2015-06-22 yuta 16 80 20000 20 1000 0 1250 33 38 32 39 35 36 34 37 41 46 40 47 43 44 42 45 16 25 17 24 18 22 20 21 26 19 28 23 29 27 30 31 13 4 9 2 5 3 1 0 7 14 6 15 8 12 11 10 48 55 49 54 50 53 51 52 56 63 57 62 58 61 59 60 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 33 38 32 39 35 36 34 37 32 16 3 41 46 40 47 43 44 42 45 32 16 3 16 25 17 24 18 22 20 21 32 16 3 26 19 28 23 29 27 30 31 32 16 3 13 4 9 2 5 3 1 0 32 16 3 7 14 6 15 8 12 11 10 32 16 3 48 55 49 54 50 53 51 52 32 16 3 56 63 57 62 58 61 59 60 32 16 3 1 2 2 2 2 3 ---- ---- ---- ---- ---- 2 4 ---- ---- ---- ---- ---- 2 5 -------------------------------------- -------------------------------------- -------------------------------------- -------------------------------------- -------------------------------------- 4 2 4 3 ---- ---- ---- ---- ---- 6 2 -- -- -- -- -- 0.2 32 16 0 #00b3ff #00b3ff #00b3ff 0 0 1 #00b3ff #00b3ff #00b3ff 1 0 2 #00b3ff #00b3ff #00b3ff 2 0 3 #00b3ff #00b3ff #00b3ff 3 0 4 #00b3ff #00b3ff #00b3ff 4 0 5 #00b3ff #00b3ff #00b3ff 5 0 6 #00ff95 #00ff95 #00ff95 6 0 7 #00ff95 #00ff95 #00ff95 7 0 8 #00ff95 #00ff95 #00ff95 8 0 9 #00b3ff #00b3ff #00b3ff 9 0 10 #00ff95 #00ff95 #00ff95 10 0 11 #00ff95 #00ff95 #00ff95 11 0 12 #00ff95 #00ff95 #00ff95 12 0 13 #00b3ff #00b3ff #00b3ff 13 0 14 #00ff95 #00ff95 #00ff95 14 0 15 #00ff95 #00ff95 #00ff95 15 0 16 #8f06ff #8f06ff #8f06ff 16 0 17 #8f06ff #8f06ff #8f06ff 17 0 18 #8f06ff #8f06ff #8f06ff 18 0 19 #0105ff #0105ff #0105ff 19 0 20 #8f06ff #8f06ff #8f06ff 20 0 21 #8f06ff #8f06ff #8f06ff 21 0 22 #8f06ff #8f06ff #8f06ff 22 0 23 #0105ff #0105ff #0105ff 23 0 24 #8f06ff #8f06ff #8f06ff 24 0 25 #8f06ff #8f06ff #8f06ff 25 0 26 #0105ff #0105ff #0105ff 26 0 27 #0105ff #0105ff #0105ff 27 0 28 #0105ff #0105ff #0105ff 28 0 29 #0105ff #0105ff #0105ff 29 0 30 #0105ff #0105ff #0105ff 30 0 31 #0105ff #0105ff #0105ff 31 0 32 #ff0004 #0080ff #0080ff 32 0 33 #ff0004 #0080ff #0080ff 33 0 34 #ff0004 #0080ff #0080ff 34 0 35 #ff0004 #0080ff #0080ff 35 0 36 #ff0004 #0080ff #0080ff 36 0 37 #ff0004 #0080ff #0080ff 37 0 38 #ff0004 #0080ff #0080ff 38 0 39 #ff0004 #0080ff #0080ff 39 0 40 #ff17d9 #ff17d9 #ff17d9 40 0 41 #ff17d9 #ff17d9 #ff17d9 41 0 42 #ff17d9 #ff17d9 #ff17d9 42 0 43 #ff17d9 #ff17d9 #ff17d9 43 0 44 #ff17d9 #ff17d9 #ff17d9 44 0 45 #ff17d9 #ff17d9 #ff17d9 45 0 46 #ff17d9 #ff17d9 #ff17d9 46 0 47 #ff17d9 #ff17d9 #ff17d9 47 0 48 #d5ff00 #d5ff00 #d5ff00 48 0 49 #d5ff00 #d5ff00 #d5ff00 49 0 50 #d5ff00 #d5ff00 #d5ff00 50 0 51 #d5ff00 #d5ff00 #d5ff00 51 0 52 #d5ff00 #d5ff00 #d5ff00 52 0 53 #d5ff00 #d5ff00 #d5ff00 53 0 54 #d5ff00 #d5ff00 #d5ff00 54 0 55 #d5ff00 #d5ff00 #d5ff00 55 0 56 #ff9500 #ff9500 #ff9500 56 0 57 #ff9500 #ff9500 #ff9500 57 0 58 #ff9500 #ff9500 #ff9500 58 0 59 #ff9500 #ff9500 #ff9500 59 0 60 #ff9500 #ff9500 #ff9500 60 0 61 #ff9500 #ff9500 #ff9500 61 0 62 #ff9500 #ff9500 #ff9500 62 0 63 #ff9500 #ff9500 #ff9500 63 0 64 #0080ff #0080ff #000000 64 0 65 #0080ff #0080ff #000000 65 0 66 #0080ff #0080ff #000000 66 0 67 #0080ff #0080ff #000000 67 0 68 #0080ff #0080ff #000000 68 0 69 #0080ff #0080ff #000000 69 0 70 #0080ff #0080ff #000000 70 0 71 #0080ff #0080ff #000000 71 0 72 #0080ff #0080ff #000000 72 0 73 #0080ff #0080ff #000000 73 0 74 #0080ff #0080ff #000000 74 0 75 #0080ff #0080ff #000000 75 0 76 #0080ff #0080ff #000000 76 0 77 #0080ff #0080ff #000000 77 0 78 #0080ff #0080ff #000000 78 0 79 #0080ff #0080ff #000000 79 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 - spikesFromDatBool: set to 1 if you want detrended spikes from wideband dat file; set to 0 if from high-passed fil file 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 YutaMouse39-150804 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. 1 YutaMouse39-150804-01 YutaMouse39-150804-02 YutaMouse39-150804-03 YutaMouse39-150804-04 YutaMouse39-150804-05 YutaMouse39-150804-06 YutaMouse39-150804-07 YutaMouse39-150804-08 YutaMouse39-150804-09 YutaMouse39-150804-10 YutaMouse39-150804-11