2015-07-10
brendon
16
97
20000
20
1000
0
1250
1250
lfp
1
6
0
7
3
4
2
5
9
14
8
15
11
12
10
13
16
23
17
22
18
21
19
20
24
31
25
30
26
29
27
28
65
70
64
71
67
68
66
69
73
78
72
79
75
74
76
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
96
1
6
0
7
3
4
2
5
32
16
3
9
14
8
15
11
12
10
13
32
16
3
16
23
17
22
18
21
19
20
32
16
3
24
31
25
30
26
29
27
28
32
16
3
65
70
64
71
67
68
66
69
32
16
3
73
78
72
79
75
74
76
77
32
16
3
48
57
49
56
50
54
52
53
32
16
3
58
51
60
55
61
59
62
63
32
16
3
45
36
41
34
37
35
33
32
32
16
3
39
46
38
47
40
44
43
42
32
16
3
80
87
81
86
82
85
83
84
32
16
3
88
95
89
94
90
93
91
92
32
16
3
2
2
CTX
2
3
CTX
2
4
CTX
4
2
CTX
4
3
CTX
4
4
CTX
4
5
CTX
4
6
CTX
4
7
CTX
7
2
HPC
7
3
HPC
7
4
HPC
7
5
HPC
8
2
HPC
8
3
HPC
9
2
HPC
9
3
HPC
10
2
HPC
1
2
CTX
0.200000
32
16
0
#ff0004
#ff0004
#ff0004
0
0
1
#ff0004
#ff0004
#ff0004
1
0
2
#ff0004
#ff0004
#ff0004
2
0
3
#ff0004
#ff0004
#ff0004
3
0
4
#ff0004
#ff0004
#ff0004
4
0
5
#ff0004
#ff0004
#ff0004
5
0
6
#ff0004
#ff0004
#ff0004
6
0
7
#ff0004
#ff0004
#ff0004
7
0
8
#f700ff
#f700ff
#f700ff
8
0
9
#f700ff
#f700ff
#f700ff
9
0
10
#f700ff
#f700ff
#f700ff
10
0
11
#f700ff
#f700ff
#f700ff
11
0
12
#f700ff
#f700ff
#f700ff
12
0
13
#f700ff
#f700ff
#f700ff
13
0
14
#f700ff
#f700ff
#f700ff
14
0
15
#f700ff
#f700ff
#f700ff
15
0
16
#2a00ff
#2a00ff
#2a00ff
16
0
17
#2a00ff
#2a00ff
#2a00ff
17
0
18
#2a00ff
#2a00ff
#2a00ff
18
0
19
#2a00ff
#2a00ff
#2a00ff
19
0
20
#2a00ff
#2a00ff
#2a00ff
20
0
21
#2a00ff
#2a00ff
#2a00ff
21
0
22
#2a00ff
#2a00ff
#2a00ff
22
0
23
#2a00ff
#2a00ff
#2a00ff
23
0
24
#009dff
#009dff
#009dff
24
0
25
#009dff
#009dff
#009dff
25
0
26
#009dff
#009dff
#009dff
26
0
27
#009dff
#009dff
#009dff
27
0
28
#009dff
#009dff
#009dff
28
0
29
#009dff
#009dff
#009dff
29
0
30
#009dff
#009dff
#009dff
30
0
31
#009dff
#009dff
#009dff
31
0
32
#00ddff
#00ddff
#00ddff
32
0
33
#00ddff
#00ddff
#00ddff
33
0
34
#00ddff
#00ddff
#00ddff
34
0
35
#00ddff
#00ddff
#00ddff
35
0
36
#00ddff
#00ddff
#00ddff
36
0
37
#00ddff
#00ddff
#00ddff
37
0
38
#00ff11
#00ff11
#00ff11
38
0
39
#00ff11
#00ff11
#00ff11
39
0
40
#00ff11
#00ff11
#00ff11
40
0
41
#00ddff
#00ddff
#00ddff
41
0
42
#00ff11
#00ff11
#00ff11
42
0
43
#00ff11
#00ff11
#00ff11
43
0
44
#00ff11
#00ff11
#00ff11
44
0
45
#00ddff
#00ddff
#00ddff
45
0
46
#00ff11
#00ff11
#00ff11
46
0
47
#00ff11
#00ff11
#00ff11
47
0
48
#8903ff
#8903ff
#8903ff
48
0
49
#8903ff
#8903ff
#8903ff
49
0
50
#8903ff
#8903ff
#8903ff
50
0
51
#0080ff
#0080ff
#0080ff
51
0
52
#8903ff
#8903ff
#8903ff
52
0
53
#8903ff
#8903ff
#8903ff
53
0
54
#8903ff
#8903ff
#8903ff
54
0
55
#0080ff
#0080ff
#0080ff
55
0
56
#8903ff
#8903ff
#8903ff
56
0
57
#8903ff
#8903ff
#8903ff
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
#ff0004
#ff0004
#ff0004
64
0
65
#ff0004
#ff0004
#ff0004
65
0
66
#ff0004
#ff0004
#ff0004
66
0
67
#ff0004
#ff0004
#ff0004
67
0
68
#ff0004
#ff0004
#ff0004
68
0
69
#ff0004
#ff0004
#ff0004
69
0
70
#ff0004
#ff0004
#ff0004
70
0
71
#ff0004
#ff0004
#ff0004
71
0
72
#ff00ae
#ff00ae
#ff00ae
72
0
73
#ff00ae
#ff00ae
#ff00ae
73
0
74
#ff00ae
#ff00ae
#ff00ae
74
0
75
#ff00ae
#ff00ae
#ff00ae
75
0
76
#ff00ae
#ff00ae
#ff00ae
76
0
77
#ff00ae
#ff00ae
#ff00ae
77
0
78
#ff00ae
#ff00ae
#ff00ae
78
0
79
#ff00ae
#ff00ae
#ff00ae
79
0
80
#e6ff00
#e6ff00
#e6ff00
80
0
81
#e6ff00
#e6ff00
#e6ff00
81
0
82
#e6ff00
#e6ff00
#e6ff00
82
0
83
#e6ff00
#e6ff00
#e6ff00
83
0
84
#e6ff00
#e6ff00
#e6ff00
84
0
85
#e6ff00
#e6ff00
#e6ff00
85
0
86
#e6ff00
#e6ff00
#e6ff00
86
0
87
#e6ff00
#e6ff00
#e6ff00
87
0
88
#ff9500
#ff9500
#ff9500
88
0
89
#ff9500
#ff9500
#ff9500
89
0
90
#ff9500
#ff9500
#ff9500
90
0
91
#ff9500
#ff9500
#ff9500
91
0
92
#ff9500
#ff9500
#ff9500
92
0
93
#ff9500
#ff9500
#ff9500
93
0
94
#ff9500
#ff9500
#ff9500
94
0
95
#ff9500
#ff9500
#ff9500
95
0
96
#0080ff
#0080ff
#0080ff
96
0
badchannels
badchannels
17 27 65 70 64 71 49 51 36 41 32 59 21 44 47 80 84 96 15 19 20 75 74 55 34 5 8 11 29 72 76 61 12 40 45 33
Mandatory
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
Templeton_032415
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.