[Mne_analysis] 1. Redefine Onset
Geller, Jason
jason-geller at uiowa.edu
Mon Nov 4 18:49:15 EST 2019
External Email - Use Caution
Thanks for the quick reply! My epochs are aligned to a specific event (onset of audio file). There is 500 ms of silence at the start of each file. What I need is a new time zero that starts at 500 ms. I can provide more information, if needed.
Jason Geller, Ph.D.
Postdoctoral Scholar
The University of Iowa
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of mne_analysis-request at nmr.mgh.harvard.edu <mne_analysis-request at nmr.mgh.harvard.edu>
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Today's Topics:
1. Re: Redefine Onset (Geller, Jason)
2. Re: Redefine Onset (Dan McCloy)
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Message: 1
Date: Mon, 4 Nov 2019 20:36:47 +0000
From: "Geller, Jason" <jason-geller at uiowa.edu>
Subject: Re: [Mne_analysis] Redefine Onset
To: "mne_analysis at nmr.mgh.harvard.edu"
<mne_analysis at nmr.mgh.harvard.edu>
Message-ID: <BEA1BBD3-CC81-45CC-8CE9-9DBF918AC3DC at uiowa.edu>
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Hello,
I have an issue where I need to realign the zero point of epochs (there is 500 ms of silence at the start of an audio event). Is there an MNE function that will allow me to do this? I thought shift_time might get me what I need, but it does not.
> On Nov 4, 2019, at 11:00 AM, mne_analysis-request at nmr.mgh.harvard.edu wrote:
>
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>
> 1. Re: How to edit time attribute in a raw object (Eric Larson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 4 Nov 2019 09:21:41 -0500
> From: Eric Larson <larson.eric.d at gmail.com>
> Subject: Re: [Mne_analysis] How to edit time attribute in a raw object
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CAGu2niUwUAU4ZUGeLYEqKCih1VN1fXBisVecpe0ii4ynrmPb8g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> If the time of recording start is properly encoded in the file and read by
> MNE (which is hopefully the case), then you should be able to use it. You
> can manually convert from relative (starting from zero) to absolute time by
> looking at `raw.info['meas_date']` and `raw.first_samp`. But the eaiser
> thing to do would be to construct an Annotations
> <https://mne.tools/stable/generated/mne.Annotations.html> class with your
> behavioral/pupil events (in whatever starting time frame you prefer), then
> set `raw.annotations = my_annotations`, which should convert it to the raw
> object's time reference in `raw.info['meas_date']`. Check out the
> Annotations tutorials -- such as this one
> <https://mne.tools/dev/auto_tutorials/raw/plot_30_annotate_raw.html#creating-annotations-programmatically>
> -- and if it's not clear from them how to do it, we should improve the
> documentation.
>
> We do not allow modifying the `raw.times` attribute intentionally. A lot of
> downstream code (e.g., epoching) would break, loudly or (worse) silently,
> in unexpected and unpredictable if users could do this.
>
> Eric
>
>
> On Mon, Nov 4, 2019 at 6:03 AM vahid.bokharaie at tuebingen.mpg.de <
> vahid.bokharaie at tuebingen.mpg.de> wrote:
>
>> External Email - Use Caution
>>
>> Hi Philip
>> Thanks for your sharp response. It calarified the situation for me.
>> And to answer to your question, for rat EEG, we record behavioural data in
>> a go/no-go task, pupil diameters and EEG. I define Events based on
>> behavioural and pupil size, and then should convert them into proper format
>> to be read in mne. So it is important that time stamps match. Of course
>> this is something that can be handled easily, but I could not believe such
>> a simple feature is not incorporated into mne. Hence spent too much time
>> trying to find the right function.
>> Regards,
>> Vahid
>>
>>
>> -------- Original Message --------
>> Subject: Re: [Mne_analysis] How to edit time attribute in a raw object
>> From: Phillip Alday
>> To: Discussion and support forum for the users of MNE Software ,Vahid
>> Bokharaie
>> CC:
>>
>>
>> The time in the raw recordings (the Raw object) are assumed to be
>> arbitrary and just a measure of time elapsed since the beginning of the
>> recording, so there's not really a way to set or manipulate them. Why do
>> you need absolute time here? Are you concatenating Raw objects?
>>
>> Best,
>> Phillip
>>
>> On 4/11/19 10:55 am, Vahid Bokharaie wrote:
>>> External Email - Use Caution
>>>
>>> Hi all
>>> I posted this question in stackoverflow but seems MNE community is not
>>> active there, hence I searched for MNE mailing list and joined it.
>>> I use MNE for analysis of both rat and human EEG recordings. The system
>>> we have for rat EEG is from a company called NeuroNexus, and they have
>>> their own Matlab script to convert the EEG recordings and the time
>>> stamps into mat files. And then I import them in python and use MNE to
>>> analyse and visualise them. This means I have to establish my EEG raw
>>> objects from the scratch and save them to file, which I can do. But a
>>> seemingly trivial thing that I have not managed to find out how to do is
>>> to incorporate the time array into the EEG raw object. When I create and
>>> save the EEG raw object, it automatically set the initial time to 0, but
>>> my initial recording time is not 0 and I need to offset that. It is
>>> important to correct this, because the time stamps of EEG and
>>> behavioural data should match.
>>> Simply typing |raw.times = new_array| leads to |AttributeError: can't
>>> set attribute. ||This should be a very simple thing to do, but I have
>>> not been able to find it although I have looked into the documentation.
>>> So, I thought to ask it in here and if it is not really possible, then
>>> dig into the source code to fix it myself. Thanks in advance.
>>> Regards,
>>> Vahid
>>> |
>>>
>>> --
>>>
>> ---------------------------------------------------------------------------------------
>>> Vahid S. Bokharaie, PhD
>>> Senior Research Scientist
>>> Max Planck Institute for Biological Cybernetics
>>> Department of Physiology of Cognitive Processes
>>> Max Planck Ring 8, 72076 Tuebingen, Germany
>>> +49 (0)7071 - 601-1644
>>> vahid.bokharaie at tuebingen.mpg.de
>>> https://www.kyb.tuebingen.mpg.de/person/59086/84548
>>>
>> --------------------------------------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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>>
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Message: 2
Date: Mon, 4 Nov 2019 15:36:28 -0800
From: Dan McCloy <dan.mccloy at gmail.com>
Subject: Re: [Mne_analysis] Redefine Onset
To: Discussion and support forum for the users of MNE Software
<mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
<CAOE0pYkNMYVb63URz1b5wR7m1BfRS_RDB81aCeDKAWTqhk6Gwg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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Do you mean that you created epochs, but now you want the epochs to include
different samples (i.e., start earlier and/or end later)? If so, you have
to go back to the Raw data and re-do epoching with different tmin/tmax
values.
Or do you mean that the *data* in the epochs is what you want, but you just
want to change the *time labels* associated with each sample? If so,
`epochs.shift_time()` should do what you want; please say more about why it
does not get you what you need. Note that behavior of `shift_time` is
currently being changed in the development version of MNE-Python;
previously time shifts were forced to be integer multiples of the sampling
period, but soon (as soon as
https://github.com/mne-tools/mne-python/pull/6996 gets merged) it will be
possible on the development version to shift by any arbitrary amount of
time.
On Mon, Nov 4, 2019 at 12:37 PM Geller, Jason <jason-geller at uiowa.edu>
wrote:
> External Email - Use Caution
>
> Hello,
>
> I have an issue where I need to realign the zero point of epochs (there is
> 500 ms of silence at the start of an audio event). Is there an MNE function
> that will allow me to do this? I thought shift_time might get me what I
> need, but it does not.
>
>
>
> > On Nov 4, 2019, at 11:00 AM, mne_analysis-request at nmr.mgh.harvard.edu
> wrote:
> >
> > Send Mne_analysis mailing list submissions to
> > mne_analysis at nmr.mgh.harvard.edu
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> > or, via email, send a message with subject or body 'help' to
> > mne_analysis-request at nmr.mgh.harvard.edu
> >
> > You can reach the person managing the list at
> > mne_analysis-owner at nmr.mgh.harvard.edu
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Mne_analysis digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: How to edit time attribute in a raw object (Eric Larson)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 4 Nov 2019 09:21:41 -0500
> > From: Eric Larson <larson.eric.d at gmail.com>
> > Subject: Re: [Mne_analysis] How to edit time attribute in a raw object
> > To: Discussion and support forum for the users of MNE Software
> > <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID:
> > <
> CAGu2niUwUAU4ZUGeLYEqKCih1VN1fXBisVecpe0ii4ynrmPb8g at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > External Email - Use Caution
> >
> > If the time of recording start is properly encoded in the file and read
> by
> > MNE (which is hopefully the case), then you should be able to use it. You
> > can manually convert from relative (starting from zero) to absolute time
> by
> > looking at `raw.info['meas_date']` and `raw.first_samp`. But the eaiser
> > thing to do would be to construct an Annotations
> > <https://mne.tools/stable/generated/mne.Annotations.html> class with
> your
> > behavioral/pupil events (in whatever starting time frame you prefer),
> then
> > set `raw.annotations = my_annotations`, which should convert it to the
> raw
> > object's time reference in `raw.info['meas_date']`. Check out the
> > Annotations tutorials -- such as this one
> > <
> https://mne.tools/dev/auto_tutorials/raw/plot_30_annotate_raw.html#creating-annotations-programmatically
> >
> > -- and if it's not clear from them how to do it, we should improve the
> > documentation.
> >
> > We do not allow modifying the `raw.times` attribute intentionally. A lot
> of
> > downstream code (e.g., epoching) would break, loudly or (worse) silently,
> > in unexpected and unpredictable if users could do this.
> >
> > Eric
> >
> >
> > On Mon, Nov 4, 2019 at 6:03 AM vahid.bokharaie at tuebingen.mpg.de <
> > vahid.bokharaie at tuebingen.mpg.de> wrote:
> >
> >> External Email - Use Caution
> >>
> >> Hi Philip
> >> Thanks for your sharp response. It calarified the situation for me.
> >> And to answer to your question, for rat EEG, we record behavioural data
> in
> >> a go/no-go task, pupil diameters and EEG. I define Events based on
> >> behavioural and pupil size, and then should convert them into proper
> format
> >> to be read in mne. So it is important that time stamps match. Of course
> >> this is something that can be handled easily, but I could not believe
> such
> >> a simple feature is not incorporated into mne. Hence spent too much time
> >> trying to find the right function.
> >> Regards,
> >> Vahid
> >>
> >>
> >> -------- Original Message --------
> >> Subject: Re: [Mne_analysis] How to edit time attribute in a raw object
> >> From: Phillip Alday
> >> To: Discussion and support forum for the users of MNE Software ,Vahid
> >> Bokharaie
> >> CC:
> >>
> >>
> >> The time in the raw recordings (the Raw object) are assumed to be
> >> arbitrary and just a measure of time elapsed since the beginning of the
> >> recording, so there's not really a way to set or manipulate them. Why do
> >> you need absolute time here? Are you concatenating Raw objects?
> >>
> >> Best,
> >> Phillip
> >>
> >> On 4/11/19 10:55 am, Vahid Bokharaie wrote:
> >>> External Email - Use Caution
> >>>
> >>> Hi all
> >>> I posted this question in stackoverflow but seems MNE community is not
> >>> active there, hence I searched for MNE mailing list and joined it.
> >>> I use MNE for analysis of both rat and human EEG recordings. The system
> >>> we have for rat EEG is from a company called NeuroNexus, and they have
> >>> their own Matlab script to convert the EEG recordings and the time
> >>> stamps into mat files. And then I import them in python and use MNE to
> >>> analyse and visualise them. This means I have to establish my EEG raw
> >>> objects from the scratch and save them to file, which I can do. But a
> >>> seemingly trivial thing that I have not managed to find out how to do
> is
> >>> to incorporate the time array into the EEG raw object. When I create
> and
> >>> save the EEG raw object, it automatically set the initial time to 0,
> but
> >>> my initial recording time is not 0 and I need to offset that. It is
> >>> important to correct this, because the time stamps of EEG and
> >>> behavioural data should match.
> >>> Simply typing |raw.times = new_array| leads to |AttributeError: can't
> >>> set attribute. ||This should be a very simple thing to do, but I have
> >>> not been able to find it although I have looked into the documentation.
> >>> So, I thought to ask it in here and if it is not really possible, then
> >>> dig into the source code to fix it myself. Thanks in advance.
> >>> Regards,
> >>> Vahid
> >>> |
> >>>
> >>> --
> >>>
> >>
> ---------------------------------------------------------------------------------------
> >>> Vahid S. Bokharaie, PhD
> >>> Senior Research Scientist
> >>> Max Planck Institute for Biological Cybernetics
> >>> Department of Physiology of Cognitive Processes
> >>> Max Planck Ring 8, 72076 Tuebingen, Germany
> >>> +49 (0)7071 - 601-1644
> >>> vahid.bokharaie at tuebingen.mpg.de
> >>> https://www.kyb.tuebingen.mpg.de/person/59086/84548
> >>>
> >>
> --------------------------------------------------------------------------------------
> >>>
> >>>
> >>> _______________________________________________
> >>> Mne_analysis mailing list
> >>> Mne_analysis at nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
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