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Hi Francisco,
<div class=""><br class="">
</div>
<div class="">The fieldname ‘avg’, in the source reconstructed data has a historical reason, but is a bit unlucky and misleading. Indeed it refers to the fact that the numeric data in the sub-structure reflects an average (across a bunch observations). In your
case it is the signal power in the baseline and in the post stimulus respectively. </div>
<div class=""><br class="">
</div>
<div class="">Now, if you want to run a permutation test, you need a sufficient amount of subjects (which in this case serve as the ‘observations’). This is what Stephan refers to in his earlier reply in this thread. Given that you used only 1 subject worth
of data, the code throws an error (and correctly so), because there is not much to permute. To do a meaningful statistical inference you need at least results from 15 or so (but ideally more) subjects.</div>
<div class=""><br class="">
</div>
<div class="">If, on the other hand, you want to perform the statistics within the subject (i.e. using the individual trials as units-of-observation for the permutation) you need to set up your analysis in a slightly different way.</div>
<div class=""><br class="">
</div>
<div class="">Best wishes,</div>
<div class=""><br class="">
</div>
<div class="">Jan-Mathijs</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 18 Nov 2022, at 14:20, FRANCISCO JAVIER GÓMEZ CAMPOS via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Dear Stephan,</span></p>
<p dir="ltr" style="margin-top: 12pt; margin-bottom: 0pt; line-height: 1.2;" class="">
<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Thank you for your response, but in this case our source analysis data does not contain the average across subjects.
If you refer to the ‘avg’ structure, it is one of the outputs coming from performing the source analysis by contrasting the pre and post stimulus interval. During the process, I calculate an inverse filter calculated from both intervals together and then applied
separately to each interval, from this process I obtain the output ‘avg’, I do this for each subject and each condition.</span></p>
<p dir="ltr" style="margin-top: 12pt; margin-bottom: 0pt; line-height: 1.2;" class="">
<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">You can see it in more detail at this link</span><a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/beamformer/__;!!HJOPV4FYYWzcc1jazlU!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1IE_2mg0g$" class="ContentPasted0"><span style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;" class=""> </span><span style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(0, 0, 128); background-color: rgb(255, 255, 255); font-weight: 400; text-decoration: underline;" class="">https://www.fieldtriptoolbox.org/tutorial/beamformer/</span></a><span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;"> in
the section<span class="Apple-converted-space"> </span></span><span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400; font-style: italic;">‘Source Analysis: Contrasting activity
to another interval’.</span></p>
<p dir="ltr" style="margin-top: 12pt; margin-bottom: 0pt; line-height: 1.2;" class="">
<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Our source data are distributed as follows, for each subject I have the mean power of each voxel for each condition
independently, perhaps best understood with the following image:</span><a href="https://urldefense.com/v3/__https://gyazo.com/00af9e5ca9647bec71d561c4197eefc5__;!!HJOPV4FYYWzcc1jazlU!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1KfbWELHw$" class="ContentPasted0"><span style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;" class=""> </span></a><a href="https://urldefense.com/v3/__https://gyazo.com/39bb9c919f469d95f984a68b6dca6e18__;!!HJOPV4FYYWzcc1jazlU!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1JEfrkLwg$" class="ContentPasted0"><span style="font-size: 12pt; font-family: "Times New Roman"; color: rgb(17, 85, 204); background-color: rgb(255, 255, 255); font-weight: 400; text-decoration: underline;" class="">https://gyazo.com/39bb9c919f469d95f984a68b6dca6e18</span></a><span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;"> </span></p>
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<span style="border: none; display: inline-block; overflow: hidden; width: 704px; height: 348px;" class=""><img width="704" height="348" class="ContentPasted0" src="https://lh6.googleusercontent.com/fLsaCgJYAhYIaQRGNxzNEdwzQN7n10QBbjS-oOeTbhvP68qQ3rBW8dnFa37-Vg2pzaNbY2NiVPCW4YCNLwwed-IpPQfXo-RzL1Sh9ac7LgqEkClX4kIr79C_BAfOvGhmtIMeW-wgY5VYJ31TSbyQpcllTBTnD13S5roabFDKvjtghYDMV7sr-2Kz1Hanbg" style="margin-top: 0px;"></span>
<div style="margin-top: 0pt; margin-bottom: 0pt; line-height: 1.3090909090909089;" class="">
<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">We suspect that the problem could stem from the fact that our data structure differs from the one described in the
tutorial for ft_sourcestatistics in that we do not provide sources from each trail, but the average source of each condition instead. So, our question is whether with this data structure we can perform a nonparametric randomization test, by creating the null
hypothesis distribution shuffling voxels between conditions and then obtain an 'average' null distribution across subjects. I am not sure if this makes sense. Another way could be to shuffle conditions across subjects and obtain a null hypothesis distribution
from this shuffle.</span></div>
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<p dir="ltr" style="margin-top: 12pt; margin-bottom: 0pt; line-height: 1.3090909090909089;" class="">
<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Thank you again,</span></p>
<p dir="ltr" style="margin-top: 12pt; margin-bottom: 0pt; line-height: 1.3090909090909089;" class="">
<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Best,</span></p>
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<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Francisco Javier Gómez</span></p>
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<span class="ContentPasted0" style="font-size: 12pt; font-family: "Times New Roman"; background-color: rgb(255, 255, 255); font-weight: 400;">Instituto de Biomedicina de Sevilla(IBIS)</span></p>
</b><br class="Apple-interchange-newline ContentPasted0">
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<font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">De:</b><span class="Apple-converted-space"> </span>STEPHAN MORATTI <<a href="mailto:smoratti@psi.ucm.es" class="">smoratti@psi.ucm.es</a>><br class="">
<b class="">Enviado:</b><span class="Apple-converted-space"> </span>jueves, 17 de noviembre de 2022 14:44<br class="">
<b class="">Para:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>FRANCISCO JAVIER GÓMEZ CAMPOS <<a href="mailto:fjgomez-ibis@us.es" class="">fjgomez-ibis@us.es</a>><br class="">
<b class="">Asunto:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] Help with ft_sourcestatistics</font>
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<div dir="ltr" class="">Dear Francisco,
<div class=""><br class="">
</div>
<div class="">It seems that in your source data you probably have the average across subjects, but the individual source data for each subject is missing. You may store them in individual cells and then submit these cells to the source statistics.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Stephan</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">El jue, 17 nov 2022 a las 11:32, FRANCISCO JAVIER GÓMEZ CAMPOS via fieldtrip (<<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>>) escribió:<br class="">
</div>
<blockquote class="x_gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;">
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Dear community,<br class="">
</div>
<div style="font-family: Mangal, "Nirmala UI", "Devanagari Sangam MN", sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);" class="">
<br class="">
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<div style="font-family: Mangal, "Nirmala UI", "Devanagari Sangam MN", sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);" class="">
<div class="">I am having problems using the ft_sourcestatistics function. I would like to use this function</div>
<div class="">to conduct a within-subject analysis to establish which areas show differences between two</div>
<div class="">experimental conditions. I mainly have doubts about two aspects, the first one is about how to</div>
<div class="">attach the source analysis data, and the second one is about the design of the design matrix.</div>
<div class=""><br class="">
</div>
<div class="">Regarding the data coming from the source analysis, I have the sources separated by</div>
<div class="">conditions (obtained by following this tutorial<span class="Apple-converted-space"> </span><a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/tutorial/beamformer/__;!!HJOPV4FYYWzcc1jazlU!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1IE_2mg0g$" target="_blank" class="">https://www.fieldtriptoolbox.org/tutorial/beamformer/</a>):</div>
<div class=""><br class="">
</div>
<div class="">Source analysis data for each condition:</div>
<blockquote style="margin-top: 0px; margin-bottom: 0px;" class="">
<div class="">freq: 4.8302</div>
<div class="">cfg: [1×1 struct]</div>
<div class="">dim: [85 110 132]</div>
<div class="">inside: [1234200×1 logical]</div>
<div class="">pos: [1234200×3 double]</div>
<div class="">method: 'average'</div>
<div class="">avg: [1×1 struct]</div>
</blockquote>
<blockquote style="margin-top: 0px; margin-bottom: 0px;" class="">
<div class=""><br class="">
</div>
<div class="">avg:</div>
<blockquote style="margin-top: 0px; margin-bottom: 0px;" class="">
<div class="">pow: [1234200×1 double]</div>
<div class="">noise: [1234200×1 double]</div>
<div class="">filter: {1234200×1 cell}</div>
<div class="">label: {61×1 cell}</div>
<div class="">filterdimord: '{pos}_ori_chan'</div>
</blockquote>
</blockquote>
<div class=""><br class="">
</div>
<div class="">The code I use is the following (based on this code in this tutorial</div>
<div class=""><a href="https://urldefense.com/v3/__https://www.fieldtriptoolbox.org/example/source_statistics/__;!!HJOPV4FYYWzcc1jazlU!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1IM6xnJLg$" target="_blank" class="">https://www.fieldtriptoolbox.org/example/source_statistics/</a><span class="Apple-converted-space"> </span>)
:</div>
<div class=""><br class="">
</div>
<blockquote style="margin-top: 0px; margin-bottom: 0px;" class="">
<div class="">design=[1 2]; %for 2 conditions</div>
<div class="">% run sourcestatistics using cluster based correction %</div>
<div class="">cfg = [];</div>
<div class="">cfg.dim = sourceanalysis_condition1(1).dim;</div>
<div class=""><br class="">
</div>
<div class="">cfg.method = 'montecarlo';</div>
<div class="">cfg.statistic = 'ft_statfun_depsamplesT';</div>
<div class="">cfg.parameter = 'pow';</div>
<div class="">cfg.correctm = 'cluster';</div>
<div class="">cfg.numrandomization = 'all';</div>
<div class="">cfg.alpha = 0.05; % note that this only implies single-sided testing</div>
<div class="">cfg.tail = 0;</div>
<div class="">cfg.design(1,:) = [1:length(find(design==1)) 1:length(find(design==2))];</div>
<div class="">cfg.design(2,:) = design;</div>
<div class="">cfg.uvar = 1; % row of design matrix that contains unit variable (in this case: trials)</div>
<div class="">cfg.ivar = 2; % row of design matrix that contains independent variable (the conditions)</div>
<div class="">stat = ft_sourcestatistics(cfg, sourceanalysis_condition1, sourceanalysis_condition2)</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">When I run this code, I get the following error:</div>
<blockquote style="margin-top: 0px; margin-bottom: 0px;" class="">
<div class="">Error using ft_statfun_depsamplesT (line 83)</div>
<div class="">The data must contain at least two units of observation (trials or subjects).</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">I understand that my design matrix and/or the structure of sourceanalysis_condition are</div>
<div class="">wrong, I have tried different combinations and I cannot find the solution. I hope you can</div>
<div class="">guide me in this regard so that I can adapt it to the conditions of my study.</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Francisco Javier Gómez,</div>
Instituto de Biomedicina de Sevilla (IBIS)<br class="">
</div>
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<font face="monospace, monospace" class="">Stephan Moratti, PhD</font></div>
<div class=""><font face="monospace, monospace" class="">Profesor de Psicología Experimental</font></div>
<div class=""><font face="monospace, monospace" class="">Departamento de Psicología Experimental</font></div>
<div class=""><font face="monospace, monospace" class="">Facultad de Psicología</font></div>
<div class=""><font face="monospace, monospace" class="">Center for Cognitive and Computational Neuroscience</font></div>
<div class=""><font face="monospace, monospace" class="">Universidad Complutense de Madrid</font></div>
<div class=""><font face="monospace, monospace" class=""><a href="mailto:smoratti@ucm.es" target="_blank" class="">smoratti@ucm.es</a></font></div>
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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="">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!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1IhCnYeZw$" 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!6N5sAUOLFHX5VmnV9FuI390JcfBKDqKW5I94Eju8n6bs515XFjjjZfbDgj9-ZJOis1KRANuRDSZRpVED-QyvuI2uvBEic1IhCnYeZw$</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 class="Apple-converted-space"> </span></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="">
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