[FieldTrip] fieldtrip Digest, Vol 104, Issue 20
Paul Dhami
pdhami06 at gmail.com
Wed Jul 24 16:10:11 CEST 2019
Hi Jichen
thank you for the input.
I was talking more in regards to specifically using the cluster-based
permutation method implemented in FieldTrip, which from my understanding,
doesn't support a 2 x 2 between factors ANOVA.
Although I could extract values in a more static manner using times and
regions of interest and just inputting such values in something like SPSS
to conduct a 2 x 2 between factors ANOVA, as there is no strong a priori
hypothesis, I was hoping to do it across all electrodes and times, and thus
using the cluster method for correction for multiple comparisons.
Best,
Paul
On Wed, Jul 24, 2019 at 6:06 AM <fieldtrip-request at science.ru.nl> wrote:
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> Today's Topics:
>
> 1. EEG electrode coordinates (Holly Rossiter)
> 2. Template 3D electrode set for Brain Products' acticap 64ch
> standard (Carolina Ogawa)
> 3. Re: 2 x 2 with Two Between Subjects- ANOVA (王寄辰)
> 4. Re: EEG electrode coordinates (Schoffelen, J.M. (Jan Mathijs))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 23 Jul 2019 12:10:28 +0000
> From: Holly Rossiter <RossiterH at cardiff.ac.uk>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Cc: Adam Doggett <DoggettA at cardiff.ac.uk>, James Kolasinski
> <KolasinskiJ at cardiff.ac.uk>
> Subject: [FieldTrip] EEG electrode coordinates
> Message-ID:
> <
> AM6PR02MB39272DA663C647F9F981C6AEE4C70 at AM6PR02MB3927.eurprd02.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi there,
>
> Our student is using a novel method for coregistering EEG electrodes and
> fiducials using a number of cameras. We therefore have just a list of
> coordinates and fiducials that doesn't come from a standard software
> package like polhemus for example. We are having trouble reading it in to
> use in ft_electroderealign/ft_volumerealign/ft_read_headshape in a form
> that fieldtrip is happy with as it asks for units and a coordinate system
> that it recognises whereas ours is sort of arbitrary. Is there any way to
> create the correct structure so that we can use these coordinates for EEG
> coregistration with an MRI?
>
> Kind regards,
> Holly
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>
> Message: 2
> Date: Tue, 23 Jul 2019 18:12:03 -0300
> From: Carolina Ogawa <carolyogawa at gmail.com>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] Template 3D electrode set for Brain Products'
> acticap 64ch standard
> Message-ID:
> <
> CAPtXX5NVbrv_bfvGKt72rsJcZhQiSF4jeVi5wr+x5c34iVpD_Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear community,
>
> I am trying to use the function "ft_channelrepair", but I can't figure out
> how to configure the EEG electrodes position.
>
> The EEG cap I used is the "Acticap 64ch standard".
>
> I suppose it would work like this:
>
> cfg.elec = ft_read_sens(filename);
>
> data_after_interpolation = ft_channelrepair(cfg,
> data_before_interpolation);
>
>
> in which "filename" = template 3D electrode set available on <
> https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode>.
> There is no template available for the "Acticap 64ch standard" on the
> mentioned website, though.
>
> Then, I thought it would be valid editing the "easycap-M1.txt" template
> (which is available), and transforming it into the "Acticap 64ch standard",
> which apparently would involve deleting 8 channels and renaming two, as
> described on <
> http://www.fieldtriptoolbox.org/template/layout/#acticap-64ch-standard2mat
> >.
>
> However, I don't know how can I do this and I'm not sure if this would be
> the proper way to solve this.
>
> Can someone please tell me:
> 1. If this solution would be valid or if there is any other way to solve
> this?
> 2. In case it is valid, do I have do I have to download the
> "easycap-M1.txt" file, convert it into a ".m" file and then edit it?
>
>
> Thank you in advance!
>
> Carolina Ogawa
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> ------------------------------
>
> Message: 3
> Date: Wed, 24 Jul 2019 14:38:17 +0800
> From: 王寄辰 <wjcpsysci at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] 2 x 2 with Two Between Subjects- ANOVA
> Message-ID:
> <CAOfCAW2g6Q8UEx65ZpAB=
> c5hBZru7wdZ+J3ko_SjoNH512MNgw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Paul,
>
> I think just using the 2-way ANOVA is enough.
> I'm not familiar with this non-parameter test, but ANOVA is robust, even
> the assumption of distribution is not fitted perfactly
> Once you do the 2-way ANOVA, you will get the main effect and interaction,
> if the interaction is significant, you could see the simple effect in
> different level. So why are you want to know "some but not for all"
> interaction effects ?
>
> All best
> Jichen
>
>
> Paul Dhami <pdhami06 at gmail.com> 于2019年7月11日周四 上午7:45写道：
>
> > Dear Fieldtrip community,
> >
> > I have 4 groups of participants that fall into one of four
> > categories/factors:
> >
> > Clinical/Young, Clinical/Old, Healthy/Young, Healthy/Old.
> >
> > I was hoping to test an interaction in a 2-way ANOVA design, with Age
> > group and Clinical group as my two factors.
> >
> > Reading this link:
> >
> >
> http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests/
> >
> > In the first paragraph:
> >
> > You can use cluster-based permutation tests for some but not for all
> >> interaction effects. Specifically, you can only use them for testing
> >> interaction effects in factorial designs with only a single
> >> between-subjects factor
> >
> >
> > Based on the second sentence of only being possible when there is a
> single
> > between-subjects factor, is it safe to say that in my design, I wouldn't
> be
> > able to use cluster-based permutation tests?
> >
> > What would be the best way to analyze such as design than with
> > cluster-based permutation tests? Would it be just a one-way ANOVA with
> the
> > independsamplesF function?
> >
> > Thank you,
> > Paul
> >
> > _______________________________________________
> > fieldtrip mailing list
> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > https://doi.org/10.1371/journal.pcbi.1002202
> >
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> ------------------------------
>
> Message: 4
> Date: Wed, 24 Jul 2019 08:16:51 +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] EEG electrode coordinates
> Message-ID: <087A1E0F-E6F4-462B-874E-D0DD40CEA033 at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Holly,
>
> Although the coordinates might be ‘arbitrary’, they are defined with
> respect to a certain reference frame, right? If what you call the
> ‘fiducial’ locations are well-defined landmarks that are used to create one
> of the supported coordinate systems, then it would be relatively
> straightforward to map the points in your representation to coordinates
> that can be used for coregistration.
>
> Procedure:
>
> 0) write some glue code, so that you can either read in, or represent your
> point cloud in a fieldtrip-like data structure (as would be outputted by
> ft_read_headshape). That is, either write a reading function (that can be
> plugged in), or convert your point cloud into a data structure (containing
> obj.pos at least) -> needed for step 2.
> 1) use ft_headcoordinates to create a transformation matrix that maps from
> your ‘arbitrary space’ to a known coordinate system. For this you need the
> fiducials to coincide with known landmarks.
> 2) use the derived transformation matrix to transform the coordinate
> system of your headshape object into the desired coordinate system
> (ft_transform_geometry).
>
> Ideally, all steps are taken care of by ft_read_headshape, provided the
> file with the electrodes and fiducials allows for automatic extraction of
> the fiducial locations.
>
> Best wishes,
> Jan-Mathijs
>
>
> On 23 Jul 2019, at 14:10, Holly Rossiter <RossiterH at cardiff.ac.uk<mailto:
> RossiterH at cardiff.ac.uk>> wrote:
>
> Hi there,
>
> Our student is using a novel method for coregistering EEG electrodes and
> fiducials using a number of cameras. We therefore have just a list of
> coordinates and fiducials that doesn’t come from a standard software
> package like polhemus for example. We are having trouble reading it in to
> use in ft_electroderealign/ft_volumerealign/ft_read_headshape in a form
> that fieldtrip is happy with as it asks for units and a coordinate system
> that it recognises whereas ours is sort of arbitrary. Is there any way to
> create the correct structure so that we can use these coordinates for EEG
> coregistration with an MRI?
>
> Kind regards,
> Holly
> _______________________________________________
> 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 104, Issue 20
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