[FieldTrip] IMPORTANT: Bug in ft_freqstatistics

[Eelke Spaak]

Hi Ingrid,

Thanks for your question; it made me realize that my e-mail was not
clear enough. In your case, when you repaired channels that were still
present in the data, the output channel order of ft_channelrepair will
be the same as the input channel order.

The problem only occurs if you use ft_channelrepair to repair
*missing* channels, so e.g. channels switched off during acquisition
or that were discarded during preprocessing.

Groeten,
Eelke

On 20 March 2013 20:55, Ingrid Nieuwenhuis <inieuwenhuis at berkeley.edu> wrote:
> 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
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> Ingrid Nieuwenhuis PhD
> Postdoctoral Fellow
> Sleep and Neuroimaging Laboratory
> Department of Psychology
> University of California, Berkeley
> California 94720-1650
> Tolman Hall, room 5305
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip