2013-07-15 gabrielle Rat08 4 shanks in right dHPC (1-4) 8 shanks in left 'amygdala' (5-12) 8 shanks in right 'amygdala' (13-20) 161-162-163 : Accelerometer 164 : Airpuff 165-166 : rewards 16 166 20000 20 1000 0 1250 39.0625 .whl 1250 lfp 16 19 18 17 20 28 24 26 21 22 25 30 27 23 29 31 8 11 0 7 9 5 1 3 13 14 15 12 2 10 4 6 65 70 64 71 67 68 66 69 73 78 72 79 75 76 74 77 48 57 49 56 50 54 52 53 58 51 60 55 61 59 62 63 45 36 41 34 37 35 33 32 39 46 38 47 40 44 43 42 80 87 81 86 82 85 83 84 88 95 89 94 90 93 91 92 129 134 128 135 131 132 130 133 137 142 136 143 139 140 138 141 112 121 113 120 114 118 116 117 122 115 124 119 125 123 126 127 109 100 105 98 101 99 97 96 103 110 102 111 104 108 107 106 144 151 145 150 146 149 147 148 152 159 153 158 154 157 155 156 163 164 165 160 161 162 16 19 18 17 20 28 24 26 32 16 3 21 22 25 30 27 23 29 31 32 16 3 8 11 0 7 9 5 1 3 32 16 3 13 14 15 12 2 10 4 6 32 16 3 65 70 64 71 67 68 66 69 32 16 3 73 78 72 79 75 76 74 77 32 16 3 48 57 49 56 50 54 52 53 32 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#aa41ff 153 0 154 #aa41ff #aa41ff #aa41ff 154 0 155 #aa41ff #aa41ff #aa41ff 155 0 156 #aa41ff #aa41ff #aa41ff 156 0 157 #aa41ff #aa41ff #aa41ff 157 0 158 #aa41ff #aa41ff #aa41ff 158 0 159 #aa41ff #aa41ff #aa41ff 159 0 160 #d33059 #d33059 #0080ff 160 0 161 #d33059 #d33059 #0080ff 161 0 162 #d33059 #d33059 #0080ff 162 0 163 #bb0205 #bb0205 #0080ff 163 0 164 #bb0205 #bb0205 #0080ff 164 0 165 #bb0205 #bb0205 #0080ff 165 0 ndm_concatenate spotsSamplingRate 14 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_extractleds suffix Mandatory useTrackerData false Mandatory threshold 70 Mandatory extension mpg 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 Mandatory refractoryPeriod 16 Mandatory peakSearchLength 32 Mandatory start 0 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 4 Optional after 4 Optional extra false 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_start suffixes Mandatory wideband false Mandatory events false Mandatory video 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)