[FieldTrip] statistical reporting cluster based permutation

[Arnaud Delorme]

Dear Katia,

I would mention that the statistics were corrected for multiple comparisons using the cluster methods. You may report the p-value for stats and the actual difference in terms of values between the conditions for effect size.

Best,

Arno
--
Arnaud Delorme, PhD
Centre de Recherche Cerveau et Cognition - UMR 5549
Pavillon Baudot, Hopital Purpan, BP 25202
31052 Toulouse Cedex 3, France

> On Nov 15, 2015, at 7:39 PM, Kaelasha Tyler <ktyler at swin.edu.au> wrote:
> 
> Thanks Steve,
> 
> Very clear.
> K.
> 
> PhD Candidate
> Brain and Psychological Sciences Research Centre
> Swinburne University of Technology
> Melbourne
> Australia
> From: fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl <mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Stephen Politzer-Ahles [stephen.politzer-ahles at ling-phil.ox.ac.uk <mailto:stephen.politzer-ahles at ling-phil.ox.ac.uk>]
> Sent: Sunday, 15 November 2015 10:15 PM
> To: fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] statistical reporting cluster based permutation
> 
> Hello Kaelasha,
> 
> There isn't really any one absolute right way to report these; my best suggestion is to look in the literature for other papers in your area that have reported cluster based stats, and see how they do it. In my experience it's usually sufficient to report the p-value, polarity, and approximate spatiotemporal distribution of an effect (e.g., "there was a significant positive effect (p=.042) based on a cluster of fronto-central electrodes lasting from x ms to y ms..."), as is done in this paper:https://www.researchgate.net/publication/38112722_Reasoning_with_Exceptions_An_Event-related_Brain_Potentials_Study <https://www.researchgate.net/publication/38112722_Reasoning_with_Exceptions_An_Event-related_Brain_Potentials_Study>.
> I also find raster plots to be a nice way to visualize the spatiotemporal extent of a cluster; see, e.g., this paper:http://joshuakhartshorne.org/papers/HartshorneSnedekerLiemAzarKim.pdf <http://joshuakhartshorne.org/papers/HartshorneSnedekerLiemAzarKim.pdf>
> 
> See also http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test <http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test> for some suggestions about wording and interpretation of the effects.
> 
> Best,
> Steve
> 
> 
> 
> ---
> Stephen Politzer-Ahles
> University of Oxford
> Language and Brain Lab, Faculty of Linguistics, Phonetics & Philology
> http://users.ox.ac.uk/~cpgl0080/ <http://users.ox.ac.uk/~cpgl0080/>Message: 1
> Date: Sun, 15 Nov 2015 01:07:30 +0000
> From: Kaelasha Tyler <ktyler at swin.edu.au <mailto:ktyler at swin.edu.au>>
> To: "fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl <mailto:fieldtrip at science.ru.nl>>
> Subject: [FieldTrip] statistical reporting cluster based permutation
>         tests
> Message-ID:
>         <FB8747C478C3AF489C8F5164C02011B9E48CAE50 at gsp-ex01.ds.swin.edu.au <mailto:FB8747C478C3AF489C8F5164C02011B9E48CAE50 at gsp-ex01.ds.swin.edu.au>>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi all,
> 
> I am writing up results for cluster based permutation tests that I ran on masked priming meg data.
> 
> I have to admit I am not entirely sure the exact form for reporting the stats on these.
> 
> For example, when comparing two conditions, with n=20,  I have one significant positive cluster over left frontal and parietal areas. The stats for this cluster read:
> 
> prob: 0.0420
> clusterstat: 1.2443e+04
> stddev: 0.0063
> cirange: 0.0124
> 
> Has anyone else completed and rerooted on results, having used cluster based permutation tests?
> Mean values don't seem to be appropriate here, so would it simply be the p value and standard deviation for the significant clusters that would be reported on?
> 
> Thanks,
> K
> 
> PhD Candidate
> Brain and Psychological Sciences Research Centre
> Swinburne University of Technology
> Melbourne
> Australia
> 
> 
> 
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