- -- 1 15 ---- ---- ---- ---- ---- 1 16 ------ ------ ------ ------ ------ 1 17 ---- ---- ---- ---- ---- 2 2 2 3 2 4 2 5 -------------------------------------- -------------------------------------- -------------------------------------- -------------------------------------- -------------------------------------- 2 6 -------- -------- -------- -------- -------- 2 7 ---- ---- ---- ---- ---- 2 8 2 9 -------------------- -------------------- -------------------- -------------------- -------------------- 2 10 -- -- -- -- -- 2 11 -------------- -------------- -------------- -------------- -------------- 3 2 3 3 3 4 ---------------- ---------------- ---------------- ---------------- ---------------- 3 5 ---- ---- ---- ---- ---- 3 6 ------ ------ ------ ------ ------ 3 7 ------ ------ ------ ------ ------ 3 8 -- -- -- -- -- 3 9 ------ ------ ------ ------ ------ 4 2 4 3 -- -- -- -- -- 4 4 ------ ------ ------ ------ ------ 4 5 ---- ---- ---- ---- ---- 4 6 -------- -------- -------- -------- -------- 6 2 6 3 6 4 -- -- -- -- -- 7 2 7 3 7 4 7 5 7 6 7 7 7 8 7 9 7 10 ------------ ------------ ------------ ------------ ------------ 7 11 -- -- -- -- -- 0.2 Z:/Buzsakilabspace/Datasets/RoyerS/RoyerS_som2/som2_1/som2_1.dat 32 16 0 #0080ff #0080ff #0080ff 0 0 1 #0080ff #0080ff #0080ff 1 0 2 #0080ff #0080ff #0080ff 2 0 3 #0080ff #0080ff #0080ff 3 0 4 #0080ff #0080ff #0080ff 4 0 5 #0080ff #0080ff #0080ff 5 0 6 #0080ff #0080ff #0080ff 6 0 7 #0080ff #0080ff #0080ff 7 0 8 #0080ff #0080ff #0080ff 8 0 9 #0080ff #0080ff #0080ff 9 0 10 #0080ff #0080ff #0080ff 10 0 11 #0080ff #0080ff #0080ff 11 0 12 #0080ff #0080ff #0080ff 12 0 13 #0080ff #0080ff #0080ff 13 0 14 #0080ff #0080ff #0080ff 14 0 15 #0080ff #0080ff #0080ff 15 0 16 #0080ff #0080ff #0080ff 16 0 17 #0080ff #0080ff #0080ff 17 0 18 #0080ff #0080ff #0080ff 18 0 19 #0080ff #0080ff #0080ff 19 0 20 #0080ff #0080ff #0080ff 20 0 21 #0080ff #0080ff #0080ff 21 0 22 #0080ff #0080ff #0080ff 22 0 23 #0080ff #0080ff #0080ff 23 0 24 #0080ff #0080ff #0080ff 24 0 25 #0080ff #0080ff #0080ff 25 0 26 #0080ff #0080ff #0080ff 26 0 27 #0080ff #0080ff #0080ff 27 0 28 #0080ff #0080ff #0080ff 28 0 29 #0080ff #0080ff #0080ff 29 0 30 #0080ff #0080ff #0080ff 30 0 31 #0080ff #0080ff #0080ff 31 0 32 #0080ff #0080ff #0080ff 32 0 33 #0080ff #0080ff #0080ff 33 0 34 #0080ff #0080ff #0080ff 34 0 35 #0080ff #0080ff #0080ff 35 0 36 #0080ff #0080ff #0080ff 36 0 37 #0080ff #0080ff #0080ff 37 0 38 #0080ff #0080ff #0080ff 38 0 39 #0080ff #0080ff #0080ff 39 0 40 #0080ff #0080ff #0080ff 40 0 41 #0080ff #0080ff #0080ff 41 0 42 #0080ff #0080ff #0080ff 42 0 43 #0080ff #0080ff #0080ff 43 0 44 #0080ff #0080ff #0080ff 44 0 45 #0080ff #0080ff #0080ff 45 0 46 #0080ff #0080ff #0080ff 46 0 47 #0080ff #0080ff #0080ff 47 0 48 #0080ff #0080ff #0080ff 48 0 49 #0080ff #0080ff #0080ff 49 0 50 #0080ff #0080ff #0080ff 50 0 51 #0080ff #0080ff #0080ff 51 0 52 #0080ff #0080ff #0080ff 52 0 53 #0080ff #0080ff #0080ff 53 0 54 #0080ff #0080ff #0080ff 54 0 55 #0080ff #0080ff #0080ff 55 0 56 #0080ff #0080ff #0080ff 56 0 57 #0080ff #0080ff #0080ff 57 0 58 #0080ff #0080ff #0080ff 58 0 59 #0080ff #0080ff #0080ff 59 0 60 #0080ff #0080ff #0080ff 60 0 61 #0080ff #0080ff #0080ff 61 0 62 #0080ff #0080ff #0080ff 62 0 63 #0080ff #0080ff #0080ff 63 0 64 #0080ff #0080ff #0080ff 64 0 65 #0080ff #0080ff #0080ff 65 0 66 #0080ff #0080ff #0080ff 66 0 67 #0080ff #0080ff #0080ff 67 0 68 #0080ff #0080ff #0080ff 68 0 69 #0080ff #0080ff #0080ff 69 0 70 #0080ff #0080ff #0080ff 70 0 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 �µs). 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)