[FieldTrip] MEG Time-Frequency testing (ft_freqstatistics)

Tue Dec 21 08:20:55 CET 2010

Hi Kambiz,

I don't fully understand your question. Do you want to know what the 
fields mean that come out of ft_freqstatistics, or did you hacked some 
output, and want to know how to make the file in a way that FieldTrip 
can plot it? In either case, check out this tutorial:
"Cluster-based permutation tests on time-frequency data"
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq
Here you can find description of ft_freqstatistics with the cluster 
permutation routine, and it points to where you can find output items 
for ft_freqstatistics on the ftp server
"The output can also be obtained from 
ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/cluster_permutation_freq/stat_freq_planar_FICvsFC.mat."

Hope this helps,
Ingrid

Ingrid Nieuwenhuis PhD
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650

On 20-12-2010 13:46, Tavabi, Kambiz wrote:
> Greetings - where can I find a description of the output items for ft_freqstatistics? Or atleast the essential fields necessary for sensibly plotting results of the cluster permutation routine?
> -K.
> -------------------------------------------------------------
> Kambiz Tavabi PhD
> Biomedical Imaging Laboratory
> The Children's Hospital of Philadelphia
> 34th Street and Civic Center Boulevard
> Philadelphia, Pa. 19104
> Tel: 267.426.0302
> email: tavabik at email.chop.edu
> -------------------------------------------------------------
> ________________________________________
> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Nathan Weisz [nathanweisz at mac.com]
> Sent: Thursday, December 16, 2010 4:48 AM
> To: Email discussion list for the FieldTrip project
> Subject: Re: [FieldTrip] MEG Time-Frequency testing (ft_freqstatistics)
>
> hi kambiz,
>
> did you look at the actual p-values of you clusters?
>
> the code that you posted plots only the positive cluster (doesn't mean it's significant). so it's no surprise that you don't see a blue blob, because you masked it. look at data structure and there should also be a field 'negclusters' and a 'negclusterlabelmat'.
>
> good luck,
> n
>
> On 16.12.2010, at 09:21, Eric Maris wrote:
>
>> Kambiz,
>>
>>>> Have a look at the (channel,frequency)-specific paired t-tests.
>>> I am not sure exactly what you mean. By 'specific' do you mean sample
>>> wise testing in a narrow frequency range?
>> Sorry, I forgot that you have time resolution. I mean the
>> (channel,time,frequency)-specific paired t-tests, which are in the output of
>> freqstatistics.
>>
>>
>> Best,
>>
>> Eric
>>
>>
>>> -K.
>>> -------------------------------------------------------------
>>> Kambiz Tavabi PhD
>>> Biomedical Imaging Laboratory
>>> The Children's Hospital of Philadelphia
>>> 34th Street and Civic Center Boulevard
>>> Philadelphia, Pa. 19104
>>> Tel: 267.426.0302
>>> email: tavabik at email.chop.edu
>>> -------------------------------------------------------------
>>> ________________________________________
>>> From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl]
>>> On Behalf Of Eric Maris [e.maris at donders.ru.nl]
>>> Sent: Wednesday, December 15, 2010 5:36 PM
>>> To: 'Email discussion list for the FieldTrip project'
>>> Subject: Re: [FieldTrip] MEG Time-Frequency testing (ft_freqstatistics)
>>>
>>> Dear Kambiz,
>>>
>>>
>>>> Greetings Fieldstrippers
>>> "Fieldtrippers" may have connotations that a scientist does not always
>>> appreciate, but what to think of "Fieldstrippers"?
>>>
>>>> My problem with the results in the attachment is that in the grand
>>>> averages there is an obvious event related desynchrony (cold colors,
>>>> negative values) difference between 0.4-0.8sec; 10-40hz which somehow
>>>> doesn't get picked up, but the small blip of noise/event-related
>>>> synchrony (hot colors, positive values) c. 0.5sec at 50Hz is revealed
>>>> as different between conditions by the permutations!
>>> Have a look at the (channel,frequency)-specific paired t-tests. Do
>>> these
>>> detect the big cold blob? If not, the variance across subjects is
>>> probably
>>> large.
>>>
>>>
>>> Best,
>>>
>>> Eric Maris
>>>
>>>
>>>
>>>
>>>
>>>
>>> To carry out the
>>>> permutations I used
>>>> cfg.method           = 'montecarlo';
>>>> cfg.statistic        = 'depsamplesT';
>>>> cfg.correctm         = 'cluster';
>>>> cfg.clusteralpha     = 0.05;
>>>> cfg.clusterstatistic = 'maxsum';
>>>> cfg.neighbours       = [ ];
>>>> cfg.tail             = 0;
>>>> cfg.clustertail      = 0;
>>>> cfg.alpha            = 0.05;
>>>> cfg.numrandomization = 500;
>>>> So I presume that the result is not due to a signs (pos/neg values)
>>>> issue, if I am using a two-tailed test. Changing cfg.tail&
>>>> cfg.clustertail to 1 makes little to no difference, and a value of -1
>>>> results in errors. Basically, I'd appreciate if someone, based on
>>> what
>>>> is observable in the grand averages, could confirm that the
>>> permutation
>>>> result makes sense? And if not then some advice on what I am doing
>>>> wrong. Thank you. -Kambiz
>>>>
>>>> -K.
>>>> ------------------------------------------------------------
>>>> Kambiz Tavabi PhD
>>>> Biomedical Imaging Laboratory
>>>> The Children's Hospital of Philadelphia
>>>> 34th Street and Civic Center Boulevard
>>>> Philadelphia, Pa. 19104
>>>> Tel: 267.426.0302
>>>> email: tavabik at email.chop.edu<mailto:tavabik at email.chop.edu>
>>>> ------------------------------------------------------------
>>>
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