[Mne_analysis] TFCE parameters

Eric Larson larson.eric.d at gmail.com
Mon Jul 18 12:56:52 EDT 2016
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Excellent -- if you have time, feel free to open a Pull Request on GitHub
to improve the documentation of that function.

Eric


On Mon, Jul 18, 2016 at 12:52 PM, Cushing, Cody <CCUSHING1 at mgh.harvard.edu>
wrote:

> Aha!  That's perfect.  Thank you.  I had actually been trying to figure it
> out from that very paper, I just had failed to make the connection between
> start/step and the integral.  Thanks so much.
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu [
> mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Natalie Klein [
> neklein at andrew.cmu.edu]
> *Sent:* Monday, July 18, 2016 10:06 AM
> *To:* Discussion and support forum for the users of MNE Software
> *Subject:* Re: [Mne_analysis] TFCE parameters
>
> Hi Cody, it might help to read this paper on TFCE:
>
> Smith, S. M., & Nichols, T. E. (2009). Threshold-free cluster enhancement:
> Addressing problems of smoothing, threshold dependence and localisation in
> cluster inference. *NeuroImage*, *44*(1), 83–98.
> http://doi.org/10.1016/j.neuroimage.2008.03.061
>
> The definition of TFCE in equation (1) is an integral, with range "start"
> to the height at a given point; in software, this is simply approximated as
> a sum, so you choose the "start" (typically 0 makes sense) and then the
> step for how many discrete steps to choose to approximate the integral as a
> sum. I think the paper is very helpful for getting the intuition.
>
>
>
>
> On Mon, Jul 18, 2016 at 10:02 AM, Cushing, Cody <CCUSHING1 at mgh.harvard.edu
> > wrote:
>
>> Hi all,
>>
>> My apologies if the documentation exists somewhere and I am just unable
>> to find it, but what do the start/step parameters when using TFCE
>> explicitly control?  I couldn't find much in the manual or the archives.
>>
>> Cheers,
>> Cody
>>
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