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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi FT community,<br>
<br>
So I had a look into this and it seems the filter used between SPM<>FieldTrip is different. In SPM a FIR filter was used whereas in FieldTrip I was using a Butterworth filter (for some reason I assumed a FIR filter). When defaulting everything to the same filter,
both pre-processing steps seemed much more in-line with one another as well as analysis results.<br>
<br>
Many thanks,<br>
Cihan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Cihan Dogan via fieldtrip<br>
<b>Sent:</b> 07 August 2021 12:55<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Cihan Dogan <CDogan1994@hotmail.co.uk><br>
<b>Subject:</b> Re: [FieldTrip] Discrepancy between FieldTrip and SPM artefact rejection functions (thresholding)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Jan,<br>
<br>
Many thanks for getting back to me so promptly.<br>
<br>
So the overall number of trials is approximately 430 trials per participant. I do call ft_preprocessing after the code I linked. In terms of the typo, I manually typed the commands into email, my bad! Finally, the baseline subtraction and filtering should
be the same between platforms, I’ll double check this today. And indeed, both are using the same 118 electrodes.<br>
<br>
I’ll have a closer look into this today/tomorrow and return with my findings.<br>
<br>
Thanks for the help!<br>
Cihan<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs) via fieldtrip<br>
<b>Sent:</b> 06 August 2021 09:27<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] Discrepancy between FieldTrip and SPM artefact rejection functions (thresholding)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Cihan, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I never use SPM myself, so I cannot comment on what is going on under the hood there.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Just one or two pointers and questions for now:<o:p></o:p></p>
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<p class="MsoNormal">- what’s the overall number of trials? To get a feel about the discrepancy, it would be relevant to know this.<o:p></o:p></p>
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<p class="MsoNormal">- just to be sure: after specifying the cfg for preprocessing, you actually call ft_preprocessing, right? The code you pasted in your e-mail does not mention that.<o:p></o:p></p>
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<p class="MsoNormal">- there’s a typo in the cfg for ft_artifact_threshold: ‘continious' should read ‘continuous', although that would probably not explain your observations.<o:p></o:p></p>
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<p class="MsoNormal">- one potential difference in the processing steps between SPM and FT could be the order of the filtering and baseline subtraction.<o:p></o:p></p>
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<p class="MsoNormal">- the set of channels used in both SPM and FT are the same?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Anyway, no definitive answer here, but if you want to get to the bottom of this, I’d first compare the ‘preprocessed’ data, without the whole thresholding machinery applied. Just inspect the time courses for offset differences etc. This
would then give pointers as to why the numbers are so different.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best wishes,<o:p></o:p></p>
</div>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 6 Aug 2021, at 00:26, Cihan Dogan via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.55pt">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.<span class="apple-converted-space"> </span><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" style="margin-bottom:8.0pt;line-height:11.55pt"><b>FieldTrip Configuration Summary:</b><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.55pt"><b>Preprocessing:</b><o:p></o:p></p>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg = []<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.demean = ‘yes’;<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.baselinewindow = [-0.2, 0];<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.lpfilter = ‘yes’;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.hpfilter = ‘yes’;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.lpfreq = 30;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.hpfreq = 0.1<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.lpfiltord = 5;<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.hpfiltord = 5;<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt"><b>Artefact Rejection:</b><o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt"><b> </b><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"><i>Thresholding -100 to 100 uV</i><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:11.55pt"><b> </b><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg = [];<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.continious = ‘no’;<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.artfctdef.threshold.min = -100;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.artfctdef.threshold.max = 100;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.artfctdef.threshold.channel = get_eeg_channels(data);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt">cfg.artfctdef.threshold.bpfilter = ‘no’;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">[cfg, artifact] = ft_artifact_threshold(cfg, data);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">cfg = [];<o:p></o:p></p>
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<div>
<p class="MsoNormal">cfg.artfctdef.reject = 'complete';<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">cfg.artfctdef.zvalue.artifact = artifact; % this doesn’t make a difference given we only have 1 set of artifacts<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">postprocessed = ft_rejectartifact(cfg, data);<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.55pt"><b>SPM Configuration Summary:</b><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.55pt"><i>Filtering 0.1 30 Hz</i><o:p></o:p></p>
<div>
<p class="MsoNormal" style="line-height:11.55pt">matlabbatch{1}.spm.meeg.preproc.filter.type = 'butterworth';<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="line-height:11.55pt">matlabbatch{1}.spm.meeg.preproc.filter.band = 'bandpass';<o:p></o:p></p>
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<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.filter.freq = [0.1 30];<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.filter.dir = 'twopass';<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.filter.order = 5;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"><i>baseline -200 to 0 ms</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.bc.timewin = [-200 0];<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"><i>Thresholding -100 to 100 uV</i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"><i> </i><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.artefact.mode = 'reject';<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.artefact.badchanthresh = 0.5;<o:p></o:p></p>
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<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.artefact.append = true;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.artefact.methods.channels{1}.type = 'EEG';<o:p></o:p></p>
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<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.artefact.methods.fun.threshchan.threshold = 100;<o:p></o:p></p>
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<div>
<p class="MsoNormal">matlabbatch{1}.spm.meeg.preproc.artefact.methods.fun.threshchan.excwin = 1000;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
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<div>
<p class="MsoNormal"><b>6 Participant Example</b><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="line-height:11.55pt"><i> </i><o:p></o:p></p>
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<p class="MsoNormal" align="center" style="text-align:center">Participant<o:p></o:p></p>
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<p class="MsoNormal" align="center" style="text-align:center">SPM Reject<o:p></o:p></p>
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<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="text-align:center">FieldTrip Reject<o:p></o:p></p>
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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="text-align:center">23<o:p></o:p></p>
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<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="text-align:center">221<o:p></o:p></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="text-align:center">141<o:p></o:p></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="text-align:center">24<o:p></o:p></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="text-align:center">257<o:p></o:p></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="text-align:center">295<o:p></o:p></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="text-align:center">25<o:p></o:p></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="text-align:center">260<o:p></o:p></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="text-align:center">227<o:p></o:p></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="text-align:center">26<o:p></o:p></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="text-align:center">80<o:p></o:p></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="text-align:center">55<o:p></o:p></p>
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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="text-align:center">27<o:p></o:p></p>
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<p class="MsoNormal" align="center" style="text-align:center">284<o:p></o:p></p>
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<p class="MsoNormal" align="center" style="text-align:center">271<o:p></o:p></p>
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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="text-align:center">28<o:p></o:p></p>
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<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="text-align:center">178<o:p></o:p></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="text-align:center">164<o:p></o:p></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="text-align:center">39<o:p></o:p></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="text-align:center">159<o:p></o:p></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="text-align:center">128<o:p></o:p></p>
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</tr>
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<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.55pt"><span style="color:white"> </span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:8.0pt;line-height:11.55pt"> <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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</span><a href="https://urldefense.com/v3/__https:/doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!vLTGG-Iql13sRmyQWAgFmTmxPKaUG9bo3LN8yj1yKhaKO18YQKRI0lDKyoX-yez0GP2aD5WfTxqxQdY$"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!vLTGG-Iql13sRmyQWAgFmTmxPKaUG9bo3LN8yj1yKhaKO18YQKRI0lDKyoX-yez0GP2aD5WfTxqxQdY$</span></a><o:p></o:p></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
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