[Mne_analysis] The issue of converting EDF to FIF format

Xiaoxiao Bai baixx013 at gmail.com
Thu Jul 3 09:17:39 EDT 2014
Search archives: 
HI Denis,

Thank you for your help.

Best

Xiaoxiao


On Thu, Jul 3, 2014 at 8:57 AM, Denis-Alexander Engemann <
denis.engemann at gmail.com> wrote:

> Hi Xiaoxiao,
>
> it turns out I misread your question.
> If you want to add the electrode positions manually
> you have to update the corresponding fields in the raw.info['chs'] for
> each channel. It's the first three entries in the 'loc' and the the first
> row of the matrix in 'eeg_loc'.
>
> To give an example:
>
>
> https://github.com/dengemann/mne-python/blob/montage/mne/montages/montage.py#L166
>
> HTH,
> Denis
>
>
>
>
>
>
> On Thu, Jul 3, 2014 at 2:15 AM, 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
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Mne_analysis mailing list
>>>>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The information in this e-mail is intended only for the person to
>>>>>>>>> whom it is
>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>>>> the e-mail
>>>>>>>>> contains patient information, please contact the Partners
>>>>>>>>> Compliance HelpLine at
>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent
>>>>>>>>> to you in error
>>>>>>>>> but does not contain patient information, please contact the
>>>>>>>>> sender and properly
>>>>>>>>> dispose of the e-mail.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Mne_analysis mailing list
>>>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>>
>>>>>>>>
>>>>>>>> The information in this e-mail is intended only for the person to
>>>>>>>> whom it is
>>>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>>> the e-mail
>>>>>>>> contains patient information, please contact the Partners
>>>>>>>> Compliance HelpLine at
>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>> you in error
>>>>>>>> but does not contain patient information, please contact the sender
>>>>>>>> and properly
>>>>>>>> dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Mne_analysis mailing list
>>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>
>>>>>>>
>>>>>>> The information in this e-mail is intended only for the person to
>>>>>>> whom it is
>>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>> the e-mail
>>>>>>> contains patient information, please contact the Partners Compliance
>>>>>>> HelpLine at
>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>> you in error
>>>>>>> but does not contain patient information, please contact the sender
>>>>>>> and properly
>>>>>>> dispose of the e-mail.
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mne_analysis mailing list
>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>
>>>>>>
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>> the e-mail
>>>>>> contains patient information, please contact the Partners Compliance
>>>>>> HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and properly
>>>>>> dispose of the e-mail.
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Mne_analysis mailing list
>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to whom
>>>>> it is
>>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Mne_analysis mailing list
>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140703/174fed5b/attachment.html

More information about the Mne_analysis mailing list