[FieldTrip] fieldtrip Digest, Vol 115, Issue 5
Andrade Rey René
rene.andrade at edu.uah.es
Thu Jun 4 14:06:03 CEST 2020
> On 4 Jun 2020, at 12:29, "fieldtrip-request at science.ru.nl" <fieldtrip-request at science.ru.nl> wrote:
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> Today's Topics:
>
> 1. definetrial error (Andrade Rey René)
> 2. Re: definetrial error (Schoffelen, J.M. (Jan Mathijs))
> 3. Fwd: Question (Bahar Saadatmehr)
> 4. Re: Question (Schoffelen, J.M. (Jan Mathijs))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Jun 2020 17:37:02 +0000
> From: Andrade Rey René <rene.andrade at edu.uah.es>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] definetrial error
> Message-ID:
> <VE1PR03MB5901C6D571B1CB08CB6D7AD1AF880 at VE1PR03MB5901.eurprd03.prod.outlook.com>
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>
> Dear FieldtripToolbox experts:
> I am presenting myself as I am new in the community. I am a student of Medicine in University of Alcala de Henares in Madrid Spain.
> I have a problem when running the dipole fitting tutorial. I have downloaded and set to path this trialfun_oddball_stimlocked.m file.
>
>>> cfg=ft_definetrial(cfg)
> evaluating trialfunction 'trialfun_oddball_stimlocked'
> Warning: channels with different sampling rate not supported, selecting subset of 33 channels at 250.000000 Hz
> Warning: channels with different sampling rate not supported, selecting subset of 33 channels at 250.000000 Hz
> Error using ft_definetrial (line 196)
> no trials were defined, see FT_DEFINETRIAL for help
>
>
> I am running on Temple University Hospital TUH EEG dataset of epilepsy.
>
> Thank you for your help in advance!
> Best,
> Rene Andrade.
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> ------------------------------
>
> Message: 2
> Date: Wed, 3 Jun 2020 19:43:07 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] definetrial error
> Message-ID: <DFAE80EC-E7F7-4FD6-A401-B6C6138AF57E at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear René,
>
> It is not clear what you want to do exactly,
I want to find the origin of focal or more complex seizures of epilepsy
> but in general you should not expect that a tutorial that was written for task based data, for instance an oddball task, works as is for any other data, in your case a clinical EEG dataset.
I understand
my question would be then how to proceed (see below)
> There are several reasons for this. First of all, an experimental dataset typically contains markers at specified timepoints in the data, that indicate certain events happening, for instance the onset of a visual stimulus on the screen, or a button pressed by the participant. Using this event information (which is represented in a dataset specific way) the experimenter can determine which chunks of the data are interesting for further investigation. The definition of the chunks of interest is done in ft_definetrial (which is the function that throws the error), but this only works if the data aligns with the instructions that the function is given. Now, given that you input clinical EEG data in combination with an event extraction recipe (’trialfun_oddball_stimlocked') that has no relation whatsoever with any event information stored in the EEG data file, it is bound to fail.
>
> So the question now is whether you want to learn about dipole fitting, or whether you want to learn about epilepsy data analysis, or about a combination thereof.
>
I need the combination because sometimes the focal seizure location is in the ROI of maximum activity and there is no need for dipole fitting but sometimes there is propagation and it is required to do analysis with dipole to know where it came from
> We don’t have a lot of teaching material about epilepsy, but a good start might be http://www.fieldtriptoolbox.org/tutorial/epilepsy/, rather than the tutorial you referred to. Note, however, that this tutorial concerns MEG data, and some parts of it are not relevant in case of EEG data. On the other hand, it might give you some handles on how this type of data can be analyzed.
>
I will check for the tutorial but please tell me what changes do I need to do or what data do I need, to run dipole fitting in epilepsy dataset.
Also I have data from epilepsy that shows no epileptic seizure or epileptic activity whatsoever (that is healthy subjects) is it easier to analyse eeg with dipole fitting in that case? How should I proceed?
Thank you for your kindness and dedication!!
> Best wishes,
> Jan-Mathijs
>
>
>
>
> On 3 Jun 2020, at 19:37, Andrade Rey René <rene.andrade at edu.uah.es<mailto:rene.andrade at edu.uah.es>> wrote:
>
> Dear FieldtripToolbox experts:
> I am presenting myself as I am new in the community. I am a student of Medicine in University of Alcala de Henares in Madrid Spain.
> I have a problem when running the dipole fitting tutorial. I have downloaded and set to path this trialfun_oddball_stimlocked.m file.
>
>>> cfg=ft_definetrial(cfg)
> evaluating trialfunction 'trialfun_oddball_stimlocked'
> Warning: channels with different sampling rate not supported, selecting subset of 33 channels at 250.000000 Hz
> Warning: channels with different sampling rate not supported, selecting subset of 33 channels at 250.000000 Hz
> Error using ft_definetrial (line 196)
> no trials were defined, see FT_DEFINETRIAL for help
>
>
> I am running on Temple University Hospital TUH EEG dataset of epilepsy.
>
> Thank you for your help in advance!
> Best,
> Rene Andrade.
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
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> Message: 3
> Date: Thu, 4 Jun 2020 12:41:44 +0430
> From: Bahar Saadatmehr <saadatmehr.b at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Fwd: Question
> Message-ID:
> <CAFP59Yz-9rEHJMCBMEpYU=J0D=5eVU-Md7sBi-yaUv4_Hd7E9Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ---------- Forwarded message ---------
> From: Bahar Saadatmehr <saadatmehr.b at gmail.com>
> Date: Mon, 1 Jun 2020, 13:06
> Subject: Question
> To: <fieldtrip at science.ru.nl>
>
>
> Hello. I was wondering if I could have your help.
> How can I put electrode positions in the .elc format to use it with CURRY?
>
> Thank you in advance for your help.
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> ------------------------------
>
> Message: 4
> Date: Thu, 4 Jun 2020 08:19:53 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Question
> Message-ID: <3600C155-E580-4EAF-A55A-26A981F31D21 at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Bahar,
>
> In general, it does not make sense to forward or resend a message to the discussion in case you haven’t received a reply. The reason for this is that people who invest their time and efforts to answer questions on this list, do so on a voluntary basis. Besides this, your question was so unspecific that I guess nobody knows how to provide an sufficiently informative answer.
>
> I suggest that you 1) try and search on the fieldtrip website yourself, there should be information there which already points into the direction of a solution, and 2) carefully read some of the linked pages on http://www.fieldtriptoolbox.org/discussion_list/, which give you some information about the best way of asking questions on these types of lists.
>
> Best wishes and good luck,
> Jan-Mathijs
>
>
>
> J.M.Schoffelen, MD PhD
> Associate PI, VIDI-fellow - PI, language in interaction
> Telephone: +31-24-3614793
> Physical location: room 00.028
> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>
>
>
>
> On 4 Jun 2020, at 10:11, Bahar Saadatmehr <saadatmehr.b at gmail.com<mailto:saadatmehr.b at gmail.com>> wrote:
>
>
> ---------- Forwarded message ---------
> From: Bahar Saadatmehr <saadatmehr.b at gmail.com<mailto:saadatmehr.b at gmail.com>>
> Date: Mon, 1 Jun 2020, 13:06
> Subject: Question
> To: <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
>
>
> Hello. I was wondering if I could have your help.
> How can I put electrode positions in the .elc format to use it with CURRY?
>
> Thank you in advance for your help.
>
> _______________________________________________
> fieldtrip mailing list
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> https://doi.org/10.1371/journal.pcbi.1002202
>
>
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> End of fieldtrip Digest, Vol 115, Issue 5
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