[Mne_analysis] problem with triggers
Mark Williams
mwilliam at maccs.mq.edu.au
Fri Jul 25 22:03:39 EDT 2008
Hi Matti,
We are using a KIT system and we transform the data using mne_kit2fif
However when we do the averaging for example 3 events which are coded
on 3 separate channels we only get events for the first 2 channels.
If we do the transformation and only put in the 3rd channel then we
get all the events for it so it's not due to the threshold or missing
events.
Any idea why?
See all the details below:
bash-3.2$ mne_kit2fiff --elp 048_ar.elp --hsp 048_ar.hsp --sns
KIT_Sensors.txt -
-hpi 048_ME008_preB1-coreg.txt --raw 048_ME008_B1-export.txt --out
ar_run1.fif -
-stim 177:178:179
mne_kit2fiff version 1.3 compiled at Apr 5 2007 16:06:51
elp file : 048_ar.elp
hpi file : 048_ME008_preB1-coreg.txt
HPI coil alignment tolerance : 5.0 mm
head shape file : 048_ar.hsp
raw data file : 048_ME008_B1-export.txt
sfreq : 1000.0 Hz
bandpass : 0.0 ... 200.0 Hz
stimulus channels : 177:178:179
threshold : 1.000
output file : ar_run1.fif
Transformed 5 locations to the Neuromag head coordinate frame.
Transformed 2243 head shape points to the Neuromag head coordinate
frame.
5 HPI coils in 048_ar.elp
5 HPI coil positions read from 048_ME008_preB1-coreg.txt
Procrustes matching (desired vs. transformed) :
-68.72 -1.90 1.80 mm <-> -71.11 -0.20 1.58 mm
diff = 2.94
5 mm
68.79 0.20 -0.60 mm <-> 71.81 0.52 0.72 mm
diff = 3.31
7 mm
-6.78 95.01 51.20 mm <-> -5.76 93.21 51.23 mm
diff = 2.06
9 mm
-41.00 79.16 46.40 mm <-> -40.19 78.47 47.95 mm
diff = 1.87
8 mm
33.60 83.25 53.20 mm <-> 31.14 83.71 50.52 mm
diff = 3.67
0 mm
160 MEG channels and 32 other channels read from KIT_Sensors.txt
Coordinate transformation: CTF/4D/KIT head -> head
0.001443 -0.999999 0.000000 -0.12 mm
0.999999 0.001443 0.000000 0.00 mm
-0.000000 -0.000000 1.000000 -0.00 mm
0.000000 0.000000 0.000000 1.00
Coordinate transformation: MEG device -> head
0.996493 -0.059802 0.058530 6.33 mm
0.056177 0.996510 0.061740 -2.95 mm
-0.062017 -0.058235 0.996375 38.29 mm
0.000000 0.000000 0.000000 1.00
The output file will contain a total of 158 channels including the
synthetic STI
014
Writing meas info...done.
Writing raw
data................................................................
........................................................................
........
........................................................................
........
........................................................................
........
........................................................................
........
........................................................................
........
........................................................................
........
.........................................[done]
Closing file..[Done]
Adding directory to ar_run1.fif...[done]
ar_run1.fif ready
Thank you for stopping by.
bash-3.2$ mne_process_raw --raw ar_run1.fif --decim 4 --save
ar_run1_dec.fif
Warning: MNE-suite, version 2.0
Your license will expire on 07/31/08.
Please contact your system administrator.
mne_process_raw version 1.36 compiled at Apr 5 2007 16:06:19
32-bit architecture. Using 600.00 Mbytes for ring buffers
--- Setting up the filter ---
Using a 4096-point FFT in filtering of raw data with 2048-sample tapers
bandpass = 0.0 ( 0.0) ... 40.0 ( 5.0) Hz
filter is on
--- Opening ar_run1.fif ---
STI 014 range set to 1.000000
Compensation in file : uncompensated
Setting up compensation data...
No compensation set. Nothing more to do.
No compensation was requested.
A new compensation value (uncompensated) was assigned to 157 MEG
channels.
No SSS data in ar_run1.fif
0 bad channels read from ar_run1.fif
Ring buffer structure with 995 entries initialized
144 filter buffers needed
Ring buffer structure with 121 entries initialized
filter : 0.000 ... 40.0 Hz bins : 0 ... 327 of 4097 hpw : 3
lpw : 20
Highpass filter will work as specified.
Raw data file ar_run1.fif:
nchan = 158
nsamp = 585000
sfreq = 1000.000 Hz
length = 585.000 sec
Finding triggers (trigger channel = STI 014) ...[done]
88 events found in ar_run1.fif
88 events written to ar_run1-eve.fif
No projection operator found in ar_run1.fif
--- Saving data to ar_run1_dec.fif (decim = 4) ---
8000 / 585000 samples read, 2000 saved
16000 / 585000 samples read, 4000 saved
24000 / 585000 samples read, 6000 saved
32000 / 585000 samples read, 8000 saved
40000 / 585000 samples read, 10000 saved
48000 / 585000 samples read, 12000 saved
56000 / 585000 samples read, 14000 saved
64000 / 585000 samples read, 16000 saved
72000 / 585000 samples read, 18000 saved
80000 / 585000 samples read, 20000 saved
88000 / 585000 samples read, 22000 saved
96000 / 585000 samples read, 24000 saved
104000 / 585000 samples read, 26000 saved
112000 / 585000 samples read, 28000 saved
120000 / 585000 samples read, 30000 saved
128000 / 585000 samples read, 32000 saved
136000 / 585000 samples read, 34000 saved
144000 / 585000 samples read, 36000 saved
152000 / 585000 samples read, 38000 saved
160000 / 585000 samples read, 40000 saved
168000 / 585000 samples read, 42000 saved
176000 / 585000 samples read, 44000 saved
184000 / 585000 samples read, 46000 saved
192000 / 585000 samples read, 48000 saved
200000 / 585000 samples read, 50000 saved
208000 / 585000 samples read, 52000 saved
216000 / 585000 samples read, 54000 saved
224000 / 585000 samples read, 56000 saved
232000 / 585000 samples read, 58000 saved
240000 / 585000 samples read, 60000 saved
248000 / 585000 samples read, 62000 saved
256000 / 585000 samples read, 64000 saved
264000 / 585000 samples read, 66000 saved
272000 / 585000 samples read, 68000 saved
280000 / 585000 samples read, 70000 saved
288000 / 585000 samples read, 72000 saved
296000 / 585000 samples read, 74000 saved
304000 / 585000 samples read, 76000 saved
312000 / 585000 samples read, 78000 saved
320000 / 585000 samples read, 80000 saved
328000 / 585000 samples read, 82000 saved
336000 / 585000 samples read, 84000 saved
344000 / 585000 samples read, 86000 saved
352000 / 585000 samples read, 88000 saved
360000 / 585000 samples read, 90000 saved
368000 / 585000 samples read, 92000 saved
376000 / 585000 samples read, 94000 saved
384000 / 585000 samples read, 96000 saved
392000 / 585000 samples read, 98000 saved
400000 / 585000 samples read, 100000 saved
408000 / 585000 samples read, 102000 saved
416000 / 585000 samples read, 104000 saved
424000 / 585000 samples read, 106000 saved
432000 / 585000 samples read, 108000 saved
440000 / 585000 samples read, 110000 saved
448000 / 585000 samples read, 112000 saved
456000 / 585000 samples read, 114000 saved
464000 / 585000 samples read, 116000 saved
472000 / 585000 samples read, 118000 saved
480000 / 585000 samples read, 120000 saved
488000 / 585000 samples read, 122000 saved
496000 / 585000 samples read, 124000 saved
504000 / 585000 samples read, 126000 saved
512000 / 585000 samples read, 128000 saved
520000 / 585000 samples read, 130000 saved
528000 / 585000 samples read, 132000 saved
536000 / 585000 samples read, 134000 saved
544000 / 585000 samples read, 136000 saved
552000 / 585000 samples read, 138000 saved
560000 / 585000 samples read, 140000 saved
568000 / 585000 samples read, 142000 saved
576000 / 585000 samples read, 144000 saved
584000 / 585000 samples read, 146000 saved
585000 / 585000 samples read, 146250 saved
--- Complete ---
bash-3.2$ mne_process_raw --raw ar_run1_dec.fif --ave Localiser.ave --
cov Localiser.cov --projoff --gave ar1.fif --gcov ar1.fif.co
v
Warning: MNE-suite, version 2.0
Your license will expire on 07/31/08.
Please contact your system administrator.
mne_process_raw version 1.36 compiled at Apr 5 2007 16:06:19
32-bit architecture. Using 600.00 Mbytes for ring buffers
--- Setting up the filter ---
Using a 4096-point FFT in filtering of raw data with 2048-sample tapers
bandpass = 0.0 ( 0.0) ... 40.0 ( 5.0) Hz
filter is on
--- Opening ar_run1_dec.fif ---
STI 014 range set to 1.000000
Compensation in file : uncompensated
Setting up compensation data...
No compensation set. Nothing more to do.
No compensation was requested.
A new compensation value (uncompensated) was assigned to 157 MEG
channels.
No SSS data in ar_run1_dec.fif
0 bad channels read from ar_run1_dec.fif
Ring buffer structure with 497 entries initialized
37 filter buffers needed
Ring buffer structure with 121 entries initialized
filter : 0.000 ... 40.0 Hz bins : 0 ... 1310 of 4097 hpw : 3
lpw : 82
Highpass filter will work as specified.
Raw data file ar_run1_dec.fif:
nchan = 158
nsamp = 146250
sfreq = 250.000 Hz
length = 585.000 sec
88 events found in ar_run1_dec-eve.fif
No projection operator found in ar_run1_dec.fif
--- Averaging according to Localiser.ave ---
Localiser :
grad reject : 2000.0 fT/cm
mag reject : 3000.0 fT
EEG reject : -1.0 uV
EOG reject : 150.0 uV
ECG reject : -1.0 mV
stim ignore : -1.0 ms
output file : Localiser.fif
log file : Localiser.log
Body :
t = -200.0 ... 1000.0 ms
event = 1
ignore = 0
Body_m :
t = -200.0 ... 1000.0 ms
event = 2
ignore = 0
BodyPart_Arm :
t = -200.0 ... 1000.0 ms
event = 3
ignore = 0
Body : nave = 19
Body_m : nave = 11
BodyPart_Arm : nave = 0
Saved log to Localiser.log
Saved averages to Localiser.fif
--- Computing covariance matrix according to Localiser.cov ---
grad reject : 2000.0 fT/cm
mag reject : 3000.0 fT
EEG reject : -1.0 uV
EOG reject : 150.0 uV
ECG reject : -1.0 mV
output file : Localiser-cov.fif
log file : Localiser-cov.log
event = 1
ignore = 0
t = -200.0 ... -20.0 ms
base = -200.0 ... -20.0 ms
event = 2
ignore = 0
t = -200.0 ... -20.0 ms
base = -200.0 ... -20.0 ms
event = 3
ignore = 0
t = -200.0 ... -20.0 ms
base = -200.0 ... -20.0 ms
Computing...
A total of 1426 samples used for the covariance matrix:
20 x 46 = 920 samples from category # 1
11 x 46 = 506 samples from category # 2
Saved covariance matrix to Localiser-cov.fif
Saved log to Localiser-cov.log
--- Complete ---
Mark A. Williams, PhD
Macquarie Centre for Cognitive Science (MACCS)
Macquarie University
Sydney NSW 2109
Email: mark.williams at maccs.mq.edu.au
Phone: +61 (0)2 9850 4438
Fax: +61 (0)2 9850 6059
Office: C5C 404
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