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<p class=MsoNormal><span lang=EN-US>Dear fieldtrip users!<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>May I ask for your support because of a
problem concerning my within-subject permutation test (EEG-Data)?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>The goal is to compare two grandaverages
with two different conditions, each grandaverage consisting of 4 datasets from
4 subjects, each dataset about 40-50 single trials.<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>I did the preprocessing, timelock and
grandaverage: 4 datasets (called x1, … x4) for the first condition with the
following command:<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>…<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>cfg = [];</span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>cfg.keeptrials = </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'yes'</span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:black'>;</span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>timelock1 =
timelockanalysis(cfg, x1);</span><span lang=EN-US style='font-size:8.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>timelock2 =
timelockanalysis(cfg, x2);</span><span lang=EN-US style='font-size:8.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>timelock3 =
timelockanalysis(cfg, x3);</span><span lang=EN-US style='font-size:8.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>timelock4 =
timelockanalysis(cfg, x4);</span><span lang=EN-US style='font-size:8.0pt;
font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'> </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'> </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>cfg.channel = </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'all'</span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>cfg.latency = </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>'all'</span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>cfg.keepindividual
= </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";
color:#A020F0'>'yes'</span><span lang=EN-US style='font-size:8.0pt;font-family:
"Courier New";color:black'> </span><span lang=EN-US style='font-size:
8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>cfg.normalizevar
= </span><span lang=EN-US style='font-size:8.0pt;font-family:"Courier New";
color:#A020F0'>'N-1'</span><span lang=EN-US style='font-size:8.0pt;font-family:
"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'> </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>da_test1=
timelockgrandaverage (cfg, timelock1, timelock2, timelock3, timelock4) </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New"'><o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:black'>save </span><span
lang=EN-US style='font-size:8.0pt;font-family:"Courier New";color:#A020F0'>da_test1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:10.0pt;font-family:"Courier New";color:#A020F0'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:12.0pt'>Same way for the second condition: da_test2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:12.0pt'>Now I start the permutation test (file attached). As result
there are no significant clusters highlighted (although there are quite
large differences in the ERP-plot). I think because there is a mistake
concerning the number of single-trials which fieldtrip takes as the basis for
the statistic test.<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:12.0pt'>Because the output in the command window shows:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:12.0pt'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>…<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>selected 30 channels<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>selected 2501 time bins<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>selected 1 frequency bins<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>…<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>total number of
measurements = 8<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>total number of
variables = 2<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>number of independent
variables = 1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>number of unit
variables = 1<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>number of within-cell
variables = 0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>number of control
variables = 0<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>using a permutation
resampling approach<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>repeated measurement in
variable 1 over 4 levels<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>number of repeated
measurements in each level is 2 2 2 2 <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>computing a parmetric threshold
for clustering<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>computing statistic<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>estimated time per
randomization is 0 seconds<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>computing statistic 1 from
100<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>…<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>found 7 positive clusters in
observed data<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>found 11 negative clusters in
observed data<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>…<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>stat = <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
prob: [30x2501 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
posclusters: [1x7 struct]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
posclusterslabelmat: [30x2501 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
posdistribution: [1x100 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
negclusters: [1x11 struct]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
negclusterslabelmat: [30x2501 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
negdistribution: [1x100 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
mask: [30x2501 logical]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
stat: [30x2501 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
ref: [30x2501 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
dimord: 'chan_time'<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
label: {30x1 cell}<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
time: [1x2501 double]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>
cfg: [1x1 struct]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>cfg = <o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'> xlim: [0
0.1000]<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'> zlim:
'maxmin'<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>the input is timelock data
with 30 channels and 4000 timebins<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>applying preprocessing
options<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>averaging trials<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><b><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:red'>averaging trial 1
of 4<o:p></o:p></span></b></p>
<p class=MsoNormal style='text-autospace:none'><b><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:red'>averaging trial 2
of 4<o:p></o:p></span></b></p>
<p class=MsoNormal style='text-autospace:none'><b><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:red'>averaging trial 3
of 4<o:p></o:p></span></b></p>
<p class=MsoNormal style='text-autospace:none'><b><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New";color:red'>averaging trial 4
of 4<o:p></o:p></span></b></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:8.0pt;font-family:"Courier New"'>reading layout from file
easycap32ch-avg.lay<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span lang=EN-US
style='font-size:12.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>So, could this be the mistake that
fieldtrip guesses “4” to be the number of all trials (perhaps
because 4 datasets in each grandaverage??) And how can I solve this problem?
Is there a way to account for the single-trial number when using the
permutation test?<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Thank you very much for your help!!<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Kind regards <o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Thomas Sauvigny<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US>Tübingen University<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p>
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<p>----------------------------------</p>
<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>