[Eeglablist] Network Based Statistics (NBS) thresholds

[Makoto Miyakoshi]

Thanks Luca for your prompt response.
Ramtin, it's a good chance to ask anything to Luca :-)

Makoto

On Tue, Jul 31, 2018 at 4:17 PM Luca Cocchi <
Luca.Cocchi at qimrberghofer.edu.au> wrote:

> Hi Makoto, I trust you are well. Let’s see if I can help:
>
>
>
> The initial threshold (F or T values) should be defined based on the
> expected effect size of the effect of interest. It is not a good practice
> to choose the threshold arbitrarily or explore a large range of possible
> thresholds. Technically, exploring a range of thresholds introduces an
> additional multiple comparison problem. In its essence, the approach used
> in the NBS (initial thresholding and subsequent cluster statistic on
> surviving edges) is not different from what is done in other popular
> analysis packages (e.g., SPM, recommended search threshold of p<0.001).
>
>
>
> In the field called “Significance” the user can define the desired NBS
> (network-wise FWE corrected) threshold. Typically, this threshold is set to
> 0.05. Just to be clear, this is not the initial “search” threshold but the
> threshold ascribed to define a significant network at the given value. Note
> that significance is ascribed at the level of the whole network and not
> individual edges.
>
>
>
> Further information can be found in the NBS manual and the related forum.
>
>
>
> Cheers, Luca
>
>
>
>
>
> *From:* Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> *Sent:* Wednesday, August 1, 2018 3:26 AM
> *To:* R.Mehraram2 at newcastle.ac.uk; Luca Cocchi <
> Luca.Cocchi at qimrberghofer.edu.au>; andrewzalesky at gmail.com
> *Cc:* EEGLAB List <eeglablist at sccn.ucsd.edu>
> *Subject:* Re: [Eeglablist] Network Based Statistics (NBS) thresholds
>
>
>
> Dear Andrew and Luca,
>
>
>
> It's been a while since we met in Tokyo. How are you doing? I wonder if
> you have time to kindly help Ramtin.
>
>
>
> Makoto
>
>
>
> On Thu, Jul 26, 2018 at 2:33 AM Ramtin Mehraram (Student) <
> R.Mehraram2 at newcastle.ac.uk> wrote:
>
> Hi all,
>
>
>
> I am struggling in understanding what the threshold values in the NBS
> toolbox mean. I hope you can help me.
>
>
>
> To my knowledge, the value which in the toolbox GUI is defined as
> “Threshold” should be arbitrarily chosen, but I am not sure in which way
> that value influences the output. Is it a threshold on the t values?
>
>
>
> On the bottom, there is a field called “Significance”, which is supposedly
> the max p-value to be considered significant. However I change that value,
> the output seems not to be affected at all, showing always p<0.001 in the
> viewer window.
>
>
>
> Am I missing something?
>
>
>
> Thank you in advance for your help.
>
>
>
> B.
>
>
>
> Ramtin Mehraram
>
> PhD Student @ramtinTVT
>
> Biomedical Research Building 3rd floor
>
> Institute of Neuroscience
>
> Newcastle University
>
> NE4 5PL, United Kingdom
>
> www.lewybodylab.org
>
> https://www.newcastlebrc.nihr.ac.uk/research-themes/dementia/
>
>
>
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>
>
> --
>
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>


-- 
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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