2007-06-28
kenji
16
99
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
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
0.200000
32
16
0
#45fff3
#45fff3
#ff5101
0
0
1
#45fff3
#45fff3
#ff5101
1
0
2
#45fff3
#45fff3
#ff5101
2
0
3
#ff2706
#45fff3
#ff5101
3
0
4
#45fff3
#45fff3
#ff5101
4
0
5
#45fff3
#45fff3
#ff5101
5
0
6
#45fff3
#45fff3
#ff5101
6
0
7
#45fff3
#45fff3
#ff5101
7
0
8
#fff201
#fff201
#fff201
8
0
9
#fff201
#fff201
#fff201
9
0
10
#fff201
#fff201
#fff201
10
0
11
#ff1b06
#fff201
#fff201
11
0
12
#fff201
#fff201
#fff201
12
0
13
#fff201
#fff201
#fff201
13
0
14
#fff201
#fff201
#fff201
14
0
15
#fff201
#fff201
#fff201
15
0
16
#4aff08
#4aff08
#4aff08
16
0
17
#4aff08
#4aff08
#4aff08
17
0
18
#4aff08
#4aff08
#4aff08
18
0
19
#ce1fff
#4aff08
#4aff08
19
0
20
#ff0d05
#4aff08
#4aff08
20
0
21
#4aff08
#4aff08
#4aff08
21
0
22
#4aff08
#4aff08
#4aff08
22
0
23
#4aff08
#4aff08
#4aff08
23
0
24
#ffff03
#01ffd9
#01ffd9
24
0
25
#01ffd9
#01ffd9
#01ffd9
25
0
26
#01ffd9
#01ffd9
#01ffd9
26
0
27
#01ffd9
#01ffd9
#01ffd9
27
0
28
#ff3b0f
#01ffd9
#01ffd9
28
0
29
#01ffd9
#01ffd9
#01ffd9
29
0
30
#01ffd9
#01ffd9
#01ffd9
30
0
31
#ffea05
#01ffd9
#01ffd9
31
0
32
#d103ff
#d103ff
#d103ff
32
0
33
#d103ff
#d103ff
#d103ff
33
0
34
#ff2511
#d103ff
#d103ff
34
0
35
#d103ff
#d103ff
#d103ff
35
0
36
#d103ff
#d103ff
#d103ff
36
0
37
#d103ff
#d103ff
#d103ff
37
0
38
#d103ff
#d103ff
#d103ff
38
0
39
#d103ff
#d103ff
#d103ff
39
0
40
#ff1803
#011aff
#011aff
40
0
41
#011aff
#011aff
#011aff
41
0
42
#011aff
#011aff
#011aff
42
0
43
#011aff
#011aff
#011aff
43
0
44
#011aff
#011aff
#011aff
44
0
45
#011aff
#011aff
#011aff
45
0
46
#011aff
#011aff
#011aff
46
0
47
#011aff
#011aff
#011aff
47
0
48
#ff1008
#11ff21
#ff055d
48
0
49
#11ff21
#11ff21
#ff055d
49
0
50
#11ff21
#11ff21
#ff055d
50
0
51
#11ff21
#11ff21
#ff055d
51
0
52
#11ff21
#11ff21
#ff055d
52
0
53
#11ff21
#11ff21
#ff055d
53
0
54
#11ff21
#11ff21
#ff055d
54
0
55
#11ff21
#11ff21
#ff055d
55
0
56
#ff0303
#ffbc03
#ffbc03
56
0
57
#ffbc03
#ffbc03
#ffbc03
57
0
58
#ffbc03
#ffbc03
#ffbc03
58
0
59
#ffbc03
#ffbc03
#ffbc03
59
0
60
#ffbc03
#ffbc03
#ffbc03
60
0
61
#ffbc03
#ffbc03
#ffbc03
61
0
62
#ffbc03
#ffbc03
#ffbc03
62
0
63
#ffbc03
#ffbc03
#ffbc03
63
0
64
#05ff16
#05ff16
#05ff16
64
0
65
#05ff16
#05ff16
#05ff16
65
0
66
#05ff16
#05ff16
#05ff16
66
0
67
#05ff16
#05ff16
#05ff16
67
0
68
#ff1a05
#05ff16
#05ff16
68
0
69
#05ff16
#05ff16
#05ff16
69
0
70
#05ff16
#05ff16
#05ff16
70
0
71
#05ff16
#05ff16
#05ff16
71
0
72
#00ffd9
#00ffd9
#00ffd9
72
0
73
#00ffd9
#00ffd9
#00ffd9
73
0
74
#00ffd9
#00ffd9
#00ffd9
74
0
75
#00ffd9
#00ffd9
#00ffd9
75
0
76
#00ffd9
#00ffd9
#00ffd9
76
0
77
#00ffd9
#00ffd9
#00ffd9
77
0
78
#ff1164
#00ffd9
#00ffd9
78
0
79
#00ffd9
#00ffd9
#00ffd9
79
0
80
#68ff03
#68ff03
#68ff03
80
0
81
#68ff03
#68ff03
#68ff03
81
0
82
#68ff03
#68ff03
#68ff03
82
0
83
#68ff03
#68ff03
#68ff03
83
0
84
#68ff03
#68ff03
#68ff03
84
0
85
#68ff03
#68ff03
#68ff03
85
0
86
#ff2908
#68ff03
#68ff03
86
0
87
#68ff03
#68ff03
#68ff03
87
0
88
#ffee37
#ffee37
#ff016f
88
0
89
#ffee37
#ffee37
#ff016f
89
0
90
#ffee37
#ffee37
#ff016f
90
0
91
#ff0d0d
#ffee37
#ff016f
91
0
92
#ffee37
#ffee37
#ff016f
92
0
93
#ffee37
#ffee37
#ff016f
93
0
94
#ffee37
#ffee37
#ff016f
94
0
95
#ffee37
#ffee37
#ff016f
95
0
96
#0080ff
#0080ff
#0080ff
96
0
97
#0080ff
#0080ff
#0080ff
97
0
98
#0080ff
#0080ff
#0080ff
98
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
6
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
1
Mandatory
mergeBaseName
ec014.171_188
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.