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<div class="moz-cite-prefix">Le 19/12/2024 à 14:57, Schoffelen, J.M.
(Jan Mathijs) via fieldtrip a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:FB284698-802A-4564-B6AA-9F6F9F463336@donders.ru.nl">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Anne,
<div><br>
</div>
<div>I don’t know what’s going on. </div>
<div><br>
</div>
<div>Have you tried cfg.neighbours = {} (i.e. curly rather than
square brackets), and/or explicitly defined cfg.connectivity =
[]; ?</div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br id="lineBreakAtBeginningOfMessage">
<div>Hi Jan-Mathijs, <br>
</div>
</div>
</blockquote>
<p>When I try cfg.neighbours = {}, instead of [], a bug appears
earlier at <br>
</p>
<p>Unrecognized field name "label".<br>
<br>
Error in channelconnectivity (line 91)<br>
[seld] = match_str(chans, neighbours(chan).label);</p>
<p>I solved it with cfg.chanel = {ROI} in order to overlap the
field .label of the data structure, and with cfg.neighbours = [];
<br>
</p>
<p>after this function (channelconnectivity) and go back to <br>
</p>
<p>I have for the cfg structure and these 3 fields : <br>
</p>
<p> channel: {'V5_R'}<br>
neighbours: []<br>
connectivity: 0</p>
<p>With cfg.neighbours={}; , in the function channelconnectivity,
the bug appears at line 91<br>
</p>
<p>line 90 for chan=1:length(neighbours)<br>
line 91 [seld] = match_str(chans,
neighbours(chan).label);<br>
</p>
<p>in fact with cfg.neighbours={} , the variable 'neighbours' is a
struct with no field, so length(neighbours)=1 , and the loop
begins and it's bug.</p>
<p>So I go back cfg.chanel = {'V5_R'} and cfg.neighbours=[]
(cfg.connectivity = [] has
<style type="text/css">.rtcContent { padding: 30px; }.lineNode {font-size: 10pt; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-style: normal; font-weight: normal; }</style>no
impact), I find the same bug again, at the function <font
size="2"> 'findcluster'. <br>
</font></p>
<p><font size="2">But, I think that the problem comes from the
expected input data onoff of the function findcluster : </font>
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<p><font size="2">onoff = is a 3D boolean matrix
with size N1xN2xN3</font></p>
<p><font size="2">three dimensions are expected for chan freq and
time, but in my case there are only two dimensions freq and
time. So I changed the indut data like this (for example for the
first subject) :</font></p>
<p><font size="2">ftAllFiles{1}<br>
<br>
ans = <br>
<br>
struct with fields:<br>
<br>
dimord: 'chan_freq_time'<br>
avg: [1×29×401 double]<br>
time: [-0.2000 -0.1990 -0.1980 -0.1970 -0.1960 -0.1950
-0.1940 -0.1930 -0.1920 -0.1910 -0.1900 -0.1890 -0.1880 -0.1870
-0.1860 … ]<br>
freq: [6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
24 25 26 27 28 29 30 31 32 33 34]<br>
label: {'V5_R'} <br>
</font></p>
<p><font size="2">with a first dimension as a scalar (only one
chanel). <br>
</font></p>
<p><font size="2">It now seems to be working properly. but I must
verify the results to be sure.<br>
</font></p>
<p><font size="2">The moral of the story is that you always have to
define a “chan” dimension, even if there's only one chanel, and
that it's not theoretically necessary to encode the data in this
case. </font></p>
<p><font size="2">Thank you. </font></p>
<p><font size="2">Best regards. </font></p>
<p><font size="2">Anne <br>
</font></p>
<blockquote type="cite"
cite="mid:FB284698-802A-4564-B6AA-9F6F9F463336@donders.ru.nl">
<div>
<div>
<blockquote type="cite">
<div>On 19 Dec 2024, at 12:18, Anne Guérin via fieldtrip <a
class="moz-txt-link-rfc2396E"
href="mailto:fieldtrip@science.ru.nl"><fieldtrip@science.ru.nl></a>
wrote:</div>
<br class="Apple-interchange-newline">
<div>
<p
style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;">
<font size="2">Hi,<span class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">I would like to use the FT permutations
test with cluster based correction on 2D data freq x
time with a within subject design. Data are obtained
after sources reconstruction and are for example
related to a particular ROI (e.g. V5_R). The first
dimension is a frequency dimension but not the
oscillatory brain frequency. This dimension is linked
to a temporal frequency of the input visual stimulus.
the second dimension is time (sRate = 1kHz) and data
are timelocked ERP for different values of this
temporale frequency (by step of 1Hz). The data
therefore has the same structure as if it had been
obtained by time-frequency analysis on a particular
electrode.<span class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">For example, here's the data for one
participant:<br>
ftAllFiles{1}<br>
<br>
ans =<span class="Apple-converted-space"> </span><br>
<br>
struct with fields:<br>
<br>
dimord: 'freq_time'<br>
avg: [29×401 double]<br>
time: [-0.2000 -0.1990 -0.1980 -0.1970 -0.1960
-0.1950 -0.1940 -0.1930 -0.1920 -0.1910 -0.1900
-0.1890 -0.1880 -0.1870 -0.1860 … ]<br>
freq: [6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
21 22 23 24 25 26 27 28 29 30 31 32 33 34]<br>
label: {'V5_R'}<br>
There are 29 participants for each conditions.
ftAllFiles have 2x29 cells, the first 29 correspond to
the first condition and the last 29 to the second
condition.<span class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">Here is the configuration :<span
class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">>> statcfg<br>
<br>
statcfg =<span class="Apple-converted-space"> </span><br>
<br>
struct with fields:<br>
<br>
frequency: 'all'<br>
parameter: 'avg'<br>
avgoverfreq: 'no'<br>
avgoverchan: 'no'<br>
latency: 'all'<br>
method: 'montecarlo'<br>
statistic: 'ft_statfun_depsamplesT'<br>
correctm: 'cluster'<br>
clusteralpha: 0.0500<br>
clusterstatistic: 'maxsum'<br>
minnbchan: 0<br>
tail: 1<br>
clustertail: 1<br>
alpha: 0.0500<br>
numrandomization: 100000<br>
ivar: 1<br>
uvar: 2<br>
design: [2×58 double]<br>
channel: 'all'<br>
neighbours: []<br>
avgovertime: 'no'</font></p>
<p
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<font size="2">When I run ftStat =
ft_freqstatistics(statcfg, ftAllFiles{:}); , the
program stops at the step 'findcluster':</font></p>
<p
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<font size="2">posclusobs = findcluster(tmp, connmat,
cfg.minnbchan);</font></p>
<p
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<font size="2">In fact tmp is 2D boolean table (29
frequency samples x 401 time samples), connmat is 4x4
matrix with 0 and <span class="Apple-converted-space"> </span></font><font
size="2">cfg.minnbchan=0. So bug with<span
class="Apple-converted-space"> </span></font><font
size="2">findcluster. See below.<span
class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">When I plot tmp (image(tmp)), the result
doesn't look ridiculous.<span
class="Apple-converted-space"> </span><br>
<br>
</font></p>
<p
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<font size="2">How to have a good configuration of
neighborhood for this single-sensor time-frequency
permutation test ? </font></p>
<p
style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;">
<font size="2">Thank you for your help. </font></p>
<p
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<font size="2">Best regards. </font></p>
<p
style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; 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;">
<font size="2">Anne</font></p>
<p
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<font size="2">ps : <span class="Apple-converted-space"> </span><br>
</font></p>
<div
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<br class="webkit-block-placeholder">
</div>
<p
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<font size="2">>> ftStat =
ft_freqstatistics(statcfg, ftAllFiles{:});<br>
the call to "ft_selectdata" took 0 seconds<br>
using "ft_statistics_montecarlo" for the statistical
testing<br>
using "ft_statfun_depsamplesT" for the single-sample
statistics<br>
constructing randomized design<br>
total number of measurements = 58<br>
total number of variables = 2<br>
number of independent variables = 1<br>
number of unit variables = 1<br>
number of within-cell variables = 0<br>
number of control variables = 0<br>
using a permutation resampling approach<br>
repeated measurement in variable 2 over 29 levels<br>
number of repeated measurements in each level is 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2<span
class="Apple-converted-space"> </span><br>
the maximum number of unique permutations is 536870912<br>
generated 100000 random permutations<br>
computing a parametric threshold for clustering<br>
computing statistic<br>
estimated time per randomization is 0.00 seconds<br>
computing statistic 100000 from 100000<br>
<br>
Error using findcluster<br>
invalid dimension of spatdimneighbstructmat<br>
<br>
Error in clusterstat (line 214)<br>
posclusobs = findcluster(tmp, connmat,
cfg.minnbchan);<br>
<br>
Error in ft_statistics_montecarlo (line 364)<br>
[stat, cfg] = clusterstat(cfg, statrand, statobs);<br>
<br>
Error in ft_freqstatistics (line 194)<br>
[stat, cfg] = statmethod(cfg, dat, design);<br>
</font></p>
<p
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<font size="2"> <br>
</font></p>
<p
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<font size="2"><br>
</font></p>
<pre class="moz-signature" cols="72"
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Anne Guérin-Dugué
PR Emérite Université Grenoble Alpes (UGA)
GIPSA-lab / PSD / Equipe ViBS
Bureau B146
Site Ampère
11 rue des Mathématiques
BP 46
F - 38042 GRENOBLE
tel : +33 (0)4 76 57 43 73
mel :<a href="mailto:anne.guerin@gipsa-lab.grenoble-inp.fr"
moz-do-not-send="true" class="moz-txt-link-freetext">anne.guerin@gipsa-lab.grenoble-inp.fr</a></pre>
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<pre wrap="" class="moz-quote-pre">_______________________________________________
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<pre class="moz-signature" cols="72">--
Anne Guérin-Dugué
PR Emérite Université Grenoble Alpes (UGA)
GIPSA-lab / PSD / Equipe ViBS
Bureau B146
Site Ampère
11 rue des Mathématiques
BP 46
F - 38042 GRENOBLE
tel : +33 (0)4 76 57 43 73
mel :anne.guerin@gipsa-lab.grenoble-inp.fr</pre>
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