[Mne_analysis] mne_brain_vision2fiff Losing Events?

Sat Aug 25 05:31:22 EDT 2012

hi Christian

after further investigation there is clearly a bug when writing events
in the C code.
Try offsetting by 1 the forgotten events and they will appear magically.
Before we fix the bug in the C code I would use Python to parse the vrmk file
and fix the stim channel with mne-python. Something like

mne_brain_vision_fix_stim.py --raw --vrmk file.vrmk

that would do read/write on the raw after using some raw[stim_idx,
time_idx] = 128.

HTH
Alex

On Tue, Aug 21, 2012 at 7:11 PM, Christian Brodbeck <cmb650 at nyu.edu> wrote:
> 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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