[FieldTrip] plotting neighbours
victoria schroeder
vic.schroeder2 at gmail.com
Mon Jan 18 17:45:22 CET 2016
Dear Tzvetan
I get your point. I am only using that gradiometers. However, in the text
which i copied into the previous email it is stated that ft_combineplanar
is used for 'plotting the two different gradiometers together'. They
mention gradiometers specifically. Also when running the code it is clear
that the gradiometers not the magnetometers are combined. This is the
resulting matrix when running the tutorial :
[image: Inline-Bild 1]
With this in mind, can you clarify why the toturial only uses
magnetometers? As i understand it , it uses gradiometers.
Thank you a lot
Victoria
2016-01-18 12:59 GMT+00:00 Tzvetan Popov <tzvetan.popov at uni-konstanz.de>:
> Hi Victoria,
> well if you work with the magnetometers yes. Maybe I misunderstood your
> previous posts. Yet this configuration from your post below cfg.channel =
> 'MEGGRAD’; results in time-frequency representation of power on the planar
> gradiometers only. In that case neither ft_megplanar nor ft_combineplanar
> are appropriate since the data stems from planar gradiometers. The tutorial
> you mentioned deals only with the magnetometers thus ft_megplanar and
> ft_combineplanar are used.
>
> best
> tzvetan
>
>
> Dear Tzvetan
>
> Are you sure about that in the tutorial
> http://www.fieldtriptoolbox.org/tutorial/natmeg/preprocessing neuromag
> data is used and ft_combineplanar is used to combine the gradiometers. This
> is a paragraph from this tutorial:
>
> In fact, we are now plotting the two different gradiometers together. You
> can see the channel locations being in pairs, one above the other. They are
> in reality, however, at the same location but oriented differently -
> radially and axially *with respect to the surface of the helmet*. They
> can thereby pick up both radial orientations of the magnetic fields. To use
> them properly for the purpose of plotting, we should therefor combine them
> first, adding their fields.
>
> TFR_left_MEG_comb = ft_combineplanar([],TFR_left_MEG);
> TFR_right_MEG_comb = ft_combineplanar([],TFR_right_MEG);
>
> cfg = [];
> cfg.baseline = [-0.5 -0.1];
> cfg.baselinetype = 'absolute';
> cfg.xlim <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/xlim.html> = [0.4 0.8];
> cfg.ylim <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/ylim.html> = [15 25];
> cfg.zlim <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/zlim.html> = [-4e-24 4e-24];
> cfg.marker = 'on';
> cfg.layout = 'neuromag306cmb.lay';
> figure <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/figure.html>;
> ft_topoplotTFR(cfg, TFR_left_MEG_comb);print <http://www.mathworks.com/access/helpdesk/help/techdoc/ref/print.html> -dpng natmeg_freq13.png
>
> Thus, it should be possible to use ft_combineplanar for neuromag data.
> What do you think?
>
> Cheers
> Victoria
>
> 2016-01-16 18:00 GMT+00:00 Tzvetan Popov <tzvetan.popov at uni-konstanz.de>:
>
>> Dear Victoria,
>> you should remove the ft_combineplanar step from your analysis pipeline.
>> This function takes input from ft_megplanar. The latter is applied only to
>> magnetometers or axial gradiometers.
>>
>> best
>> tzvetan
>>
>>
>> Hi !
>>
>> I am working with a neuromag system and want to do cluster based
>> permutation tests with time frequency data. However, before running the
>> stats i would like to check the clusters which are formed by
>> ft_prepare_neighbours. Thus i use ft_neighbourplot. When looking at the
>> plot and clicking on the channels i would expect to see something like :
>>
>> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623,
>> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123,
>> MEG1242+1243*
>>
>> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433,
>> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833,
>> MEG2242+2243*
>>
>> however what i see is:
>>
>> *Selected channel MEG0741, which has 0 neighbours: *
>> *Selected channel MEG0731, which has 0 neighbours: *
>> *Selected channel MEG0742+0743, which has 7 neighbours: MEG0432+0433,
>> MEG0712+0713, MEG0722+0723, MEG0732+0733, MEG1822+1823, MEG1832+1833,
>> MEG2242+2243*
>> *Selected channel MEG0711, which has 0 neighbours: *
>> *Selected channel MEG0741, which has 0 neighbours: *
>>
>> It is absolutely random when the correct output occurs. When clicking on
>> a particular channel it would randomly show me the following results:
>>
>> *Selected channel MEG1032+1033, which has 7 neighbours: MEG0622+0623,
>> MEG1012+1013, MEG1022+1023, MEG1042+1043, MEG1112+1113, MEG1122+1123,
>> MEG1242+1243*
>>
>> or
>>
>> *Selected channel MEG1031, which has 0 neighbours: *
>>
>> Do you have any suggestions why this happen? Are the channels not grouped
>> correctly?
>>
>> Below is the code starting from the time-frequency analysis of the data.
>>
>> Thank you very much
>> Victoria
>>
>> cfg = [];
>> cfg.output = 'pow';
>> cfg.channel = 'MEGGRAD';
>> cfg.method = 'mtmconvol';
>> cfg.taper = 'hanning';
>> cfg.foi = [2:2:30];
>> %cfg.keeptrials = 'yes'; for stats keep trials
>> cfg.t_ftimwin = ones(length(cfg.foi),1).*0.5; % length of time
>> window = 0.5 sec
>> cfg.toi = [-1.3:0.05:1];
>> cfg.keeptrials = 'yes';
>> FreqCon = ft_freqanalysis(cfg, Con_clean);
>> FreqIncon = ft_freqanalysis(cfg, Incon_clean);
>>
>> %combine planar
>> cfg = [];
>> cfg.method ='sum';
>> ComCon = ft_combineplanar(cfg,FreqCon);
>> ComIncon = ft_combineplanar(cfg, FreqIncon);
>>
>> % plot neighbours
>> cfg=[];
>> cfg.method = 'triangulation';
>> cfg.layout = 'neuromag306cmb.lay';
>> ft_neighbourplot(cfg,ComCon)
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