2016-02-09 daniel 16 64 20000 20 1000 0 1250 25 22 20 27 21 26 18 29 19 28 16 31 17 30 23 24 10 9 6 13 5 14 4 15 2 11 1 7 0 3 8 12 55 52 51 56 48 59 49 58 53 60 57 63 61 62 50 54 40 39 37 42 36 43 35 44 34 45 33 46 32 47 38 41 25 22 20 27 21 26 18 29 19 28 16 31 17 30 23 24 32 16 3 10 9 6 13 5 14 4 15 2 11 1 7 0 3 8 12 32 16 3 55 52 51 56 48 59 49 58 53 60 57 63 61 62 50 54 32 16 3 40 39 37 42 36 43 35 44 34 45 33 46 32 47 38 41 32 16 3 1 2 1 3 1 4 1 5 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 2 16 2 17 2 18 2 19 2 20 2 21 3 2 3 3 3 4 3 5 3 6 3 7 3 8 -------------- -------------- -------------- -------------- -------------- 4 2 4 3 4 4 ------ ------ ------ ------ ------ 5 2 5 3 5 4 5 5 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 5 15 5 16 5 17 5 18 5 19 5 20 5 21 -- -- -- -- -- 0.2 32 16 0 #ff00ff #ff00ff #ff00ff 0 0 1 #ff00ff #ff00ff #ff00ff 1 0 2 #ff00ff #ff00ff #ff00ff 2 0 3 #ff00ff #ff00ff #ff00ff 3 0 4 #ff00ff #ff00ff #ff00ff 4 0 5 #ff00ff #ff00ff #ff00ff 5 0 6 #ff00ff #ff00ff #ff00ff 6 0 7 #ff00ff #ff00ff #ff00ff 7 0 8 #ff00ff #ff00ff #ff00ff 8 0 9 #ff00ff #ff00ff #ff00ff 9 0 10 #ff00ff #ff00ff #ff00ff 10 0 11 #ff00ff #ff00ff #ff00ff 11 0 12 #ff00ff #ff00ff #ff00ff 12 0 13 #ff00ff #ff00ff #ff00ff 13 0 14 #ff00ff #ff00ff #ff00ff 14 0 15 #ff00ff #ff00ff #ff00ff 15 0 16 #00aa00 #00aa00 #00aa00 16 0 17 #00aa00 #00aa00 #00aa00 17 0 18 #00aa00 #00aa00 #00aa00 18 0 19 #00aa00 #00aa00 #00aa00 19 0 20 #00aa00 #00aa00 #00aa00 20 0 21 #00aa00 #00aa00 #00aa00 21 0 22 #00aa00 #00aa00 #00aa00 22 0 23 #00aa00 #00aa00 #00aa00 23 0 24 #00aa00 #00aa00 #00aa00 24 0 25 #00aa00 #00aa00 #00aa00 25 0 26 #00aa00 #00aa00 #00aa00 26 0 27 #00aa00 #00aa00 #00aa00 27 0 28 #00aa00 #00aa00 #00aa00 28 0 29 #00aa00 #00aa00 #00aa00 29 0 30 #00aa00 #00aa00 #00aa00 30 0 31 #00aa00 #00aa00 #00aa00 31 0 32 #f2ff59 #f2ff59 #f2ff59 32 0 33 #f2ff59 #f2ff59 #f2ff59 33 0 34 #f2ff59 #f2ff59 #f2ff59 34 0 35 #f2ff59 #f2ff59 #f2ff59 35 0 36 #f2ff59 #f2ff59 #f2ff59 36 0 37 #f2ff59 #f2ff59 #f2ff59 37 0 38 #f2ff59 #f2ff59 #f2ff59 38 0 39 #f2ff59 #f2ff59 #f2ff59 39 0 40 #f2ff59 #f2ff59 #f2ff59 40 0 41 #f2ff59 #f2ff59 #f2ff59 41 0 42 #f2ff59 #f2ff59 #f2ff59 42 0 43 #f2ff59 #f2ff59 #f2ff59 43 0 44 #f2ff59 #f2ff59 #f2ff59 44 0 45 #f2ff59 #f2ff59 #f2ff59 45 0 46 #f2ff59 #f2ff59 #f2ff59 46 0 47 #f2ff59 #f2ff59 #f2ff59 47 0 48 #5555ff #5555ff #5555ff 48 0 49 #5555ff #5555ff #5555ff 49 0 50 #5555ff #5555ff #5555ff 50 0 51 #5555ff #5555ff #5555ff 51 0 52 #5555ff #5555ff #5555ff 52 0 53 #5555ff #5555ff #5555ff 53 0 54 #5555ff #5555ff #5555ff 54 0 55 #5555ff #5555ff #5555ff 55 0 56 #5555ff #5555ff #5555ff 56 0 57 #5555ff #5555ff #5555ff 57 0 58 #5555ff #5555ff #5555ff 58 0 59 #5555ff #5555ff #5555ff 59 0 60 #5555ff #5555ff #5555ff 60 0 61 #5555ff #5555ff #5555ff 61 0 62 #5555ff #5555ff #5555ff 62 0 63 #5555ff #5555ff #5555ff 63 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 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 0 Mandatory mergeBaseName PV_ChR2_2 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 1 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 1 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.