[FieldTrip] marking artifacts by channel + trial
Tim Meehan
timeehan at gmail.com
Wed Mar 8 18:04:27 CET 2017
Thanks for sharing! I'm just taking a look now. It looks like you're doing
mostly automated rejection. Or are you also doing visual rejection along
with the z-value thresholding?
Thanks again,
Tim
On Fri, Mar 3, 2017 at 5:31 PM, Teresa Madsen <braingirl at gmail.com> wrote:
> Here's a rough sketch of my approach, with one custom function attached.
> If you or others find it useful, maybe we can think about ways to
> incorporate it into the FieldTrip code. I've been working mostly with
> scripts, but you've inspired me to work on functionizing the rest of it so
> it's more shareable.
>
> So, assuming raw multichannel data has been loaded into FieldTrip
> structure 'data' with unique trial identifiers in data.trialinfo...
>
> for ch = 1:numel(data.label)
> %% pull out one channel at a time
> cfg = [];
> cfg.channel = data.label{ch};
>
> datch{ch} = ft_selectdata(cfg, data);
>
> %% identify large z-value artifacts and/or whatever else you might want
>
> cfg = [];
> cfg.artfctdef.zvalue.channel = 'all';
> cfg.artfctdef.zvalue.cutoff = 15;
> cfg.artfctdef.zvalue.trlpadding = 0;
> cfg.artfctdef.zvalue.fltpadding = 0;
> cfg.artfctdef.zvalue.artpadding = 0.1;
> cfg.artfctdef.zvalue.rectify = 'yes';
>
> [~, artifact.zvalue] = ft_artifact_zvalue([], datch{ch});
>
> %% replace artifacts with NaNs
> cfg = [];
> cfg.artfctdef.zvalue.artifact = artifact.zvalue;
> cfg.artfctdef.reject = 'nan';
>
> datch{ch} = ft_rejectartifact(cfg,datch{ch});
> end
>
> %% re-merge channels
> data = ft_appenddata([],datch);
>
> %% mark uniform NaNs as artifacts when they occur across all channels
> % and replace non-uniform NaNs (on some but not all channels) with zeroes,
> saving times
> [artifact,data,times] = artifact_nan2zero_TEM(data) % custom function, see
> attached
>
> %% reject artifacts by breaking into sub-trials
> cfg = [];
> cfg.artfctdef.nan2zero.artifact = artifact;
> cfg.artfctdef.reject = 'partial';
>
> data = ft_rejectartifact(cfg,data);
>
> %% identify real trials
> trlinfo = unique(data.trialinfo,'rows','stable');
>
> for tr = 1:size(trlinfo,1)
>
> %% calculate trial spectrogram
>
> cfg = [];
>
> cfg.trials = ismember(data.trialinfo, trlinfo(tr,:), 'rows');
> cfg.keeptrials = 'no'; % refers to sub-trials
>
> cfg.method = 'mtmconvol';
>
> cfg.output = 'powandcsd';
>
> cfg.foi = 2.^(0:0.1:log2(300)); % 83 freqs, log2 spaced, 1-300 Hz
> cfg.tapsmofrq = cfg.foi/10; % smooth by 10%
> cfg.t_ftimwin = 2./cfg.tapsmofrq; % for 3 tapers (K=3), T=2/W
> cfg.toi = '50%';
> cfg.pad = 'nextpow2';
>
>
> freq = ft_freqanalysis(cfg,data);
>
> %% replace powspctrm & crsspctrum values with NaNs
> % where t_ftimwin (or wavlen for wavelets) overlaps with artifact
> for ch = 1:numel(freq.label)
> badt = [times{tr,ch}];
> if ~isempty(badt) && any(...
> badt > (min(freq.time) - max(freq.cfg.t_ftimwin)) & ...
> badt < (max(freq.time) + max(freq.cfg.t_ftimwin)))
> ci = find(any(strcmp(freq.label{ch}, freq.labelcmb)));
> for t = 1:numel(freq.time)
> for f = 1:numel(freq.freq)
> mint = freq.time(t) - freq.cfg.t_ftimwin(f);
> maxt = freq.time(t) + freq.cfg.t_ftimwin(f);
> if any(badt > mint & badt < maxt)
> freq.powspctrm(ch,f,t) = NaN;
> freq.crsspctrm(ci,f,t) = NaN;
> end
> end
> end
> end
> end
>
> %% save corrected output
>
> save(['trial' num2str(tr) 'mtmconvolTFA.mat'], 'freq', '-v7.3');
> end
>
>
>
> On Thu, Mar 2, 2017 at 9:55 AM, Tim Meehan <timeehan at gmail.com> wrote:
>
>> Hi Teresa,
>>
>> Thanks for the reply. I'll take a look at your example if you don't mind
>> sharing. Thanks!
>>
>> Tim
>>
>> On Thu, Mar 2, 2017 at 9:53 AM, Teresa Madsen <braingirl at gmail.com>
>> wrote:
>>
>>> No, not really. The only way I've found to do that is to loop through
>>> my artifact rejection process on each trial individually, then merge them
>>> back together with NaNs filling in where there are artifacts, but then that
>>> breaks every form of analysis I want to do. :-P
>>>
>>> I wonder if it would work to fill in the artifacts with 0s instead of
>>> NaNs....I might play with that. Let me know if you're interested in some
>>> example code.
>>>
>>> ~Teresa
>>>
>>>
>>> On Wed, Mar 1, 2017 at 3:55 PM, Tim Meehan <timeehan at gmail.com> wrote:
>>>
>>>> Hello All,
>>>>
>>>> When performing visual artifact rejection, I want to be able to mark
>>>> artifacts that occur during some specific trials and only on some specific
>>>> channels. In the tutorials I see only ways to mark bad channels (i.e.
>>>> across all trials) or bad trials (i.e. across all channels). Does FieldTrip
>>>> handle marking artifacts restricted to some channel/trial combination?
>>>>
>>>> Thanks,
>>>> Tim
>>>>
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>>
>>> --
>>> Teresa E. Madsen, PhD
>>> Research Technical Specialist: *in vivo *electrophysiology & data
>>> analysis
>>> Division of Behavioral Neuroscience and Psychiatric Disorders
>>> Yerkes National Primate Research Center
>>> Emory University
>>> Rainnie Lab, NSB 5233
>>> 954 Gatewood Rd. NE
>>> Atlanta, GA 30329
>>> (770) 296-9119
>>> braingirl at gmail.com
>>> https://www.linkedin.com/in/temadsen
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
> Teresa E. Madsen, PhD
> Research Technical Specialist: *in vivo *electrophysiology & data
> analysis
> Division of Behavioral Neuroscience and Psychiatric Disorders
> Yerkes National Primate Research Center
> Emory University
> Rainnie Lab, NSB 5233
> 954 Gatewood Rd. NE
> Atlanta, GA 30329
> (770) 296-9119
> braingirl at gmail.com
> https://www.linkedin.com/in/temadsen
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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