[Mne_analysis] Issue with tfce

[Eric Larson]

        External Email - Use Caution        

It is possible we don't do the re-negation step. Can you open an issue on
GitHub? If you can show the problem on some tiny toy data (3 "subjects", 2
"vertices", 2 "time points"?) that would help.

Eric


On Mon, Apr 27, 2020 at 10:19 AM Fleur GAUDFERNAU <
fleur.gaudfernau at pasteur.fr> wrote:

>         External Email - Use Caution
>
> Hello,
> I am actually wondering if something might be wrong with the way the tfce
> is performed.
> Almost all values in my array are negative, and I get only positive t
> values. I get exactly the same result when performing a test with tfce on X
> and on -X. Which means that the sign of the t values is wrong (for some of
> them at least), unless I'm missing something.
>
> (I'm using 2-tailed cluster permutation test with tfce =
> dict(start=0., step=0.5)).
> Kind regards,
> Fleur
>
>
>
> ------------------------------
> *De :* mne_analysis-bounces at nmr.mgh.harvard.edu <
> mne_analysis-bounces at nmr.mgh.harvard.edu> de la part de Dan McCloy <
> dan at mccloy.info>
> *Envoyé :* vendredi 24 avril 2020 16:01
> *À :* Discussion and support forum for the users of MNE Software
> *Objet :* Re: [Mne_analysis] Issue with tfce
>
>
>         External Email - Use Caution
>
> Hi Fleur,
> Quoting from Smith & Nichols 2009 (
> https://doi.org/10.1016/j.neuroimage.2008.03.061):
>
> "By default, voxels that were originally negative will be given zero TFCE
> score. However, if it is desired to apply the enhancement to both negative
> and positive values, the original image can be simply negated, passed
> through the enhancement, re-negated and combined (via addition) with the
> positive enhancement."
>
> As far as I know, MNE-Python's implementation does *not* do this for you
> automatically.
>
> -- dan
> Daniel McCloy
> https://dan.mccloy.info
> Research Scientist
> Institute for Learning and Brain Sciences
> University of Washington
>
>
> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
> On Friday, April 24, 2020 7:48 AM, Fleur GAUDFERNAU <
> fleur.gaudfernau at pasteur.fr> wrote:
>
> *        External Email - Use Caution        *
>
>
> Dear mne community,
>
> I'm doing 1 sample permutation cluster t-tests (two tailed) between 2
> conditions.
>
> Most of the values in my array data (difference between conditions) are
> negative, hence I'm expecting negative T values (which is what I get when
> I'm not using tfce). However, when using tfce, the test returns only
> positive T values. Is there a way to overcome this issue?
>
> Thanks in advance,
>
> Fleur
>
>
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