[FieldTrip] Cluster-based analysis - different steps in different tutorials

[MILÁN MAILLO, IRIS]

Hi everyone,

I am a newbie in Fieldtrip and I'm trying to do a cluster-based permutation
test within subjects. I am looking at these two tutorials:
http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/
http://www.fieldtriptoolbox.org/tutorial/eventrelatedstatistics/

In the two of them, it is said that the steps to follow are (in order):
ft_timelockanalysis, ft_timelockgrandaverage, and ft_timelockstatistics.

However, in
http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/ they
seem to perform ft_timelockanalysis followed by ft_timelockstatistics and
after that, they do ft_timelockgrandaverage (this is not what is proposed
in the other tutorial). I don't know if this makes a big difference or not,
but inconsistencies across tutorials are confusing. Moreover, in the
within-subjects part (
http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/), it
is said that the configuration in neighbours creation is the same as in the
between-trials:



“cfg.neighbours = neighbours;  % same as defined for the between-trials
experiment”

Nevertheless, in the between-trials experiment, they use the GA_FC to do
the neighbours structure, but in the within-subjects trial it is not
possible to do so, because the grandaverage is only done after the
permutation test. So what we need to do?

In sum, my questions are:

1.      When does one need to do the grandaverage?

2.      If the grandaverage is done after the permutation analysis, what do
we write in the neighbours’ structure? The output from ft_timelockanalysis
(i.e. allsubjFC)?



Thanks in advance,



Iris
-- 
*Iris Milán Maillo*

PhD Student
Speech Production and Bilingualism (SPB) <https://www.upf.edu/web/spb>
Center for Brain and Cognition (CBC) <http://cbc.upf.edu/cbc.upf.edu/>

Carrer de Ramon Trias Fargas, 25-27, 08005 Barcelona | Edifici Merce
Rodoreda, (room 24.311)
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https://doi.org/10.1371/journal.pcbi.1002202