[FieldTrip] Grand mean
Sarah Kirchler
sarah.kirchler at gmail.com
Fri May 15 09:51:38 CEST 2020
Hi Jan-Mathijs,
thank you for your answer, I do my best to explain your questions.
The Problem is, that I don't have datastructures that I can combine (but I
would like to have them). So that's the primary question.
These are the steps I already did:
I measured, as mentioned before, with an EEG the visual stimulation via two
frequencies (SSVEP).
I preprocessed my data with ft_preprocessing (cuttet it in segments, did
filtering, concenated the cfg-Matrix with the trialinfo of my clean
preprocessed data and then, with a loop, I made the SSVEP-analysis for all
my subjects (ft_timelockanalysis and ft_frequencyanalysis).
I made the timelockanalysis for the two frequencies separately and for the
control-target (which in this case is something like a baseline-condition
for measuring the average activation of the subject-brains, so I can differ
the target-activation from it. Now I added the Grand Mean:
gm_1 = ft_timelockgrandaverage(cfggm, tl1); gm_2 =
ft_timelockgrandaverage(cfggm, tl2);)
separately for the two frequencies.
I am now failing when trying to make the grand mean for the difference and
the sum of the two frequencies. I tried to make something like this for the
sum:
gm_3 =ft_timelockgrandaverage(cfggm, tl1, tl2)
but I don't think it's correct.
So I tried to make the difference like that:
cfg = [];
cfg.parameter = 'avg';
cfg.operation = 'x1-x2';
difftopo12 = ft_math(cfg, gm_1, gm_2);
figure
cfg=[];
cfg.xlim = [0.1:0.05:0.5];
cfg.zlim = [-2 2];
cfg.layout = '63equidistant_lay.mat';
ft_topoplotER(cfg, difftopo12);
But for this procedure I need datastructures for x1 and x2, which I don't
have.
(Fieldtrip: In the specification of the mathematical operation, x1 is the
parameter obtained
from the first input data structure, x2 from the second, etc.)
So I have a way that would work but not the datastructures.
I tried to make the datastructures like this:
tl1{vpn} = ft_timelockanalysis(cfg,data) (vpn is the name I gave the
subjects when looping them for the timelock- and frequencyanalysis. --> for
for vpn = 1:length(cleannames)...)
and then to make the grand mean like this:
gm_1 = ft_timelockgrandaverage(cfg, tl1{:});
but it doesn't work.
I would be really thankfull if you yould give me some help to find the
error,
Sarah
Am Do., 14. Mai 2020 um 19:12 Uhr schrieb Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl>:
> Dear Sarah,
>
> Thanks for clarifying your question. Now, could you provide the readership
> with some additional information about how you constructed these data
> structures, and how you tried to combine them, otherwise we (i.e. the
> people who’d want to think along with you to fix your problem) don’t know
> where to start.
>
> Jan-Mathijs
>
>
> On 14 May 2020, at 09:32, Sarah Kirchler <sarah.kirchler at gmail.com> wrote:
>
> Dear Jan-Mathijs,
>
> thank you for your answer. I see, i expressed myself not very clear.
> I'd like to make the Grand mean for the difference and the sum between two
> specific frequencies I measured visually wih a SSVEP.
> I'd like to do this because I'm interested in how the frequencies are
> processed in the brain regarding each other and a control measurement.
> I'm not sure if I can make the difference already when I make the GM or
> later, when I plot the topography.
> I tried to make this by building a datastructure that contains the GM of
> the one and the other frequency and then usw ft_math to compare them. But
> this doesn't work for me.
> Maybe thats enough information for you to understand the problem better,
> I'm a beginner so I often explain my problems a little bit confusing, sorry
> for that.
>
> Best,
>
> Sarah
>
> Am Mi., 13. Mai 2020 um 15:30 Uhr schrieb Schoffelen, J.M. (Jan Mathijs) <
> jan.schoffelen at donders.ru.nl>:
>
>> Dear Sarah,
>>
>> It is not clear what error message you get, nor why you think you should
>> ft_timelockanalysis/ft_timelockgrandaverage/ft_topoplotER.
>>
>> Some pointers:
>> -For a mathematical operation to be applied to numeric data that resides
>> within a fieldtrip-style data structure you’d use ft_math.
>> -What you want to do (i.e. adding or subtracting estimates of frequency
>> specific power estimated for different frequency bins) probably requires
>> some manual intervention with the data, because FT will likely prevent you
>> to do so, since it checks whether the frequency bins for the to-be-combined
>> data structures match. I could type some recipe now, but since you are not
>> too clear on the details so I’d rather not spend time on that now. Also,
>> I’d like to give other people the opportunity to chime in here :).
>>
>> Best wishes,
>> Jan-Mathijs
>>
>> On 11 May 2020, at 16:43, sarah.kirchler at gmail.com wrote:
>>
>> Dear Fieldtrip Users,
>>
>> thank you for all the help you’ve given me already.
>> Now I am trying to make the sum and the difference of the Grand mean
>> from/between two frequencies I measured with an EEG.
>> I read that it is possible to make a datastructure using {} within
>> ft_timelockbaseline and then use the option cfg.operation(x1-x2 and so on)
>> as a operation of function ft_topoplotER to make this sum/these differences.
>>
>> Now my Problem is that I don’t need to make the baselinecorrection via
>> ft_timelockbaseline because I don’t have the baseline in the datasegment
>> I’m interested in. So I tried to build the datastructure for cfg.operation
>> within ft_timelockanalysis but Fieldtrip doesn’t allow this and I get an
>> error message.
>>
>> My questions are now:
>> 1. Can I make the difference also within the ft_timelockgrandavverage
>> function or do I have to make the difference lawer in ft_topoplotER?
>> 2. If so, how can I or form a datastructure I can use in cfg.operation or
>> make the difference differently with some other function?
>>
>> I hope you understand me,
>> to all you extraordinary brains: thank you in advance,
>>
>> Sarah
>>
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