[Mne_analysis] mne_brain_vision2fiff Losing Events?

Christian Brodbeck cmb650 at nyu.edu
Tue Aug 21 13:11:44 EDT 2012
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Hello, 

Thanks for looking into this Alex! Based on a comparison of indexes, the events that are missing from the fif file are Mk292 and Mk1582. As far as I can see these events are not different from other events, neither in the text file::

	Mk291=Stimulus,S128,97717,1,0
	Mk292=Stimulus,S128,98000,1,0
	Mk293=Stimulus,S128,98300,1,0
	...
	Mk1581=Stimulus,S128,531684,1,0
	Mk1582=Stimulus,S128,532000,1,0
	Mk1583=Stimulus,S128,532300,1,0

nor when printing the line content as Python string::

	>>> p = [291, 292, 1582]
	>>> for line in open('/Volumes/Iomega/ereftests/raw_eeg converted vmrk/R0458_eref3h.vmrk'):
	...     if any(line.startswith('Mk%s' % pi) for pi in p):
	...         print repr(line)
	...     
	'Mk291=Stimulus,S128,97717,1,0\n'
	'Mk292=Stimulus,S128,98000,1,0\n'
	'Mk1582=Stimulus,S128,532000,1,0\n'

The Stim channel at these time points is simply flat, at 0 (https://dl.dropbox.com/u/659990/R0458%20eref3h/missing_events.py).

Best,

Christian



On Aug 20, 2012, at 11:12, Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu> wrote:

> Christian,
> 
> do you know which events are missed?
> 
> do you see the stim channel rising from 0 at these time points?
> 
> @matti : any idea what may be happening?
> 
> Best,
> Alex
> 
> On Fri, Aug 17, 2012 at 2:25 PM, Alexandre Gramfort
> <gramfort at nmr.mgh.harvard.edu> wrote:
>> hi Christian,
>> 
>> I confirm that I find 1958 events in your file with both
>> mne_process_raw and mne-python
>> 
>> $mne_brain_vision2fiff --header R0458_eref3h.vhdr --out test.fif
>> 
>> indeed reports 1960 events although with
>> 
>> $mne_process_raw --raw test_raw.fif --events test-eve.fif
>> 
>> and loading test-eve.fif in Python I get only 1958
>> 
>>>>> import mne
>>>>> ev = mne.read_events('test_raw-eve.fif')
>>>>> len(ev[ev[:, 2] == 128])
>> 1958
>> 
>> I therefore suspect an issue in the C code maybe while writing the
>> stim channel to fif.
>> 
>> We'll have to dig in the C code and maybe Matti can give us a hand.
>> 
>> Alex
>> 
>> On Wed, Aug 15, 2012 at 6:50 PM, Christian Brodbeck <cmb650 at nyu.edu> wrote:
>>> Hello,
>>> 
>>> When converting with mne_brain_vision2fiff, the resulting fif files seem to be missing events on occasion. My recordings should all contain 1960 events. mne_brain_vision2fiff says "nevent = 1960" (for the complete output see below), however, when opening the resulting fiff files in mne-python, up to 3 events are missing. The conversion seems to lose events consistently (i.e. when I repeat the command the same number of events get lost):
>>> 
>>> n events found by mne-python for my different subjects:
>>> 1959   R0040_eref3h_raw.fif
>>> 1958   R0458_eref3h_raw.fif
>>> 1957   R0425_eref3h_raw.fif
>>> 1957   R0355_eref3h_raw.fif
>>> 1960   R0273_eref3h_raw.fif
>>> 1960   R0541_eref3h_raw.fif
>>> 
>>> The event channel data reflects that (for a recording with 1958 events):
>>> 
>>>>>> np.unique(data)
>>> array([   0.,  128.])
>>>>>> np.sum(np.diff(data) > 0)
>>> 1958
>>>>>> np.sum(np.diff(data) < 0)
>>> 1958
>>> 
>>> I also tried the nightly version of mne with the same result. In case someone can have a look, I uploaded a set of files (10 mb): https://dl.dropbox.com/u/659990/R0458%20eref3h.zip
>>> 
>>> Thanks
>>> 
>>> Christian
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> $ mne_brain_vision2fiff --header R0458_eref3h.vhdr --out R0458_eref3h.fif
>>> 
>>> mne_brain_vision2fiff version 1.7 compiled at Jan  7 2011 02:26:21
>>> 
>>> header  file           : R0458_eref3h.vhdr
>>> output file            : R0458_eref3h.fif
>>> 
>>> Read header file : R0458_eref3h.vhdr
>>> Read header file : R0458_eref3h.vmrk
>>> 
>>> nchan           = 5
>>> sfreq           = 500.0  Hz
>>> raw data file   = R0458_eref3h.eeg
>>> raw binary      = true
>>> raw binary type = 16
>>> raw endian      = little
>>> raw nsamp       = -1
>>> nevent          = 1960
>>> eXimia          = false
>>> 
>>> Data will be split into <= 1907.3 MByte pieces
>>> 
>>> Writing header to R0458_eref3h_raw.fif ... [done]
>>> Writing raw data to R0458_eref3h_raw.fif ... Number of samples deduced from the raw file size : 671230
>>> [done]
>>> Wrote 1...671230 of 671230 samples total to R0458_eref3h_raw.fif
>>> Adding directory to R0458_eref3h_raw.fif...[done]
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