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Hi Marta,
<div class=""><br class="">
<div>You say: "<span style="font-family: Calibri, sans-serif; font-size: 11pt;" class="">I’ve run a loop over the trial field in the output of the ft_timelockanalysis as well as ft_preprocessing to check for NaNs in my 10-second data structs, but I didn’t find
any when running this loop.</span><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">”</span></font></div>
<div><span lang="EN-US" class="" style="font-family: Calibri, sans-serif; font-size: 11pt;"><br class="">
</span></div>
<div><span lang="EN-US" class="" style="font-family: Calibri, sans-serif; font-size: 11pt;">This is at odds with your earlier statement that you got a warning that the data contains NaNs. </span></div>
</div>
<div><span lang="EN-US" class="" style="font-family: Calibri, sans-serif; font-size: 11pt;"><br class="">
</span></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">The NaNs have probably been introduced in your attempt to ‘glue together’ the 2-second epochs into longer snippets of 10 seconds. If the time axes of the
original small snippets does not entirely match up (i.e. if there were gaps) then ft_redefinetrial might have filled those gaps with NaNs, while creating the 10 second snippets.</span></font></div>
<div><br class="">
</div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">FieldTrip functions that operate on data containing NaNs often gracefully ignore them, but in many occasions the NaNs will affect the output. For instance
(as is likely in your case), I think that the computation of the covariance in ft_timelockanalysis is not NaN-aware. This may cause downstream problems, when you use an all-NaN covariance matrix for the computation of spatial filters, which consequently will
by construction also be all-NaN, as will be the virtual channel data that you try to derive from it. </span></font></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class=""><br class="">
</span></font></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">The relevant question to ask here is: why do you want to stitch together the 2 second snippets of data?</span></font></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class=""><br class="">
</span></font></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">Good luck and best wishes,</span></font></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class="">Jan-Mathijs</span></font></div>
<div><font face="Calibri, sans-serif" class=""><span style="font-size: 14.666666984558105px;" class=""><br class="">
</span></font></div>
<div class=""><span lang="EN-US" class="" style="font-family: Calibri, sans-serif; font-size: 11pt;"><br class="">
</span></div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 7 Mar 2023, at 21:09, Marta Stojanović via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1; 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;">
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hi Fieldtrip community, <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
I’m reaching out with a question about a warning I encountered when redefining trial length from resting-state MEG data using ft_definetrial and ft_redefine trial.<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Namely, I redefined the length of input data from a resting-state MEG file from two-second trials to longer trials of 10-second length. I successfully used the ft_definetrial and ft_redefinetrial functions to do so, using the ‘trl’ field from the struct where
I define the trial to input as a configuration for the ft_redefinetrial function.<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
With the two-second length I have 144 trials from the data, while with the ten-second length there are 28 trials.<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
The pipeline and structs look like the following: <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
%% define trials with 10-second length <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
clear ten_seconds;<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg = [];<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.dataset = restfile; % refers to resting-state file of a single subject<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.trialdef.beginning = 0; % start at the beginning of the recording<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.trialdef.length = 10; % 10-second trial length<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.trialdef.overlap = 0; % no overlap between trials<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
ten_seconds = ft_definetrial(cfg);<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
%% redefine trials to 10 seconds<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
clear redef_data;<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg = [];<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.trl = ten_seconds.trl; % use trl from defined trial<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
redef_data = ft_redefinetrial(cfg,data);<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
%% preprocess redefined 10-second trials<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
clear ten_sec_trls;<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg = [];<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.demean = 'yes';<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg.baselinewindow = 'all';<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
% cfg.baselinewindow = [0 1018];<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
ten_sec_trls = ft_preprocessing(cfg,redef_data);<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
These are the associated structs with their fields:<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
redef_data = <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
fsample: 508.6275<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
grad: [1×1 struct]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
label: {244×1 cell}<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg: [1×1 struct]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
hdr: [1×1 struct]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
trial: {1×28 cell}<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
time: {1×28 cell}<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
trialinfo: [28×2 double]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
sampleinfo: [28×2 double]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
ten_sec_trls = <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
fsample: 508.6275<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
grad: [1×1 struct]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
hdr: [1×1 struct]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
trialinfo: [28×2 double]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
trial: {1×28 cell}<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
time: {1×28 cell}<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
label: {244×1 cell}<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
cfg: [1×1 struct]<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
When I plug the redefined data (i.e., with redefined length, ten_sec_trls) into ft_timelockanalysis, I receive the<span class="Apple-converted-space"> </span><span lang="EN-US" class="">following<span class="Apple-converted-space"> </span></span>warning:<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Warning: data contains NaN values <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In ft_preproc_polyremoval at line 75<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In ft_preproc_baselinecorrect at line 52<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In ft_timelockanalysis at line 174<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
the call to "ft_selectdata" took 0 seconds and required the additional allocation of an estimated 22 MB<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Warning: inconsistent sampleinfo <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In makessense at line 115<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In ft_datatype_timelock at line 72<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In ft_checkdata at line 479<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
In ft_timelockanalysis at line 207<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
I’ve run a loop over the trial field in the output of the ft_timelockanalysis as well as ft_preprocessing to check for NaNs in my 10-second data structs, but I didn’t find any when running this loop.<span lang="EN-US" class=""><span class="Apple-converted-space"> </span>I’ve
checked the relevant lines from the Fieldtrip functions but couldn’t find a way to solve the warning from there.<span class="Apple-converted-space"> </span></span>I’ve also checked the sampleinfo, but I sense the warning may be due to the sampleinfo in the
configuration being inconsistent with the actual data due to the removal of non-MEG channels from the sampleinfo in the resting file.<span lang="EN-US" class=""><o:p class=""></o:p></span></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
The warning message might influence later analyses, so I’m wondering if anyone has faced the same and/or has an explanation. <o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Thanks a lot in advance!<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
All the best,<br class="">
Marta<o:p class=""></o:p></div>
</div>
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<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!44dPKLWAx3oGspX-Q-IZx8b_gfPmQbTd45nbdyM61ROZgOiO2314lg4aY5eGcvDpKtQW3t1ilWOQcQ56Yd02ltXfOme3MNrQw0Ahfg$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!44dPKLWAx3oGspX-Q-IZx8b_gfPmQbTd45nbdyM61ROZgOiO2314lg4aY5eGcvDpKtQW3t1ilWOQcQ56Yd02ltXfOme3MNrQw0Ahfg$</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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