[Mne_analysis] TFCE parameters

[Cushing, Cody]

I'll make sure to make the time to get that done.

Just to add on to this, one of the old emails from the archive I found on the topic stated that a good default place to set start & step at is (start=2.0, step=0.2).  Is there any motivation behind start>0 other than trying to reduce computation time?  Altering that changes the resultant p values rather drastically in some cases I've noticed.  The source paper lists the start as typically being 0 without stating any reason to go above that.  So I'm just curious what the motivation behind this is?  Why are these the 2 parameters we have control for TFCE?  What's to be gained/lost?

Cheers,
Cody
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Eric Larson [larson.eric.d at gmail.com]
Sent: Monday, July 18, 2016 12:56 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] TFCE parameters

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<mailto: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<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu> [mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>] on behalf of Natalie Klein [neklein at andrew.cmu.edu<mailto: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<mailto: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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