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<p class="MsoNormal">Dear Fieldtrip Experts,<br>
<br>
Recently I have been in the process of moving my pre-processing pipeline from SPM to Fieldtrip. Originally, I started my analysis in SPM, then moved over to Fieldtrip, however, I was using functions provided by FieldTrip to convert the SPM data straight to
FieldTrip removing the need for me to reprocess my data.<br>
<br>
I decided to move this pre-processing over to FieldTrip rather than relying on two analysis programs. I am facing an issue whereby a large difference exists for the number of trials rejected using FieldTrips ‘ft_artifact_threshold’ versus SPM which I do not
understand given my parameters for pre-processing are the same, and thresholding is a relatively simple process.
<br>
<br>
I could understand slight differences, but not this large. To double check I also reprocessed my files in SPM since it had been a while (no change).I linked below an example of how many trials get rejected for six participants (I have a dataset of 40). As seen,
the discrepancy is quite large in some cases, for example participant 23.<br>
<br>
I hope I am making a silly mistake somewhere and missing a setting, hopefully an expert can spot it!<br>
<br>
Thanks in advance,<br>
Cihan<o:p></o:p></p>
<p class="MsoNormal"><b>FieldTrip Configuration Summary:<o:p></o:p></b></p>
<p class="MsoNormal"><b>Preprocessing:<o:p></o:p></b></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg = []<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.demean = ‘yes’;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.baselinewindow = [-0.2, 0];<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.lpfilter = ‘yes’;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.hpfilter = ‘yes’;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.lpfreq = 30;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.hpfreq = 0.1<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.lpfiltord = 5;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.hpfiltord = 5;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<b>Artefact Rejection:<o:p></o:p></b></p>
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<b><o:p> </o:p></b></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<i>Thresholding -100 to 100 uV<o:p></o:p></i></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<b><o:p> </o:p></b></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg = [];<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.continious = ‘no’;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.artfctdef.threshold.min = -100;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.artfctdef.threshold.max = 100;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.artfctdef.threshold.channel = get_eeg_channels(data);<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
cfg.artfctdef.threshold.bpfilter = ‘no’;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
[cfg, artifact] = ft_artifact_threshold(cfg, data);<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
cfg = [];<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
cfg.artfctdef.reject = 'complete';<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
cfg.artfctdef.zvalue.artifact = artifact; % this doesn’t make a difference given we only have 1 set of artifacts<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
postprocessed = ft_rejectartifact(cfg, data);<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal"><b>SPM Configuration Summary:<o:p></o:p></b></p>
<p class="MsoNormal"><i>Filtering 0.1 30 Hz<o:p></o:p></i></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
matlabbatch{1}.spm.meeg.preproc.filter.type = 'butterworth';<b><o:p></o:p></b></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
matlabbatch{1}.spm.meeg.preproc.filter.band = 'bandpass';<b><o:p></o:p></b></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.filter.freq = [0.1 30];<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.filter.dir = 'twopass';<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.filter.order = 5;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<i>baseline -200 to 0 ms<o:p></o:p></i></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.bc.timewin = [-200 0];<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<i>Thresholding -100 to 100 uV<o:p></o:p></i></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<i><o:p> </o:p></i></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.artefact.mode = 'reject';<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.artefact.badchanthresh = 0.5;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.artefact.append = true;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.artefact.methods.channels{1}.type = 'EEG';<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.artefact.methods.fun.threshchan.threshold = 100;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
matlabbatch{1}.spm.meeg.preproc.artefact.methods.fun.threshchan.excwin = 1000;<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
<o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;line-height:normal;text-autospace:none">
<b>6 Participant Example</b><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:0cm;margin-top:0cm;mso-margin-bottom-alt:8.0pt;mso-margin-top-alt:0cm;mso-add-space:auto">
<i><o:p> </o:p></i></p>
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" width="256" style="width:192.0pt;border-collapse:collapse">
<tbody>
<tr style="height:15.0pt">
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<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">Participant<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border:solid windowtext 1.0pt;border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">SPM Reject<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border:solid windowtext 1.0pt;border-left:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">FieldTrip Reject<o:p></o:p></span></p>
</td>
</tr>
<tr style="height:15.0pt">
<td width="75" nowrap="" valign="bottom" style="width:56.0pt;border:solid windowtext 1.0pt;border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">23<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">221<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">141<o:p></o:p></span></p>
</td>
</tr>
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<td width="75" nowrap="" valign="bottom" style="width:56.0pt;border:solid windowtext 1.0pt;border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">24<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">257<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">295<o:p></o:p></span></p>
</td>
</tr>
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<td width="75" nowrap="" valign="bottom" style="width:56.0pt;border:solid windowtext 1.0pt;border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">25<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">260<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">227<o:p></o:p></span></p>
</td>
</tr>
<tr style="height:15.0pt">
<td width="75" nowrap="" valign="bottom" style="width:56.0pt;border:solid windowtext 1.0pt;border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">26<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">80<o:p></o:p></span></p>
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<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">55<o:p></o:p></span></p>
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<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">27<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">284<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">271<o:p></o:p></span></p>
</td>
</tr>
<tr style="height:15.0pt">
<td width="75" nowrap="" valign="bottom" style="width:56.0pt;border:solid windowtext 1.0pt;border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">28<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">178<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">164<o:p></o:p></span></p>
</td>
</tr>
<tr style="height:15.0pt">
<td width="75" nowrap="" valign="bottom" style="width:56.0pt;border:solid windowtext 1.0pt;border-top:none;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">39<o:p></o:p></span></p>
</td>
<td width="76" nowrap="" valign="bottom" style="width:57.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">159<o:p></o:p></span></p>
</td>
<td width="105" nowrap="" valign="bottom" style="width:79.0pt;border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;padding:0cm 5.4pt 0cm 5.4pt;height:15.0pt">
<p class="MsoNormal" align="center" style="margin-bottom:0cm;text-align:center;line-height:normal">
<span style="color:black;mso-fareast-language:EN-GB">128<o:p></o:p></span></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
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