[Mne_analysis] The issue of converting EDF to FIF format

Xiaoxiao Bai baixx013 at gmail.com
Thu Jul 3 09:18:26 EDT 2014
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Hi Dgw,

Thanks a lot.

Best

Xiaoxiao


On Wed, Jul 2, 2014 at 10:24 PM, <dgwakeman at gmail.com> wrote:

> Hi
>
> You can add the digitizer data from the raw kit data to the raw egi data.
> There are no built in functions for this but it shouldn't be too hard just
> be sure to match them up correctly. However currently raw data from one MEG
> and a different EEG system can't be combined because a lot of checks and
> potentially some corrections need to be done to combine these data. The
> kind of approximation the epic hung code makes is not safe to use on long
> stretches of data like you have in raw files.
> Hth
> D
>
> Sent from my phone
>
> On Jul 2, 2014, at 20:15, Xiaoxiao Bai <baixx013 at gmail.com> wrote:
>
> Dear Denis,
>
> Thank you for your help.
>
> elc = mne.fiff.kit.read_elp() get electrode locations acquired from
> Polhemus system.
>
> raw = mne.io.egi.read_raw_egi() get fif data object from EGI raw data file.
>
> We want to add electrode locations elc into raw rather than epochs.
>
> Best
>
> Xiaoxiao
>
>
> On Wed, Jul 2, 2014 at 6:32 PM, Denis A. Engemann <
> denis.engemann at gmail.com> wrote:
>
>> Hi,
>>
>> we currently only support that at the epochs stage:
>>
>> http://martinos.org/mne/dev/generated/mne.epochs.add_channels_epochs.html
>>
>> you need compatible sampling rates
>>
>> HTH,
>> Denis
>>
>> On Jul 3, 2014, at 12:17 AM, Xiaoxiao Bai <baixx013 at gmail.com> wrote:
>>
>> Dear Denis,
>>
>> Thank you for your help. I have another simple question about saving elp
>> and EGI raw as a fif file.
>>
>> I use raw = mne.io.egi.read_raw_egi() to read EGI raw data and elc =
>> mne.fiff.kit.read_elp() to read elp file.
>>
>> How can I combine raw and elc and save them into one fif file?
>>
>> Best
>>
>> Xiaoxiao
>>
>>
>> On Wed, Jul 2, 2014 at 2:50 PM, Denis-Alexander Engemann <
>> denis.engemann at gmail.com> wrote:
>>
>>> Xiaoxiao, great!
>>>
>>> Glad to hear it worked.
>>>
>>> Best,
>>> Denis
>>>
>>>
>>> On Wed, Jul 2, 2014 at 8:36 PM, Xiaoxiao Bai <baixx013 at gmail.com> wrote:
>>>
>>>> Dear Denis,
>>>>
>>>> I have installed MNE python. It can read EGI raw file.
>>>>
>>>> Best
>>>>
>>>> Xiaoxiao
>>>>
>>>>
>>>> On Wed, Jul 2, 2014 at 12:49 PM, Denis-Alexander Engemann <
>>>> denis.engemann at gmail.com> wrote:
>>>>
>>>>>
>>>>> Hi Xiaoxiao,
>>>>>
>>>>> we meanwhile have direct reading + conversion support for EGI data
>>>>> in MNE-Python (development version),
>>>>>
>>>>> Take a look at: mne.io.egi.read_raw_egi
>>>>>
>>>>> It supports the native egi raw format.
>>>>>
>>>>> Hope this helps,
>>>>> Denis
>>>>>
>>>>>
>>>>> On Wed, Jul 2, 2014 at 6:38 PM, Xiaoxiao Bai <baixx013 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear Dgw,
>>>>>>
>>>>>> Thank you for you help. This file only includes signals of 128
>>>>>> channels with same sample rate.
>>>>>>
>>>>>> After that, I input EGI Net Station data into BrainVision and then
>>>>>> save as EDF file. This BrainVision EDF file can be converted to FIF file.
>>>>>>
>>>>>> I used matlab toolbox to read this FIF file and its header
>>>>>> information and data are correct.
>>>>>>
>>>>>> But I can not display it in the mne_browse_raw (see attached
>>>>>> screenshot).
>>>>>>
>>>>>> Best
>>>>>>
>>>>>> Xiaoxiao
>>>>>>
>>>>>>
>>>>>> On Wed, Jul 2, 2014 at 12:13 PM, dgw <dgwakeman at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Xiaoxiao,
>>>>>>>
>>>>>>> What types of data are in there? The error message suggests that
>>>>>>> there is data with different sampling rates. Do you have channels with
>>>>>>> different sampling rates? If yes, can you re-export the data removing the
>>>>>>> data with different sampling rates?
>>>>>>>
>>>>>>> HTH,
>>>>>>> D
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Jul 2, 2014 at 11:20 AM, Xiaoxiao Bai <baixx013 at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi all MEN users,
>>>>>>>>
>>>>>>>> I used Net station to save recorded EEG data to EDF format. When I
>>>>>>>> used mne_edf2fiff to convert our EDF file to FIF file, I got this error
>>>>>>>> message,
>>>>>>>>
>>>>>>>> $ mne_edf2fiff --edf Recording_9_fil.edf --fif Recording_9_fil.fif
>>>>>>>>
>>>>>>>> mne_edf2fiff version 1.6 compiled at Dec 21 2009 19:46:35
>>>>>>>>
>>>>>>>> EDF/EDF+/BDF file (input)  : Recording_9_fil.edf
>>>>>>>> No electrode position data specified.
>>>>>>>> fif file (output)          : Recording_9_fil.fif
>>>>>>>>
>>>>>>>> Parsing EDF/EDF+/BDF header...[failed]
>>>>>>>> Unequal sampling rates across data channels are not supported.
>>>>>>>>
>>>>>>>> Best
>>>>>>>>
>>>>>>>> Xiaoxiao
>>>>>>>>
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