[Mne_analysis] averaging result: "nothing accepted"
Eric Larson
larson.eric.d at gmail.com
Tue Apr 24 20:30:39 EDT 2012
I think you might have mentioned this in a previous email, but does it
actually produce the "A1_ave_log.txt" log file? That file should
record any trials that were rejected, but I'd be surprised if
rejections were the issue.
You could try running something like this (assuming the syntax is adjusted):
mne_process_raw --raw
/Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bcm_epc1.fif
--ave /$WHATEVER_THE_CORRECT_PATH_IS/A1_ec1_bcm_epc1.ave --projon
With the events (with and then without the dummy line I mentioned
before) in a text file named A1_ec1_bcm_epc1.eve, in the directory
where you're calling mne_process_raw. I believe this will cause MNE to
ignore the events in the actual FIF while doing the averaging and
instead use the text events read from the text file.
Also, it just occurred to me that I've always used a "bmin" and "bmax"
to set the baseline when doing averaging---it's possible MNE defaults
to -200ms to 0ms for the baseline if you don't tell it otherwise, in
which case I think your first epoch wouldn't be used because there is
no data for the baseline time span.
Eric
On Tue, Apr 24, 2012 at 4:44 PM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
> Eric et al.,
>
> I am using v2.7.3 on a Macintosh.
> I verified that it does read the events in properly - if I use your
> suggestion I get two events.
> I left the single event in, and saved events in a -eve.fif file. Below is
> the result of the last mne_browse_raw session. I tried to average using
> Process:Average, and all indications seem to confirm the event is in
> there, but in the end is says "nave = 0".
>
> I wonder if there are some default rejection settings that are still in
> effect and for some reason it is rejecting the epoch based on some
> artifact criteria?
>
> Thanks,
> -Jeff
>
> ********** Begin console output
> ***************************************************************************
> **
> kje-macbook:MNE jefferiksen$ mne_browse_raw &
> [1] 767
> kje-macbook:MNE jefferiksen$ 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
> 32-bit architecture. Using 1000.00 Mbytes for ring buffers
> 9 selections loaded from /Users/jefferiksen/.mne/mne_browse_raw.sel
> Current selection is GSN 1-16
> Initial settings data created.
>
> --- Opening
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1.fif ---
>
> No compensation data in
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1.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 0 MEG channels.
> No SSS data in
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1.fif
> 0 bad channels read from
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1.fif
> filter : 0.000 ... 40.0 Hz bins : 0 ... 327 of 4097 hpw : 3 lpw : 20
> Highpass filter will work as specified.
> filter : 0.000 ... 40.0 Hz bins : 0 ... 327 of 4097 hpw : 3 lpw : 20
> Highpass filter will work as specified.
> Initial dc offsets determined
> Raw data file
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1.fif:
> nchan = 257
> nsamp = 900
> sfreq = 1000.000 Hz
> length = 0.900 sec
> 1 events found in
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1-eve.fif
> Trigger channel : STI 014 max_event : 1
> Annotation file
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1-annot.fif containing 1 events read
> No projection operator found in
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1.fif
> Average EEG reference projection added.
>
> --- Projection status ---
>
> # 1 : Average EEG reference : 1 vecs : 257 chs EEG active
>
> --- Complete ---
>
> Warning:
> Name: scroll
> Class: XmScrollBar
> Specified slider size is greater than the maximum scrollbar
> value minus the minimum scrollbar value.
>
> Average :
> stim ignore : off
> grad reject : off
> mag reject : off
> EEG reject : off
> EOG reject : off
> ECG reject : off
> grad flat : off
> mag flat : off
> EEG flat : off
> EOG flat : off
> ECG flat : off
> Do not fix trigger skew
> output file : A1_ec1_bcm_epc1-ave.fif
> log file : A1_ave_log.txt
> event file : A1_ec1_bcm_epc1.eve
> ave1epoch :
> t = 0.0 ... 900.0 ms
> event = 1
> ignore = 0
>
> Event file is in the new format
> Read 1 events from A1_ec1_bcm_epc1.eve
> ave1epoch : nave = 0
> Saved 1 user-defined events to annotation file
> /Users/jefferiksen/Documents/Fair_lab/hdEEG_subjects/AIRC0001/MNE/A1_ec1_bc
> m_epc1-annot.fif
>
> ******************* end console output
> ***************************************************************************
> ***
>
>
> On 4/24/12 4:12 PM, "Eric Larson" <larson.eric.d at gmail.com> wrote:
>
>>Which version of MNE are you running? I think that one of the older
>>versions of MNE didn't recognize the last event in a text file, which
>>you could overcome by adding a dummy event line like this:
>>
>>changing the event file from:
>>
>>0 0 0 0 psuedo_event
>>10 0.009 0 1 trigger1
>>
>>to:
>>
>>0 0 0 0 psuedo_event
>>10 0.009 0 1 trigger1
>>10 0.009 0 111 trigger1
>>
>>The choice of 111 as the trigger number here is arbitrary, it's just
>>putting something there so the second-to-last line (important one)
>>actually gets picked up.
>>
>>Eric
>>
>>On Tue, Apr 24, 2012 at 4:04 PM, Jeff Eriksen <eriksenj at ohsu.edu> wrote:
>>> I have managed to insert one event into my EEG FIF file, which I want to
>>> average (yes, Nave = 1). I did this by importing a text file list of
>>>events
>>> using mne-browse-raw. I can see this event when I list them within
>>> mne-browse-raw. When I try to average inside the GUI, I get a brief
>>>display
>>> of a window that goes by too fast to read, then the message "nothing
>>> accepted"
>>>
>>> Any suggestions on debugging this? Some of my files are included below.
>>> Thanks,
>>> -Jeff
>>>
>>> Here is the event file I created:
>>>
>>> # sample time from to text
>>> 0 0 0 0 psuedo_event
>>> 10 0.009 0 1 trigger1
>>>
>>> Here is the ave file I created:
>>>
>>> average {
>>> outfile A1_ec1_bcm_epc1-ave.fif
>>> eventfile A1_ec1_bcm_epc1.eve
>>> logfile A1_ave_log.txt
>>> category {
>>> name ave1epoch
>>> event 1
>>> tmin 0.0
>>> tmax 0.9
>>> }
>>> }
>>>
>>> Here is the console output of trying to average:
>>>
>>> Event file is in the new format
>>> Read 1 events from A1_ec1_bcm_epc1.eve
>>> test : nave = 0
>>> Average :
>>> stim ignore : off
>>> grad reject : off
>>> mag reject : off
>>> EEG reject : off
>>> EOG reject : off
>>> ECG reject : off
>>> grad flat : off
>>> mag flat : off
>>> EEG flat : off
>>> EOG flat : off
>>> ECG flat : off
>>> Do not fix trigger skew
>>> output file : A1_ec1_bcm_epc1-ave.fif
>>> log file : A1_ave_log.txt
>>> event file : A1_ec1_bcm_epc1.eve
>>> test :
>>> t = 0.0 ... 900.0 ms
>>> event = 1
>>> ignore = 0
>>>
>>> Event file is in the new format
>>> Read 1 events from A1_ec1_bcm_epc1.eve
>>> test : nave = 0
>>>
>>>
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