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Hi Cihan,
<div class=""><br class="">
</div>
<div class="">I never use SPM myself, so I cannot comment on what is going on under the hood there.</div>
<div class=""><br class="">
</div>
<div class="">Just one or two pointers and questions for now:</div>
<div class="">- what’s the overall number of trials? To get a feel about the discrepancy, it would be relevant to know this.</div>
<div class="">- 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.</div>
<div class="">- there’s a typo in the cfg for ft_artifact_threshold: ‘continious' should read ‘continuous', although that would probably not explain your observations.</div>
<div class="">- one potential difference in the processing steps between SPM and FT could be the order of the filtering and baseline subtraction.</div>
<div class="">- the set of channels used in both SPM and FT are the same?</div>
<div class=""><br class="">
<div>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.</div>
<div><br class="">
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br class="">
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<div><br class="">
<blockquote type="cite" class="">
<div class="">On 6 Aug 2021, at 00:26, Cihan Dogan via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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Dear Fieldtrip Experts,<br class="">
<br class="">
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 class="">
<br class="">
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 class="">
<br class="">
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 class="">
<br class="">
I hope I am making a silly mistake somewhere and missing a setting, hopefully an expert can spot it!<br class="">
<br class="">
Thanks in advance,<br class="">
Cihan<o:p class=""></o:p></p>
<p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;">
<b class="">FieldTrip Configuration Summary:<o:p class=""></o:p></b></p>
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<b class="">Preprocessing:<o:p class=""></o:p></b></p>
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cfg = []<o:p class=""></o:p></div>
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cfg.demean = ‘yes’;<o:p class=""></o:p></div>
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cfg.baselinewindow = [-0.2, 0];<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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cfg.lpfilter = ‘yes’;<o:p class=""></o:p></div>
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cfg.hpfilter = ‘yes’;<o:p class=""></o:p></div>
<div style="margin: 0cm; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.lpfreq = 30;<o:p class=""></o:p></div>
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cfg.hpfreq = 0.1<o:p class=""></o:p></div>
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cfg.lpfiltord = 5;<o:p class=""></o:p></div>
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cfg.hpfiltord = 5;<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<b class="">Artefact Rejection:<o:p class=""></o:p></b></div>
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<b class=""><o:p class=""> </o:p></b></div>
<div style="margin: 0cm; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class="">Thresholding -100 to 100 uV<o:p class=""></o:p></i></div>
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<b class=""><o:p class=""> </o:p></b></div>
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cfg = [];<o:p class=""></o:p></div>
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cfg.continious = ‘no’;<o:p class=""></o:p></div>
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cfg.artfctdef.threshold.min = -100;<o:p class=""></o:p></div>
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cfg.artfctdef.threshold.max = 100;<o:p class=""></o:p></div>
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cfg.artfctdef.threshold.channel = get_eeg_channels(data);<o:p class=""></o:p></div>
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cfg.artfctdef.threshold.bpfilter = ‘no’;<o:p class=""></o:p></div>
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[cfg, artifact] = ft_artifact_threshold(cfg, data);<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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cfg = [];<o:p class=""></o:p></div>
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cfg.artfctdef.reject = 'complete';<o:p class=""></o:p></div>
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cfg.artfctdef.zvalue.artifact = artifact; % this doesn’t make a difference given we only have 1 set of artifacts<o:p class=""></o:p></div>
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postprocessed = ft_rejectartifact(cfg, data);<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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<b class="">SPM Configuration Summary:<o:p class=""></o:p></b></p>
<p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;">
<i class="">Filtering 0.1 30 Hz<o:p class=""></o:p></i></p>
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matlabbatch{1}.spm.meeg.preproc.filter.type = 'butterworth';<b class=""><o:p class=""></o:p></b></div>
<div style="margin: 0cm; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
matlabbatch{1}.spm.meeg.preproc.filter.band = 'bandpass';<b class=""><o:p class=""></o:p></b></div>
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matlabbatch{1}.spm.meeg.preproc.filter.freq = [0.1 30];<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.filter.dir = 'twopass';<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.filter.order = 5;<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<i class="">baseline -200 to 0 ms<o:p class=""></o:p></i></div>
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<o:p class=""> </o:p></div>
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matlabbatch{1}.spm.meeg.preproc.bc.timewin = [-200 0];<o:p class=""></o:p></div>
<div style="margin: 0cm; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<i class="">Thresholding -100 to 100 uV<o:p class=""></o:p></i></div>
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<i class=""><o:p class=""> </o:p></i></div>
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matlabbatch{1}.spm.meeg.preproc.artefact.mode = 'reject';<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.artefact.badchanthresh = 0.5;<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.artefact.append = true;<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.artefact.methods.channels{1}.type = 'EEG';<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.artefact.methods.fun.threshchan.threshold = 100;<o:p class=""></o:p></div>
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matlabbatch{1}.spm.meeg.preproc.artefact.methods.fun.threshchan.excwin = 1000;<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
<div style="margin: 0cm; line-height: normal; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class="">6 Participant Example</b><o:p class=""></o:p></div>
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<i class=""><o:p class=""> </o:p></i></div>
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<span style="" class="">Participant<o:p class=""></o:p></span></div>
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<span style="" class="">SPM Reject<o:p class=""></o:p></span></div>
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<span style="" class="">FieldTrip Reject<o:p class=""></o:p></span></div>
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<span style="" class="">164<o:p class=""></o:p></span></div>
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<span style="" class="">128<o:p class=""></o:p></span></div>
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<p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;">
<o:p class=""> </o:p></p>
<p class="MsoNormal" style="margin: 0cm 0cm 8pt; line-height: 15.399999618530273px; font-size: 11pt; font-family: Calibri, sans-serif;">
<o:p class=""> </o:p></p>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!vLTGG-Iql13sRmyQWAgFmTmxPKaUG9bo3LN8yj1yKhaKO18YQKRI0lDKyoX-yez0GP2aD5WfTxqxQdY$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!vLTGG-Iql13sRmyQWAgFmTmxPKaUG9bo3LN8yj1yKhaKO18YQKRI0lDKyoX-yez0GP2aD5WfTxqxQdY$</a><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span></div>
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