Hello,
After running mne_process_raw --raw <raw> --eventsout <output>, I wasn't
able to find the trigger code for the button presses in the event file. I
don't know if it wasn't recorded and stored during the MEG scan or if I
made a mistake on my part.
Any input is appreciated.
Thank you,
-Ricky
Hi Ricky,
Can you provide us with some more information? We can't help without
some more details like:
What version of MNE?
What was the exact command run?
What was the output of that command?
What system did the data come from (I assume the Charlestown one)?
Did you employ any special settings when collecting the data?
Did you employ any special settings in your environment, when running
the command (e.g. MNE_TRIGGER_CH_NAME)?
Thanks
Dan
Sorry about that.
1.MNE 2.7
2.the command was mne_process_raw --raw raw_data/raw.fif --eventsout
triggers/.eve
3.The data was along the lines of this:
22800 37.961 0 0
25252 42.044 0 41
26547 44.200 0 11
27674 46.076 0 2
28793 47.939 0 8
29898 49.779 0 3
30983 51.585 0 9
32118 53.475 0 14
33298 55.440 0 19
34436 57.335 0 20
35508 59.119 0 16
36649 61.019 0 13
37756 62.862 0 11 %The button presses are assigned trigger
values 64 and 128 (channels 7 and 8). A button response was supposed to
be recorded after onset of every stimuli and every stimuli was assigned a
trigger number as shown above.
4. It was from Charlestown
5. No special setting were used during data collection or when running
the command.
Thank you,
-Ricky
output:
mne_process_raw version 2.28 compiled at Dec 15 2009 08:56:37
64-bit architecture. Using 2000.00 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 raw_data/CPLEX_01_V1_raw.fif ---
No compensation data in raw_data/CPLEX_01_V1_raw.fif
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 306 MEG channels.
No SSS data in raw_data/CPLEX_01_V1_raw.fif
Data skip of 22800 samples in the beginning
0 bad channels read from raw_data/CPLEX_01_V1_raw.fif
filter : 0.000 ... 40.0 Hz bins : 0 ... 545 of 4097 hpw : 3 lpw : 34
Highpass filter will work as specified.
Initial dc offsets determined
Raw data file raw_data/CPLEX_01_V1_raw.fif:
nchan = 389
nsamp = 143400
sfreq = 600.615 Hz
length = 238.755 sec
268 events found in raw_data/CPLEX_01_V1_raw-eve.fif
Trigger channel : STI 014 max_event : 41
--- Saving events (leading edge) in text format to
triggers/CPLEX_01_V12.eve ---
--- Complete ---
-Ricky
Hi Ricky,
I think the problem may be a simple syntax issue.
The first question to answer is is there a triggers directory in the
directory you run the command from? (i.e. can you "ls ./triggers/")
Is the file written?
If the answers to these are "Yes" and "no", try using "./triggers/
CPLEX_01_V12.eve" instead of without the "./". You may want to
consider using the full path to data in future calls to commands to
avoid issues like these (environment variables can be very helpful
for keeping these simple).
Good Luck!
Dan
Thank you for the help, but I don't think it is a syntax issue. It is
more... did the scanner store the button responses in the STI channel.
When I run the command, it writes out the .eve file with relevant
information. It is just missing the critical button response information.
Is there another way to process the raw file and hopefully extract the
response triggers? Mne_browse_raw also shows no response triggers.
-Ricky
Hi Ricky
Did you see the buttons triggered in your acquisition? Sometimes, when
people use the MEG at Martinos, they don't switch back Ch.5-8 to the
correct (hold "hi" configuration... see the diagram on the side of the
equipment rack). If that was not in that configuration and if you
don't see the pulses when you acquire, then you basically didn't
record the responses.
Hope this helps.
Cheers
KC
Thank you for the help, but I don't think it is a syntax issue. It is
more... did the scanner store the button responses in the STI channel.
When I run the command, it writes out the .eve file with relevant
information. It is just missing the critical button response
information.
Is there another way to process the raw file and hopefully extract the
response triggers? Mne_browse_raw also shows no response triggers.-Ricky
Hi Ricky,
I think the problem may be a simple syntax issue.
The first question to answer is is there a triggers directory in the
directory you run the command from? (i.e. can you "ls ./triggers/")Is the file written?
If the answers to these are "Yes" and "no", try using "./triggers/
CPLEX_01_V12.eve" instead of without the "./". You may want to
consider using the full path to data in future calls to commands to
avoid issues like these (environment variables can be very helpful
for keeping these simple).Good Luck!
Danoutput:
mne_process_raw version 2.28 compiled at Dec 15 2009 08:56:37
64-bit architecture. Using 2000.00 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 raw_data/CPLEX_01_V1_raw.fif ---
No compensation data in raw_data/CPLEX_01_V1_raw.fif
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 306 MEG
channels.
No SSS data in raw_data/CPLEX_01_V1_raw.fif
Data skip of 22800 samples in the beginning
0 bad channels read from raw_data/CPLEX_01_V1_raw.fif
filter : 0.000 ... 40.0 Hz bins : 0 ... 545 of 4097 hpw : 3
lpw : 34
Highpass filter will work as specified.
Initial dc offsets determined
Raw data file raw_data/CPLEX_01_V1_raw.fif:
nchan = 389
nsamp = 143400
sfreq = 600.615 Hz
length = 238.755 sec
268 events found in raw_data/CPLEX_01_V1_raw-eve.fif
Trigger channel : STI 014 max_event : 41--- Saving events (leading edge) in text format to
triggers/CPLEX_01_V12.eve ------ Complete ---
-Ricky
What was the output when you ran the command?
Sorry about that.
1.MNE 2.7
2.the command was mne_process_raw --raw raw_data/raw.fif --
eventsout
triggers/.eve
3.The data was along the lines of this:
22800 37.961 0 0
25252 42.044 0 41
26547 44.200 0 11
27674 46.076 0 2
28793 47.939 0 8
29898 49.779 0 3
30983 51.585 0 9
32118 53.475 0 14
33298 55.440 0 19
34436 57.335 0 20
35508 59.119 0 16
36649 61.019 0 13
37756 62.862 0 11 %The button presses are assigned
trigger
values 64 and 128 (channels 7 and 8). A button response was
supposed to
be recorded after onset of every stimuli and every stimuli was
assigned a
trigger number as shown above.
4. It was from Charlestown
5. No special setting were used during data collection or when
running
the command.Thank you,
-RickyHi Ricky,
Can you provide us with some more information? We can't help
without
some more details like:What version of MNE?
What was the exact command run?
What was the output of that command?
What system did the data come from (I assume the Charlestown
one)?
Did you employ any special settings when collecting the data?
Did you employ any special settings in your environment, when
running
the command (e.g. MNE_TRIGGER_CH_NAME)?Thanks
DanHello,
After running mne_process_raw --raw <raw> --eventsout
<output>, I
wasn't
able to find the trigger code for the button presses in the
event
file. I
don't know if it wasn't recorded and stored during the MEG
scan or
if I
made a mistake on my part.Any input is appreciated.
Thank you,
-Ricky
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Adrian KC Lee, ScD
Instructor
Radiology at Harvard Medical School
Department of Radiology, MGH
Athinoula A. Martinos Center for Biomedical Imaging
Research Associate
Department of Cognitive & Neural Systems, Boston University
Director of BAMBI
Boston-Area Machine-Brain Interfaces outreach program
National Science Foundation Science of Learning Center
Center of Excellence for Learning in Education, Science and Technology
Email: akclee at alum.mit.edu
Website: www.akclee.com
Ricky,
yet another way to view the stimulus channel would be to convert the raw data into a Matlab .mat file
(using the mne_raw2mat commmand, see section 9.13 in the MNE Manual 2.6).
e.g. mne_raw2mat --raw <rawfilename> --mat <matfilename>
Then you can load the matfile, and plot and examine the stimulus channel (usually ch#313, but check MNE_raw_info).
Or use the Matlab command unique(<stimchanneldatavector>), which will give you all the different pulse values recorded on the stimulus channel.
They should include your condition/trial triggers and the response button values.
Kestas
The conversion is unnecessary (and wastes space). You can read the raw
data directly to Matlab using the MNE Matlab functions.
- Matti