[Mne_analysis] The issue of converting EDF to FIF format

dgwakeman at gmail.com dgwakeman at gmail.com
Wed Jul 2 22:24:36 EDT 2014
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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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