2012-09-12 andresg 16 134 20000 20 1000 0 1250 0 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 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 0 1 2 3 4 5 6 7 32 16 3 8 9 10 11 12 13 14 15 32 16 3 16 17 18 19 20 21 22 23 32 16 3 24 25 26 27 28 29 30 31 32 16 3 32 33 34 35 36 37 38 39 32 16 3 40 41 42 43 44 45 46 47 32 16 3 48 49 50 51 52 53 54 55 32 16 3 56 57 58 59 60 61 62 63 32 16 3 64 65 66 67 68 69 70 71 32 16 3 72 73 74 75 76 77 78 79 32 16 3 80 81 82 83 84 85 86 87 32 16 3 88 89 90 91 92 93 94 95 32 16 3 96 97 98 99 100 101 102 103 32 16 3 104 105 106 107 108 109 110 111 32 16 3 112 113 114 115 116 117 118 119 32 16 3 120 121 122 123 124 125 126 127 32 16 3 1 2 1 3 14 2 ------ ------ ------ ------ ------ 14 3 ---------------------- ---------------------- ---------------------- ---------------------- ---------------------- 14 4 ---------------------- ---------------------- ---------------------- ---------------------- ---------------------- 15 2 ------------------ ------------------ ------------------ ------------------ ------------------ 17 2 -------- -------- -------- -------- -------- 5 2 5 3 5 4 5 5 5 6 5 7 -- -- -- -- 2 2 2 3 2 4 2 5 2 6 2 7 2 8 2 9 2 10 2 11 2 12 2 13 -- -- -- -- 2 14 -- -- -- -- 2 15 6 2 6 3 6 4 6 5 6 6 6 7 6 8 6 9 6 10 6 11 6 12 6 13 6 14 -- -- -- -- 6 15 -- -- -- -- 6 16 6 17 6 18 ---- ---- -- ---- ---- 7 2 7 3 7 4 7 5 7 6 7 7 7 8 7 9 7 10 7 11 7 12 7 13 -- -- -- -- 7 14 -- -- -- -- 7 15 -------------------- -------------------- -------------------- -------------------- 7 16 -- -- -- -- 7 17 ------------ ------------ ------------ ------------ 7 18 ---------------- ---------------- ---------------- ---------------- 7 19 -- -- -- -- 7 20 ------ ------ ------ ------ 7 21 ------ ------ ------ ------ 7 22 -------- -------- -------- -------- 7 23 ------ ------ ------ ------ 7 24 ---------- ---------- ---------- ---------- 7 25 ------------------ ------------------ ------------------ ------------------ 7 26 ------------ ------------ ------------ ------------ 7 27 0.2 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 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113 #0080ff #0080ff #0080ff 113 0 114 #0080ff #0080ff #0080ff 114 0 115 #0080ff #0080ff #0080ff 115 0 116 #0080ff #0080ff #0080ff 116 0 117 #0080ff #0080ff #0080ff 117 0 118 #0080ff #0080ff #0080ff 118 0 119 #0080ff #0080ff #0080ff 119 0 120 #0080ff #0080ff #0080ff 120 0 121 #0080ff #0080ff #0080ff 121 0 122 #0080ff #0080ff #0080ff 122 0 123 #0080ff #0080ff #0080ff 123 0 124 #0080ff #0080ff #0080ff 124 0 125 #0080ff #0080ff #0080ff 125 0 126 #0080ff #0080ff #0080ff 126 0 127 #0080ff #0080ff #0080ff 127 0 128 #0080ff #0080ff #0080ff 128 0 129 #0080ff #0080ff #0080ff 129 0 130 #0080ff #0080ff #0080ff 130 0 131 #0080ff #0080ff #0080ff 131 0 132 #0080ff #0080ff #0080ff 132 0 133 #0080ff #0080ff #0080ff 133 0 process_calcThreshold executeScriptBool 1 Mandatory rmsWindowLength 2 Mandatory useage: process_calcThreshold fileBaseName electrodeNumber This script calculates the spike detection threshold and puts it in the file fileBaseName.threshold.electrodeNumber parameters: - executeScriptBool determines whether the script should be run with the next batch process. - rmsWindowLength represents the root mean square (rms) integration window for detection. process_detectSpikes executeScriptBool 1 Mandatory thresholdFactor 7 Mandatory refractoryPeriod 8 Mandatory rmsWindowLength 2 Mandatory peakWindowLength 10 Mandatory windowPeakAlign 5 Mandatory spikesFromDatBool 1 Mandatory This script does the following: * detects the spikes (creates the .res.# file), * aligns the peaks, * gets the waveforms (creates the .spk.# file), The variables used by the different programs called in this script depend on the sampling rate. The default is for a sampling rate of 10khz. All the script parameters are multiplifaction factor of 10khz except the thresholdFactor. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - refractoryPeriod represents the after detection, how many samples to skip before detecting a new spike if one is detected. - rmsWindowLength represents the root mean square (rms) integration window for detection. - peakWindowLength represents the window (number of samples to test) to search for spike peak, seams to be used for eigen calculation or finding of the true spike peak. - windowPeakAlign represents the middle of the peakWindowLength, where to take the spike peak in peakWindowLength. - thresholdFactor is a factor to compute the detection threshold: threshold = thresholdFactor * baseline process_findCommonThreshold executeScriptBool 1 Mandatory maxThreshold Mandatory useage: process_findCommonThreshold fileBaseName [fileBaseName ...] for each electrodeGroup in fileBaseName.xml the value in fileBaseName.threshold.electrodeGroup is replaced by the minimum threshold value across passed fileBaseNames. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - maxThreshold default = 500 process_merge executeScriptBool 1 Mandatory mergeBaseName gatsby140_082813_NSAll Mandatory process_merge usage: process_merge -n $mergeBaseName $fileBaseNames merges .spk .res etc for multi-file clustering. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - mergeBaseName designates the fileBaseName of the merged files. *** Requirements *** * calls process_pca_light : to do pca without presence of .fil file * calls pproc * each fileBaseName.* must be in a directory fileBaseName - which can be performed by process_dirFiles process_mhipass executeScriptBool 0 Mandatory frequency 800 Mandatory libraryPath /u16/local/matlab6.5/extern/lib/glnx86:/u16/local/matlab6.5/bin/glnx86:/u16/local/matlab6.5/sys/os/glnx86 Mandatory This script does the high-pass filtering for subsequent spike extraction. The .fil file is created by the program called in this script. The frequency parameter is the lowest frequency cut off. The highest frequency is computed based on the sampling rate as 0.95 % of the Nyquist frequency: sampling rate * 0.5 * 0.95 The program called in this script is currently a matlab program, therefore this part of the process relies on Matlab until this program is rewritten. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - libraryPath is the path for Matlab. process_mlopass executeScriptBool 1 Mandatory libraryPath /u16/local/matlab6.5/extern/lib/glnx86:/u16/local/matlab6.5/bin/glnx86:/u16/local/matlab6.5/sys/os/glnx86 Mandatory This script does the low-pass filtering (for local field potentials). The .eeg file is created by the program called in this script. It calls a resampling program which first apply an anti aliasing low pass filter to the data and then samples down to the local field potential sampling rate provided in the parameter file. The resampling program is currently a matlab program, therefore this part of the process relies on Matlab until this program is rewritten. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - libraryPath is the path for Matlab. process_multi_start cpFirstXmlBool 1 Mandatory rmFilFileBool 0 Mandatory This script starts eeg and spike data processing on a list of input fileBaseNames This script is called by: process_multi_start fileBaseName [fileBaseNames] Parameters: - rmFilFileBool 1 = remove the high pass filtered .fil file to save space - cpFirstXmlBool 1 = copy the xml file from the first fileBaseName to all other fileBaseNames to save time * Note that ideally the common threshold would be for single channels rather than single electrodes (may be a problem of process_baseline) process_mvFiles2Dirs executeScriptBool 1 Mandatory This script organizes files in preparation for process_merge by moving fileBaseName.* into a directory fileBaseName useage: process_mvFiles2Dirs fileBaseName parameters: - executeScriptBool determines whether the script should be run with the next batch process. process_pca executeScriptBool 1 Mandatory beforePeak 4 Mandatory afterPeak 4 Mandatory nSamplesInPCA 16 Mandatory This script performs the principle component analysis (PCA ). It computes the variance (creates the .m1m2.# file) and creates the .fet.# and .mm.# files. The variables used to compute the PCA depend on the sampling rate. The default is for a sampling rate of 10khz. The parameters in the parameter file are multiplifaction factor of 10khz. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - beforePeak represents the number of samples before peak to be used for the PCA. There is one value for all the electrodes. - afterPeak represents the number of samples after peak to be used for the PCA. There is one value for all the electrodes. - nSamplesInPCA represents the number of samples used for PCA. There is one value for all the electrodes. updateParFile executeScriptBool 1 Mandatory samplesInWaveform 16 Mandatory peakSample 8 Mandatory This script updates the parameter file. It adds for each spike group, the number of samples in each waveform, the sample index of the peak in a waveform and the number of feaures to use to do the PCA. The variables used by the different programs depend on the sampling rate. The default is for a sampling rate of 10khz. All the script parameters are multiplifaction factor of 10khz. parameters: - executeScriptBool determines whether the script should be run with the next batch process. - The parameter samplesInWaveform represents the number of samples in each waveform . - The parameter peakSample represents the sample index of the peak in a waveform.