<div dir="ltr">Hi Jichen<div><br></div><div>thank you for the input. </div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Best,</div><div>Paul</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 24, 2019 at 6:06 AM <<a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send fieldtrip mailing list submissions to<br>
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<br>
Today's Topics:<br>
<br>
1. EEG electrode coordinates (Holly Rossiter)<br>
2. Template 3D electrode set for Brain Products' acticap 64ch<br>
standard (Carolina Ogawa)<br>
3. Re: 2 x 2 with Two Between Subjects- ANOVA (王寄辰)<br>
4. Re: EEG electrode coordinates (Schoffelen, J.M. (Jan Mathijs))<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 23 Jul 2019 12:10:28 +0000<br>
From: Holly Rossiter <<a href="mailto:RossiterH@cardiff.ac.uk" target="_blank">RossiterH@cardiff.ac.uk</a>><br>
To: "<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Cc: Adam Doggett <<a href="mailto:DoggettA@cardiff.ac.uk" target="_blank">DoggettA@cardiff.ac.uk</a>>, James Kolasinski<br>
<<a href="mailto:KolasinskiJ@cardiff.ac.uk" target="_blank">KolasinskiJ@cardiff.ac.uk</a>><br>
Subject: [FieldTrip] EEG electrode coordinates<br>
Message-ID:<br>
<<a href="mailto:AM6PR02MB39272DA663C647F9F981C6AEE4C70@AM6PR02MB3927.eurprd02.prod.outlook.com" target="_blank">AM6PR02MB39272DA663C647F9F981C6AEE4C70@AM6PR02MB3927.eurprd02.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi there,<br>
<br>
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?<br>
<br>
Kind regards,<br>
Holly<br>
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Message: 2<br>
Date: Tue, 23 Jul 2019 18:12:03 -0300<br>
From: Carolina Ogawa <<a href="mailto:carolyogawa@gmail.com" target="_blank">carolyogawa@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Template 3D electrode set for Brain Products'<br>
acticap 64ch standard<br>
Message-ID:<br>
<<a href="mailto:CAPtXX5NVbrv_bfvGKt72rsJcZhQiSF4jeVi5wr%2Bx5c34iVpD_Q@mail.gmail.com" target="_blank">CAPtXX5NVbrv_bfvGKt72rsJcZhQiSF4jeVi5wr+x5c34iVpD_Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear community,<br>
<br>
I am trying to use the function "ft_channelrepair", but I can't figure out<br>
how to configure the EEG electrodes position.<br>
<br>
The EEG cap I used is the "Acticap 64ch standard".<br>
<br>
I suppose it would work like this:<br>
<br>
cfg.elec = ft_read_sens(filename);<br>
<br>
data_after_interpolation = ft_channelrepair(cfg, data_before_interpolation);<br>
<br>
<br>
in which "filename" = template 3D electrode set available on <<br>
<a href="https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode" rel="noreferrer" target="_blank">https://github.com/fieldtrip/fieldtrip/tree/master/template/electrode</a>>.<br>
There is no template available for the "Acticap 64ch standard" on the<br>
mentioned website, though.<br>
<br>
Then, I thought it would be valid editing the "easycap-M1.txt" template<br>
(which is available), and transforming it into the "Acticap 64ch standard",<br>
which apparently would involve deleting 8 channels and renaming two, as<br>
described on <<br>
<a href="http://www.fieldtriptoolbox.org/template/layout/#acticap-64ch-standard2mat" rel="noreferrer" target="_blank">http://www.fieldtriptoolbox.org/template/layout/#acticap-64ch-standard2mat</a>>.<br>
<br>
However, I don't know how can I do this and I'm not sure if this would be<br>
the proper way to solve this.<br>
<br>
Can someone please tell me:<br>
1. If this solution would be valid or if there is any other way to solve<br>
this?<br>
2. In case it is valid, do I have do I have to download the<br>
"easycap-M1.txt" file, convert it into a ".m" file and then edit it?<br>
<br>
<br>
Thank you in advance!<br>
<br>
Carolina Ogawa<br>
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Message: 3<br>
Date: Wed, 24 Jul 2019 14:38:17 +0800<br>
From: 王寄辰 <<a href="mailto:wjcpsysci@gmail.com" target="_blank">wjcpsysci@gmail.com</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] 2 x 2 with Two Between Subjects- ANOVA<br>
Message-ID:<br>
<CAOfCAW2g6Q8UEx65ZpAB=<a href="mailto:c5hBZru7wdZ%2BJ3ko_SjoNH512MNgw@mail.gmail.com" target="_blank">c5hBZru7wdZ+J3ko_SjoNH512MNgw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Paul,<br>
<br>
I think just using the 2-way ANOVA is enough.<br>
I'm not familiar with this non-parameter test, but ANOVA is robust, even<br>
the assumption of distribution is not fitted perfactly<br>
Once you do the 2-way ANOVA, you will get the main effect and interaction,<br>
if the interaction is significant, you could see the simple effect in<br>
different level. So why are you want to know "some but not for all"<br>
interaction effects ?<br>
<br>
All best<br>
Jichen<br>
<br>
<br>
Paul Dhami <<a href="mailto:pdhami06@gmail.com" target="_blank">pdhami06@gmail.com</a>> 于2019年7月11日周四 上午7:45写道：<br>
<br>
> Dear Fieldtrip community,<br>
><br>
> I have 4 groups of participants that fall into one of four<br>
> categories/factors:<br>
><br>
> Clinical/Young, Clinical/Old, Healthy/Young, Healthy/Old.<br>
><br>
> I was hoping to test an interaction in a 2-way ANOVA design, with Age<br>
> group and Clinical group as my two factors.<br>
><br>
> Reading this link:<br>
><br>
> <a href="http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests/" rel="noreferrer" target="_blank">http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests/</a><br>
><br>
> In the first paragraph:<br>
><br>
> You can use cluster-based permutation tests for some but not for all<br>
>> interaction effects. Specifically, you can only use them for testing<br>
>> interaction effects in factorial designs with only a single<br>
>> between-subjects factor<br>
><br>
><br>
> Based on the second sentence of only being possible when there is a single<br>
> between-subjects factor, is it safe to say that in my design, I wouldn't be<br>
> able to use cluster-based permutation tests?<br>
><br>
> What would be the best way to analyze such as design than with<br>
> cluster-based permutation tests? Would it be just a one-way ANOVA with the<br>
> independsamplesF function?<br>
><br>
> Thank you,<br>
> Paul<br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> <a href="https://doi.org/10.1371/journal.pcbi.1002202" rel="noreferrer" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><br>
><br>
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Message: 4<br>
Date: Wed, 24 Jul 2019 08:16:51 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)" <<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] EEG electrode coordinates<br>
Message-ID: <<a href="mailto:087A1E0F-E6F4-462B-874E-D0DD40CEA033@donders.ru.nl" target="_blank">087A1E0F-E6F4-462B-874E-D0DD40CEA033@donders.ru.nl</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Holly,<br>
<br>
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.<br>
<br>
Procedure:<br>
<br>
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.<br>
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.<br>
2) use the derived transformation matrix to transform the coordinate system of your headshape object into the desired coordinate system (ft_transform_geometry).<br>
<br>
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.<br>
<br>
Best wishes,<br>
Jan-Mathijs<br>
<br>
<br>
On 23 Jul 2019, at 14:10, Holly Rossiter <<a href="mailto:RossiterH@cardiff.ac.uk" target="_blank">RossiterH@cardiff.ac.uk</a><mailto:<a href="mailto:RossiterH@cardiff.ac.uk" target="_blank">RossiterH@cardiff.ac.uk</a>>> wrote:<br>
<br>
Hi there,<br>
<br>
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?<br>
<br>
Kind regards,<br>
Holly<br>
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End of fieldtrip Digest, Vol 104, Issue 20<br>
******************************************<br>
</blockquote></div>