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<p><font size="2">Hi Jan-Mathijs, <br>
</font></p>
<p><font size="2">Yes, indeed, data have been generated with
Brainstorm and additional “in-house” programs. I use fieldtrip
directly for permutation statistics. <br>
</font></p>
<p><font size="2"> Best regards. <br>
</font></p>
<p><font size="2">Anne<br>
</font></p>
<div class="moz-cite-prefix">Le 20/12/2024 à 19:46, Schoffelen, J.M.
(Jan Mathijs) via fieldtrip a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:C3FDBBDB-6C5D-4C73-A22A-3BE17AB26F22@donders.ru.nl">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Hi Anne,
<div><br>
</div>
<div>It seems as if you have solved it yourself indeed. I did not
notice that the data structure that you pasted in an earlier
e-mail indeed was fieldtrip-incompatible, with an incorrect
‘dimord’. I don’t know where this data structure came from, but
if it was created using ‘purely’ fieldtrip functions, please do
point us to where in the code this happened. Otherwise, I will
file this as a ‘user error’, thanks for letting us know, and
glad that it now works for you.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs<br id="lineBreakAtBeginningOfMessage">
<div><br>
<blockquote type="cite">
<div>On 19 Dec 2024, at 16:53, 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>
<div class="moz-cite-prefix"
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;">
<br class="Apple-interchange-newline">
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"
style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
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,<span
class="Apple-converted-space"> </span><br>
</div>
</div>
</blockquote>
<p
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When I try cfg.neighbours = {}, instead of [], a bug
appears earlier at<span class="Apple-converted-space"> </span><br>
</p>
<p
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Unrecognized field name "label".<br>
<br>
Error in channelconnectivity (line 91)<br>
[seld] = match_str(chans, neighbours(chan).label);</p>
<p
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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
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after this function (channelconnectivity) and go back to<span
class="Apple-converted-space"> </span><br>
</p>
<p
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I have for the cfg structure and these 3 fields :<span
class="Apple-converted-space"> </span><br>
</p>
<p
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channel: {'V5_R'}<br>
neighbours: []<br>
connectivity: 0</p>
<p
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With cfg.neighbours={}; , in the function
channelconnectivity, the bug appears at line 91<br>
</p>
<p
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line 90 for chan=1:length(neighbours)<br>
line 91 [seld] = match_str(chans,
neighbours(chan).label);<br>
</p>
<p
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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
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So I go back cfg.chanel = {'V5_R'} and
cfg.neighbours=[] (cfg.connectivity = [] has<span
class="Apple-converted-space"> </span>no impact), I
find the same bug again, at the function <span
class="Apple-converted-space"> </span><font size="2">'findcluster'.<span
class="Apple-converted-space"> </span><br>
</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">But, I think that the problem comes from
the expected input data onoff of the function
findcluster :<span class="Apple-converted-space"> </span></font></p>
<p
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<font size="2">onoff = is a 3D boolean
matrix with size N1xN2xN3</font></p>
<p
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<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
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<font size="2">ftAllFiles{1}<br>
<br>
ans =<span class="Apple-converted-space"> </span><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'}<span
class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">with a first dimension as a scalar (only
one chanel).<span class="Apple-converted-space"> </span><br>
</font></p>
<p
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<font size="2">It now seems to be working properly. but
I must verify the results to be sure.<br>
</font></p>
<p
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<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
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. </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<span class="Apple-converted-space"> </span><br>
</font></p>
<blockquote type="cite"
cite="mid:FB284698-802A-4564-B6AA-9F6F9F463336@donders.ru.nl"
style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div>
<div>
<blockquote type="cite">
<div>On 19 Dec 2024, at 12:18, Anne Guérin via
fieldtrip<span class="Apple-converted-space"> </span><a
class="moz-txt-link-rfc2396E"
href="mailto:fieldtrip@science.ru.nl"
moz-do-not-send="true"><fieldtrip@science.ru.nl></a><span
class="Apple-converted-space"> </span>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
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">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
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">When I plot tmp (image(tmp)),
the result doesn't look ridiculous.<span
class="Apple-converted-space"> </span><br>
<br>
</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">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
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">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
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">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>
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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 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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</blockquote>
<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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