[FieldTrip] IMPORTANT: Bug in ft_freqstatistics

[Ingrid Nieuwenhuis]

Hi Eelke,

Thanks for reporting. I did do ft_channelrepair on my EEG data for some 
subjects and subsequently used ft_freqstatistics. However, the channel 
order is indentical in all my subjects in the freq.

I repaired bad channels using the default setting (method='nearest'). 
The bad channels were included in the input data to ft_channelrepair (so 
they were not missing). I just checked, and in data_out after 
ft_channelrepair, the order of the labels of the data is identical to 
the data_in, thus the repaired channels were NOT appended to the end of 
the data. So apparently ft_channelrepair not always appends the repaired 
channels at the end. I suppose this is good news for me, meaning that 
the bug did not affect me, since the channels were ordered identically 
when calling ft_freqstatistics. Do you agree, or am I missing something? 
And for others that used ft_channelrepair, might be worth checking if 
the ordering is indeed changed after calling it, because it appears not 
always to be the case.

Thanks,
Ingrid

On 3/20/2013 2:01 AM, Eelke Spaak wrote:
> Dear FieldTrip community,
>
> Short version: if you did ft_freqstatistics across subjects with a
> different channel ordering across data sets (which is the case if you
> use ft_channelrepair), your results might have been erroneous. Read
> the following carefully.
>
> Yesterday, we discovered a possibly severe bug in a utility function
> (ft_selectdata_old) which was used by ft_freqstatistics. The bug
> entails that ft_selectdata_old assumes that the channels in all data
> input arguments are ordered identically, and does not take into
> account the order of the data.label field. This means that when
> several data input arguments with different channel orderings are
> passed to ft_selectdata_old, the resulting output structure (with a
> newly added 'rpt' dimension) will contain wrong data (i.e. data for
> channel X might end up in another channel Y). Importantly, the same
> thus holds for ft_freqstatistics: when doing statistics across
> subjects, if the different subjects' data sets have different channel
> orderings, the resulting statistics will be wrong.
>
> We expect that in many cases, the channel ordering across different
> data sets will be identical, and in those cases this bug will not have
> had any effect. However, one important case in which channel ordering
> *will* be different is when one does ft_channelrepair on a data set,
> since this function appends the repaired channels to the end of the
> data. So, if you have done ft_channelrepair on only a subset of your
> subjects' data, and/or used ft_channelrepair to repair different
> channels in different subjects, and subsequently passed the repaired
> data sets to ft_freqstatistics, there is a good chance the results you
> got were wrong.
>
> Most likely, this bug was introduced with revision 4101, in september
> 2011, so it has been in the code for quite a while. Note that
> ft_channelrepair only supports repairing missing channels since
> revision 5216 (february 2012), and that this was advised against until
> revision 6100 (june 2012), when the algorithm for doing so sensibly
> was implemented.
>
> The fix has been implemented and is now available from the FTP server
> as of fieldtrip-20130319 (Donders users: the fix is automatically
> available on the /home/common/ version of FieldTrip). Note that
> ft_selectdata_old still does not work correctly, this is something we
> will fix in the near future (ft_selectdata_old is deprecated). We
> fixed the behaviour of ft_appendfreq (the preferred replacement
> function for ft_selectdata_old when appending freq structures) and
> changed ft_freqstatistics to use this function instead.
>
> The other statistics functions, ft_timelockstatistics and
> ft_sourcestatistics, were not affected by this bug. We strongly advise
> you to upgrade to the latest version of FieldTrip. If the situation
> described above applies to you, you will need to redo your
> channel-level (time-)frequency statistics analyses.
>
> Details on the bug (and a test script) can be found here:
> http://bugzilla.fcdonders.nl/show_bug.cgi?id=2069 If you find any
> problems related to the bug, please post them there.
>
> We sincerely apologise for this bug and any trouble it might have caused.
>
> Best,
> On behalf of the FT core development team,
>
> Eelke
> _______________________________________________
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> fieldtrip at donders.ru.nl
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-- 
Ingrid Nieuwenhuis PhD
Postdoctoral Fellow
Sleep and Neuroimaging Laboratory
Department of Psychology
University of California, Berkeley
California 94720-1650
Tolman Hall, room 5305