[FieldTrip] fieldtrip Digest, Vol 92, Issue 21
zhipeng li
lizhipeng3924 at gmail.com
Tue Jul 31 15:52:11 CEST 2018
-
Thank you very much for your reply.@ Alexandre Gramfort
But with your answer, my question remains unsolved . On my computer, I
can't find any files on mne setup, including any of your list.
Following the instructions on the site, I made this step
-
But the setup file can't be found,I hope you can give me further
guidance.
-
Yours,
-
zhipeng
2018-07-30 18:00 GMT+08:00 <fieldtrip-request at science.ru.nl>:
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> Today's Topics:
>
> 1. Re: Regarding Tutorial: Preprocessing and averaging of
> multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=)
> 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort)
> 3. Postdoc position to work with human single neurons and LFPs,
> 9 days left to apply! (Simon Hanslmayr)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Jul 2018 08:47:25 +0200
> From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" <jorn at artinis.com>
> To: "'FieldTrip discussion list'" <fieldtrip at science.ru.nl>, "'Arana,
> S.L. \(Sophie\)'" <S.Arana at donders.ru.nl>
> Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and
> averaging of multi-channel NIRS data
> Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sunny,
>
>
>
> Yes, the FieldTrip NIRS plugin works for all our devices.
>
>
>
> With best regards,
>
> Jörn
>
>
>
> --
> Jörn M. Horschig, PhD, Project Leader & Software Engineer
> <http://www.artinis.com/> Artinis Medical Systems | +31 481 350 980
>
> Sign up for our NIRS newsletter <http://artinis.us3.list-
> manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46>
>
>
>
> From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Sunny p
> Sent: Friday, July 27, 2018 20:41
> To: Arana, S.L. (Sophie) <S.Arana at donders.ru.nl>
> Cc: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging
> of multi-channel NIRS data
>
>
>
> Hello Sophie,
>
>
>
> Once this tutorial is fully developed, Can we use this for OCTAMON (
> https://www.artinis.com/octamon/) ?
>
>
>
> Thanks for your understanding and support.
>
>
>
> Best Regards,
>
> Sunny
>
>
>
> On Wed, Jul 25, 2018 at 12:35 PM, Sunny p <sunnypitt1965 at gmail.com
> <mailto:sunnypitt1965 at gmail.com> > wrote:
>
> Hello Sophie,
>
>
>
> Thanks a lot for providing this code. I am making some changes that are
> useful. Can you please inform what is the variable 'data_func' in the code
> relates to. This is the last undefined variable in code.
>
>
>
> Thanks for your understanding and support.
>
>
>
> Best Regards,
>
> Sunny
>
>
>
> On Wed, Jul 25, 2018 at 8:22 AM, Sunny p <sunnypitt1965 at gmail.com <mailto:
> sunnypitt1965 at gmail.com> > wrote:
>
> Hello Sophie,
>
>
>
> Thanks a lot for your clarification. This is very useful.
>
>
>
> Sunny
>
>
>
> On Wednesday, July 25, 2018, Arana, S.L. (Sophie) <S.Arana at donders.ru.nl
> <mailto:S.Arana at donders.ru.nl> > wrote:
>
> Dear Sunny,
>
>
>
> the multi-channel NIRS data tutorial is currently under construction and
> will hopefully be fully available in a couple of weeks. Until then, there
> might still be some inconsistencies such as the one you have encountered.
>
>
>
> The variable you refer to is indeed missing. It refers to a filtered
> version of the data, and you can created it by running the following code
> before the epoching.
>
>
>
> cfg = [];
>
> cfg.hpfilter = 'yes';
>
> cfg.hpfreq = 0.01;
>
> data_flt = ft_preprocessing(cfg,data_down);
>
>
>
> This should help you to continue with the tutorial, but please do keep in
> mind that we are currently working on it and you might encounter some other
> inconsistencies still later on.
>
>
>
> Best,
>
> Sophie
>
>
>
>
> _____
>
>
> From: fieldtrip [fieldtrip-bounces at science.ru.nl <mailto:
> fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [
> sunnypitt1965 at gmail.com <mailto:sunnypitt1965 at gmail.com> ]
> Sent: Tuesday, July 24, 2018 9:24 PM
> To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of
> multi-channel NIRS data
>
> Hello All Good Day,
>
>
>
> Hope you are doing fine,
>
>
>
> Thanks a lot for providing with fieldtrip which is really useful to
> analyze fNIRS data. I have an issue in the "Preprocessing and averaging of
> multi-channel NIRS data" tutorial. Can you please help me with this issue?
>
>
>
> Issue: In the "Preprocessing and averaging of multi-channel NIRS data"
> tutorial " <http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel>
> http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel
>
>
>
> The "Epoch" section consists of a variable "data_flt.fsample" where
> "data_flt" variable is not defined. Can you please inform what is this
> variable related to? as this is needed to complete my analysis.
>
>
>
>
>
>
>
>
>
> Thanks for your understanding and support
>
>
>
> Best Regards,
> Sunny
>
>
>
>
>
>
>
>
>
>
> <http://www.avg.com/email-signature?utm_medium=email&
> utm_source=link&utm_campaign=sig-email&utm_content=emailclient>
>
> Virus-free. <http://www.avg.com/email-signature?utm_medium=email&
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>
>
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 30 Jul 2018 08:49:46 +0200
> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19
> Message-ID:
> <CADeotZqiKpnpykgvhfTQmoSONaBkEikFf9eyi379chfdzKkntg at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> it's the $MNE_ROOT/bin folder
> after setting the MNE_ROOT env variable to the folder that contains
> the MNE command line tools.
>
> HTH
> Alex
> On Mon, Jul 30, 2018 at 3:52 AM zhipeng li <lizhipeng3924 at gmail.com>
> wrote:
> >
> > External Email - Use Caution
> >
> > First of all, thank you very much for your reply @ Alexandre Gramfort .
> >
> > But none of the files you listed were found in bin
> >
> >
> > This is all the files contained in bin,
> >
> > I need your further help.
> >
> > Yours,
> > zhipeng
> >
> >
> > 2018-07-29 18:00 GMT+08:00 <fieldtrip-request at science.ru.nl>:
> >>
> >> Send fieldtrip mailing list submissions to
> >> fieldtrip at science.ru.nl
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >> or, via email, send a message with subject or body 'help' to
> >> fieldtrip-request at science.ru.nl
> >>
> >> You can reach the person managing the list at
> >> fieldtrip-owner at science.ru.nl
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of fieldtrip digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >> 1. A question about MEG source reconstruction (zhipeng li)
> >> 2. Re: A question about MEG source reconstruction
> >> (Alexandre Gramfort)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Sun, 29 Jul 2018 10:55:37 +0800
> >> From: zhipeng li <lizhipeng3924 at gmail.com>
> >> To: fieldtrip at science.ru.nl
> >> Subject: [FieldTrip] A question about MEG source reconstruction
> >> Message-ID:
> >> <CAAUszHHfd_jTwxGTnNzrbR=cBNUpremEz=PBhyCDYEhUGe=NQw@
> mail.gmail.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> Dear all,
> >> When I was about to create a sourcemodel, I ran into a problem.The
> >> documentary which I refers to is Tutorial documentation>Source
> >> reconstruction of event-related fields using minimum-norm
> >> estimation>Creating a sourcemodel for source-reconstruction of MEG or
> EEG
> >> data.When I installed MNE as their description, I found that the.sh file
> >> doesn't exist.The command I am using is posted below as a
> >> picture.Therefore, the following steps cannot be carried out.
> >> I would appreciate it if you could help me.
> >> Yours,
> >> zhipeng
> >> -------------- next part --------------
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> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Sun, 29 Jul 2018 10:03:59 +0200
> >> From: Alexandre Gramfort <alexandre.gramfort at inria.fr>
> >> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> >> Subject: Re: [FieldTrip] A question about MEG source reconstruction
> >> Message-ID:
> >> <CADeotZrzo1Z8XREpbHXOqXn3tTDQCLE1B0f0QGjrU4HZWN6x4Q at mail.
> gmail.com>
> >> Content-Type: text/plain; charset="UTF-8"
> >>
> >> hi,
> >>
> >> indeed there is a typo:
> >>
> >> $ cd $MNE_ROOT
> >> $ ls bin/mne_setup*
> >> bin/mne_setup bin/mne_setup_matlab_csh
> >> bin/mne_setup_mri bin/mne_setup_source_space
> >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh
> >>
> >> depending on your shell it can be
> >>
> >> source $MNE_ROOT/bin/mne_setup_sh
> >>
> >> HTH
> >> Alex
> >>
> >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li <lizhipeng3924 at gmail.com>
> wrote:
> >> >
> >> > External Email - Use Caution
> >> >
> >> > Dear all,
> >> > When I was about to create a sourcemodel, I ran into a problem.The
> documentary which I refers to is Tutorial documentation>Source
> reconstruction of event-related fields using minimum-norm
> estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG
> data.When I installed MNE as their description, I found that the.sh file
> doesn't exist.The command I am using is posted below as a
> picture.Therefore, the following steps cannot be carried out.
> >> > I would appreciate it if you could help me.
> >> > Yours,
> >> > zhipeng
> >> >
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > fieldtrip mailing list
> >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >> > https://doi.org/10.1371/journal.pcbi.1002202
> >> >
> >> >
> >> > 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
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> >>
> >>
> >> ------------------------------
> >>
> >> Subject: Digest Footer
> >>
> >> _______________________________________________
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> >> https://doi.org/10.1371/journal.pcbi.1002202
> >>
> >>
> >> ------------------------------
> >>
> >> End of fieldtrip Digest, Vol 92, Issue 19
> >> *****************************************
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > https://doi.org/10.1371/journal.pcbi.1002202
> >
> >
> > 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
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> > contains patient information, please contact the Partners Compliance
> HelpLine at
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> ------------------------------
>
> Message: 3
> Date: Mon, 30 Jul 2018 09:23:31 +0000
> From: Simon Hanslmayr <S.Hanslmayr at bham.ac.uk>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Postdoc position to work with human single
> neurons and LFPs, 9 days left to apply!
> Message-ID:
> <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Fieldtrippers,
>
> We are pleased to announce an open postdoc position in our group to work
> with human single neurons and LFP recordings in an exciting memory project
> funded by the ERC. The position is initially for 2 years with an option for
> 1 year extension. The negotiable start date is 1st Oct. Preliminary data
> has been collected and is waiting to be analysed. If you have strong
> electrophysiological analytical skills and are interested then please do
> not hesitate to apply here: http://www.memorybham.com/open-positions/
>
> If you have any questions then please do not hesitate to contact me.
>
> Best wishes,
> Dr. Simon Hanslmayr
> Reader in Cognitive Neuroscience
> Royal Society Wolfson Research Merit Award Holder
> School of Psychology
> Hills Building 2.37
> University of Birmingham
> Edgbaston
> Birmingham
> B15 2TT
> UK
>
> Tel +44 121 4146203
> http://www.memorybham.com/people/#/simon-hanslmayr/
> [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif]
>
>
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>
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>
> ------------------------------
>
> End of fieldtrip Digest, Vol 92, Issue 21
> *****************************************
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