[Eeglablist] Data change when updating eeglab from version 10 to 12

Mon Sep 16 14:17:48 PDT 2013

Hi Ilana,

In my experience, 1000 samples is common.
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock (which
is the documentation for Fieldtrip, but I believe is still implementing the
same method) recommends: "As a rule of thumb, use cfg.numrandomization =
500, and double this number if it turns out that the p-value differs from
the critical alpha-level (0.05 or 0.01) by less than 0.02."

Stephen Politzer-Ahles
New York University, Abu Dhabi
Neuroscience of Language Lab
http://www.nyu.edu/projects/politzer-ahles/

On Mon, Sep 16, 2013 at 11:43 AM, Ilana Podlipsky <ilana.mlist at gmail.com>
wrote:
>
> Dear Arno,
>
> Thank you for your reply.
> Would increase of the number of permutations make the result more stable?
> Is there some rule of thumb for a suggested number of permutation for a
given data set?
>
> Thank you
> Ilana
>
>
> On Sun, Sep 15, 2013 at 10:23 PM, Arnaud Delorme <arno at ucsd.edu> wrote:
>>
>> Dear Llana,
>>
>> this is because the permutation statistics use different random
permutation every time.
>> The result should be similar but not identical.
>> Best,
>>
>> Arno
>>
>> On Sep 12, 2013, at 11:33 AM, Ilana Podlipsky <ilana.mlist at gmail.com>
wrote:
>>
>> Dear Nicolas and Arno,
>> I recently ran an ANOVA statistic of ERSP maps across conditions and
encountered the same problem of inconsistency of statistics results each
time I run the analysis.
>> In short, every time I run the permutation statistics analysis I get
different significant electrodes.
>> I encountered this issue in EEGLAB 8,10 and 12 (didn't try 11).
>> I see now that Nicolas reported exactly the same problem.
>> Were you able to solve it?
>>
>> Thank you for your help,
>> Ilana
>>
>>
>>
>>
>> On Fri, May 3, 2013 at 7:33 AM, Arnaud Delorme <arno at ucsd.edu> wrote:
>>>
>>> Dear Nicolas,
>>>
>>> your problem is worth investigating. I have checked with the tutorial
STUDY, and the results with parametric statistics (EEGLAB) are strictly
identical from one call to the next when plotting channel ERSP
time-frequency images or channel ERSP scalp topographies. Also since 2010,
we have a battery of independent test that check EEGLAB statistics agains
the Matlab statistics toolbox. After adding Fieldtrip statistics to the
EEGLAB graphic interface  last year, we also implemented the same tests for
these new functions (which is how we discovered a bug in Anova Fieldtrip
statistics by the way - currently in the process of being fixed).
>>> This said, no program is perfect. Please upload your data to Bugzilla
so we can try reproduce the problem and see what is going on.
>>>
>>> http://sccn.ucsd.edu/eeglab/bugzilla
>>>
>>> If your data is really large (>1Gb), put it on our public FTP server
(ask Derrick Lock <dlock at ucsd.edu> for the address as I prefer to write it
here for security reasons). Let's also continue this discussion off the
list.
>>>
>>> Best regards,
>>>
>>> Arno
>>>
>>> On 2 May 2013, at 09:30, Nicolas Rochet wrote:
>>>
>>> Dear Makoto and Arno,
>>> To sum up: i'm using study analysis using channels (with GUI) to
compare two conditions. After further testings, i have similar issues with
EEGLAB version 12 and 11.05.5.4b : the stats maps (for condition
comparaison in ERSP / ITC analysis) are changing each time i replot
whatever stats option i use. Also, while ERP's topographics map are not
changing, the significant channels (when comparing the two conditions) are
changing each time i replot.
>>> Strangely, those issues only happens with EEGLAB statistic's option,
indeed when i choose Fieldtrip stat's option, i don't have this problem:
the stats map remains the same after each replotting.
>>>
>>> cordially,
>>> Nicolas
>>>
>>> Le 30/04/2013 17:00, Makoto Miyakoshi a écrit :
>>>
>>> Dear Nicolas and Arno,
>>>
>>> > some of these data, the stats are changing, whatever stats option i
used (parametric, permutations, with or without holms correction and
bonferoni correction).
>>>
>>> Permutation results may change because this approach is based on random
permutation. However parametric test result should not. Could you check it
again?
>>>
>>> > ERP's topographic map's ( the significant channels are not the same
each time i replot).
>>>
>>> Significant channels? You mean you are running STUDY analysis using
channels? If that's the case I'm not experienced with it.
>>>
>>> However, changing topographic maps is familiar with me. However, I want
to know exactly what you are doing (using ICs or channels)
>>>
>>> Makoto
>>>
>>> 2013/4/26 Nicolas Rochet <nicolas.rochet at univ-provence.fr>
>>>>
>>>> Hi Makoto,
>>>> Firstly, I recomputed ERP, ERSP and ITC after updating to version 12.
I realised that (when using the study's GUI with version 12) each time i
plot some of these data, the stats are changing, whatever stats option i
used (parametric, permutations, with or without holms correction and
bonferoni correction).
>>>> For example. when i try to compare ERSP maps in two different
condition: each time i replot it, the corresponding stat map is changing
while the ERSP map is the same. I had the same problem with ITC maps or for
ERP's topographic map's ( the significant channels are not the same each
time i replot).
>>>>
>>>> Do you have any idea ? Nobody seems to have reported similar issues
....
>>>>
>>>> Nicolas
>>>>
>>>> Le 18/04/2013 03:26, Makoto Miyakoshi a écrit :
>>>>
>>>> Dear Nicolas,
>>>>
>>>> I'd be interested in learning how much the difference was. Would you
mind explaining it to us?
>>>>
>>>> Makoto
>>>>
>>>>
>>>> 2013/4/15 Nicolas Rochet <nicolas.rochet at univ-provence.fr>
>>>>>
>>>>> Dear EEGLAB community,
>>>>> I was previously using eeglab version 10.2.2.4b. After updating EEGLAB
>>>>> to  version 12.0.2.0b (with SVN) the SAME data (ie  ERP, ERSP and ITC
>>>>> grand average) processed with the study protocol are different with
the
>>>>> two version
>>>>> Does anybody encountered similar issues ?
>>>>>
>>>>> Thanks,
>>>>> Nicolas
>>>>>
>>>>> --
>>>>> Nicolas Rochet, PhD Student
>>>>> Laboratoire de Neurosciences Cognitives, UMR 7291
>>>>>
>>>>> Université de Provence / CNRS
>>>>> Pôle 3C - Case C
>>>>> 3 place Victor Hugo
>>>>> 13331 Marseille Cedex 03
>>>>> France
>>>>>
>>>>> tel : (+33) 04 13 55 09 00
>>>>>
>>>>> _______________________________________________
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>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Makoto Miyakoshi
>>>> Swartz Center for Computational Neuroscience
>>>> Institute for Neural Computation, University of California San Diego
>>>>
>>>>
>>>>
>>>> --
>>>> Nicolas Rochet, PhD Student
>>>> Laboratoire de Neurosciences Cognitives, UMR 7291
>>>>
>>>> Université de Provence / CNRS
>>>> Pôle 3C - Case C
>>>> 3 place Victor Hugo
>>>> 13331 Marseille Cedex 03
>>>> France
>>>>
>>>> tel : (+33) 04 13 55 09 00
>>>>
>>>>
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>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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>>>
>>>
>>>
>>>
>>> --
>>> Makoto Miyakoshi
>>> Swartz Center for Computational Neuroscience
>>> Institute for Neural Computation, University of California San Diego
>>>
>>>
>>>
>>> --
>>> Nicolas Rochet, PhD Student
>>> Laboratoire de Neurosciences Cognitives, UMR 7291
>>>
>>> Université de Provence / CNRS
>>> Pôle 3C - Case C
>>> 3 place Victor Hugo
>>> 13331 Marseille Cedex 03
>>> France
>>>
>>> tel : (+33) 04 13 55 09 00
>>>
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>>>
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>>
>>
>>
>
>
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