2007-08-01
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
1
2
1
3
1
4
1
5
--
--
--
--
1
6
--
--
--
--
1
7
--
--
--
--
1
8
--
--
--
--
1
9
--
--
--
--
1
10
----------------------------
----------------------------
----------------------------
----------------------------
1
11
------
------
--
------
------
1
12
------
------
----
------
------
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
------
------
----
------
------
3
2
3
3
--
--
--
--
3
4
--
--
--
--
3
5
--
--
--
--
3
6
--
--
--
--
3
7
--
--
--
--
3
8
----
----
----
----
3
9
----
----
----
----
3
10
--
--
--
--
3
11
--
--
--
--
3
12
--
--
--
--
3
13
------
------
--
------
------
3
14
----
----
--
----
----
3
15
--------------------
--------------------
------
--------------------
--------------------
3
16
--------
--------
----
--------
--------
4
2
4
3
4
4
------------------------------------------------
------------------------------------------------
------------------------------------------------
------------------------------------------------
------------------------------------------------
5
2
5
3
5
4
----
----
----
----
5
5
--
--
--
--
--
5
6
--
--
--
--
--
5
7
----
----
--
----
----
5
8
----
----
--
----
----
5
9
------------
------------
--------
------------
------------
5
10
--------
--------
------
--------
--------
9
2
9
3
9
4
9
5
9
6
--
--
--
--
9
7
------
------
------
------
9
8
----------
----------
----------
----------
9
9
9
10
------
------
--
------
------
9
11
--------------
--------------
----
--------------
--------------
10
2
------------------------------------------
------------------------------------------
--
------------------------------------------
------------------------------------------
10
3
--
--
--
--
--
10
4
----------------------------------------------------
----------------------------------------------------
------
----------------------------------------------------
----------------------------------------------------
11
2
11
3
--------------------
--------------------
--------------------
--------------------
11
4
--------------------------------------------------
--------------------------------------------------
--------------------------------------------------
--------------------------------------------------
11
5
----
----
----
----
11
6
----
----
----
----
----
12
2
12
3
------------------
------------------
------------------
------------------
12
4
----------------------------
----------------------------
----------------------------
----------------------------
0.2
32
16
0
#06ffda
#06ffda
#06ffda
0
0
1
#06ffda
#06ffda
#06ffda
1
0
2
#06ffda
#06ffda
#06ffda
2
0
3
#06ffda
#06ffda
#06ffda
3
0
4
#ff0d05
#06ffda
#06ffda
4
0
5
#06ffda
#06ffda
#06ffda
5
0
6
#06ffda
#06ffda
#06ffda
6
0
7
#af03ff
#06ffda
#06ffda
7
0
8
#ffea08
#ffea08
#ffea08
8
0
9
#ffea08
#ffea08
#ffea08
9
0
10
#ffea08
#ffea08
#ffea08
10
0
11
#ffea08
#ffea08
#ffea08
11
0
12
#ffea08
#ffea08
#ffea08
12
0
13
#ffea08
#ffea08
#ffea08
13
0
14
#ffea08
#ffea08
#ffea08
14
0
15
#ff0303
#ffea08
#ffea08
15
0
16
#df0cff
#df0cff
#df0cff
16
0
17
#df0cff
#df0cff
#df0cff
17
0
18
#df0cff
#df0cff
#df0cff
18
0
19
#ff2908
#df0cff
#df0cff
19
0
20
#df0cff
#df0cff
#df0cff
20
0
21
#df0cff
#df0cff
#df0cff
21
0
22
#df0cff
#df0cff
#df0cff
22
0
23
#df0cff
#df0cff
#df0cff
23
0
24
#ffb20c
#ffb20c
#ffb20c
24
0
25
#ffb20c
#ffb20c
#ffb20c
25
0
26
#ffb20c
#ffb20c
#ffb20c
26
0
27
#ffb20c
#ffb20c
#ffb20c
27
0
28
#ff1803
#ffb20c
#ffb20c
28
0
29
#ffb20c
#ffb20c
#ffb20c
29
0
30
#ffb20c
#ffb20c
#ffb20c
30
0
31
#ffb20c
#ffb20c
#ffb20c
31
0
32
#12ff0a
#12ff0a
#ff08ad
32
0
33
#ff2c0c
#12ff0a
#ff08ad
33
0
34
#12ff0a
#12ff0a
#ff08ad
34
0
35
#12ff0a
#12ff0a
#ff08ad
35
0
36
#12ff0a
#12ff0a
#ff08ad
36
0
37
#12ff0a
#12ff0a
#ff08ad
37
0
38
#12ff0a
#12ff0a
#ff08ad
38
0
39
#12ff0a
#12ff0a
#ff08ad
39
0
40
#ff0d05
#ffff06
#ffff06
40
0
41
#ffff06
#ffff06
#ffff06
41
0
42
#ffff06
#ffff06
#ffff06
42
0
43
#ffff06
#ffff06
#ffff06
43
0
44
#ffff06
#ffff06
#ffff06
44
0
45
#ffff06
#ffff06
#ffff06
45
0
46
#ffff06
#ffff06
#ffff06
46
0
47
#ffff06
#ffff06
#ffff06
47
0
48
#ff2706
#0814ff
#0814ff
48
0
49
#0814ff
#0814ff
#0814ff
49
0
50
#0814ff
#0814ff
#0814ff
50
0
51
#0814ff
#0814ff
#0814ff
51
0
52
#0814ff
#0814ff
#0814ff
52
0
53
#0814ff
#0814ff
#0814ff
53
0
54
#0814ff
#0814ff
#0814ff
54
0
55
#0814ff
#0814ff
#0814ff
55
0
56
#ff2706
#13ffb0
#ff068b
56
0
57
#13ffb0
#13ffb0
#ff068b
57
0
58
#13ffb0
#13ffb0
#ff068b
58
0
59
#13ffb0
#13ffb0
#ff068b
59
0
60
#13ffb0
#13ffb0
#ff068b
60
0
61
#13ffb0
#13ffb0
#ff068b
61
0
62
#13ffb0
#13ffb0
#ff068b
62
0
63
#13ffb0
#13ffb0
#ff068b
63
0
64
#ffd30d
#ffd30d
#ffd30d
64
0
65
#ffd30d
#ffd30d
#ffd30d
65
0
66
#ffd30d
#ffd30d
#ffd30d
66
0
67
#ffd30d
#ffd30d
#ffd30d
67
0
68
#ffd30d
#ffd30d
#ffd30d
68
0
69
#ff0606
#ffd30d
#ffd30d
69
0
70
#ffd30d
#ffd30d
#ffd30d
70
0
71
#ffd30d
#ffd30d
#ffd30d
71
0
72
#0fff83
#0fff83
#0fff83
72
0
73
#0fff83
#0fff83
#0fff83
73
0
74
#0fff83
#0fff83
#0fff83
74
0
75
#ff0505
#0fff83
#0fff83
75
0
76
#0fff83
#0fff83
#0fff83
76
0
77
#0fff83
#0fff83
#0fff83
77
0
78
#0fff83
#0fff83
#0fff83
78
0
79
#0fff83
#0fff83
#0fff83
79
0
80
#089cff
#089cff
#089cff
80
0
81
#089cff
#089cff
#089cff
81
0
82
#089cff
#089cff
#089cff
82
0
83
#089cff
#089cff
#089cff
83
0
84
#089cff
#089cff
#089cff
84
0
85
#089cff
#089cff
#089cff
85
0
86
#ff390c
#089cff
#089cff
86
0
87
#089cff
#089cff
#089cff
87
0
88
#920dff
#920dff
#920dff
88
0
89
#920dff
#920dff
#920dff
89
0
90
#920dff
#920dff
#920dff
90
0
91
#920dff
#920dff
#920dff
91
0
92
#ff2b0a
#920dff
#920dff
92
0
93
#920dff
#920dff
#920dff
93
0
94
#920dff
#920dff
#920dff
94
0
95
#920dff
#920dff
#920dff
95
0
96
#7cff24
#0080ff
#0080ff
96
0
97
#7cff24
#0080ff
#0080ff
97
0
98
#7cff24
#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
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
1
Mandatory
mergeBaseName
ec014.254_269
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
Optional
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
ec014.254
ec014.255
ec014.256
ec014.257
ec014.258
ec014.259
ec014.260
ec014.263
ec014.264
ec014.265
ec014.266
ec014.269