<div dir="ltr">Dear
Jan-Mathijs,<div>Thank you for your response. I have gone through this thread : <a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2024-March/042417.html" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/pipermail/fieldtrip/2024-March/042417.html</a><<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2024-March%2F042417.html&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C9c4ab2b947b347f889a008dc546dd5da%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638478077945050349%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fHqrXqfBaYWkJoGyr17Z496%2BuyCDk8gWHh31bqNDll4%3D&reserved=0" rel="noreferrer" target="_blank">https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2024-March%2F042417.html&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C9c4ab2b947b347f889a008dc546dd5da%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638478077945050349%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fHqrXqfBaYWkJoGyr17Z496%2BuyCDk8gWHh31bqNDll4%3D&reserved=0</a>> to find solutions and applied various methods to visualize my statistical mask. </div><div>I chose 500 randomizations as a result of computational demands when applying 1000 permutations of montecarlo cluster method to the 100 participants I have.</div><div><br></div><div>I attempted the suggestions here: <a href="https://yuval-harpaz.github.io/MEG-course/html/course12.html#4">https://yuval-harpaz.github.io/MEG-course/html/course12.html#4</a></div><div>My statistical plots were not informative. What is a suggested alternative for plotting source statistics effects when computational demands are limited ?</div><div><br></div><div>Best,</div><div>Monalisa</div><div>Cognitive Neuroscience Master Student</div><div><br></div></div><div dir="ltr"><div dir="ltr"><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Apr 4, 2024 at 12:00 PM <<a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send fieldtrip mailing list submissions to<br>
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Today's Topics:<br>
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1. Re: Invalid file identifier when reading file with<br>
fiff_read_raw_segment (Schoffelen, J.M. (Jan Mathijs))<br>
2. Plotting parametric cluster permutation (MONALISA CHIKEZIE)<br>
3. Re: Plotting parametric cluster permutation<br>
(Schoffelen, J.M. (Jan Mathijs))<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 3 Apr 2024 10:02:11 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)"<br>
<<a href="mailto:janmathijs.schoffelen@donders.ru.nl" target="_blank">janmathijs.schoffelen@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Invalid file identifier when reading file<br>
with fiff_read_raw_segment<br>
Message-ID: <<a href="mailto:E16CE576-5B9A-4DE6-B485-94D414B1127D@donders.ru.nl" target="_blank">E16CE576-5B9A-4DE6-B485-94D414B1127D@donders.ru.nl</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Alexandria,<br>
<br>
Hmm, I am not sure what might be causing this. I cannot reproduce it on my end with the data that you provided (thanks for that!).<br>
I think that you might be working with an outdated copy of the fiff-readers - as provided in fieldtrip/external/mne.<br>
<br>
Your error stack mentions the error in fiff_read_raw_segment to be thrown at line 152, which is executing fiff_read_tag(…<br>
<br>
However, the most recent version of the code (which should be in line with the ‘original’ version <a href="https://github.com/mne-tools/mne-matlab" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-matlab</a><<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-matlab&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd6ab124f41c940b268c408dc53c5214f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638477353345408413%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=PdRDm3wMmu0xz4C081eEAaoUjBWSzuEvhZRA5XNtf20%3D&reserved=0" rel="noreferrer" target="_blank">https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmne-tools%2Fmne-matlab&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd6ab124f41c940b268c408dc53c5214f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638477353345408413%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=PdRDm3wMmu0xz4C081eEAaoUjBWSzuEvhZRA5XNtf20%3D&reserved=0</a>>) with its reads something else: <a href="https://github.com/fieldtrip/fieldtrip/blob/8f99c23131e221e1958bf3632a4aa125637ed501/external/mne/fiff_read_raw_segment.m#L152" rel="noreferrer" target="_blank">https://github.com/fieldtrip/fieldtrip/blob/8f99c23131e221e1958bf3632a4aa125637ed501/external/mne/fiff_read_raw_segment.m#L152</a><<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fblob%2F8f99c23131e221e1958bf3632a4aa125637ed501%2Fexternal%2Fmne%2Ffiff_read_raw_segment.m%23L152&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd6ab124f41c940b268c408dc53c5214f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638477353349939790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=K1bwmpH9XU7OjtHCirUjGje%2By%2BfV48z%2F0OYBzCTkN1A%3D&reserved=0" rel="noreferrer" target="_blank">https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fblob%2F8f99c23131e221e1958bf3632a4aa125637ed501%2Fexternal%2Fmne%2Ffiff_read_raw_segment.m%23L152&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd6ab124f41c940b268c408dc53c5214f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638477353349939790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=K1bwmpH9XU7OjtHCirUjGje%2By%2BfV48z%2F0OYBzCTkN1A%3D&reserved=0</a>><br>
<br>
Could you update your fieldtrip version, and try whether your problem persists? If so, we can take it from there.<br>
<br>
Best wishes,<br>
<br>
Jan-Mathijs<br>
<br>
PS: I have a working matlab implementation of a ‘vanilla’ signal-space separation procedure, incorporating both a spatial and subsequent temporal projection, which I wrote to be able to apply SSS to OPM data. Drop me a direct message if you would be interested in working on this together.<br>
<br>
<br>
<br>
<br>
On 3 Apr 2024, at 01:07, Xan McPherson via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><mailto:<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>>> wrote:<br>
<br>
Hello everyone,<br>
<br>
My name is Alexandria McPherson and I am a PhD student working with the physics behind MEG at the Institute for Learning and Brain Sciences, University of Washington, Seattle. Currently, I am focusing on ways to modify the signal space separation method for use with on-scalp MEG sensor systems.<br>
<br>
I am running into some issues using FieldTrip to load raw data from .fif files. Specifically, I have been working with the example file "sample-audvis-raw.fif" which is provided by MNE-Python in their "MEG/sample" data folder. Here is a Dropbox link to the data: <a href="https://www.dropbox.com/scl/fo/gffle6d9ppa47pkmes8gj/h?rlkey=8swrsnlyiz61si5ycrxg5x9c2&dl=0" rel="noreferrer" target="_blank">https://www.dropbox.com/scl/fo/gffle6d9ppa47pkmes8gj/h?rlkey=8swrsnlyiz61si5ycrxg5x9c2&dl=0</a><<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fscl%2Ffo%2Fgffle6d9ppa47pkmes8gj%2Fh%3Frlkey%3D8swrsnlyiz61si5ycrxg5x9c2%26dl%3D0&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd6ab124f41c940b268c408dc53c5214f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638477353349939790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=%2Fz85DWhK31J4Shu5NPAYZm30ObapTTDSsIX6X0uF650%3D&reserved=0" rel="noreferrer" target="_blank">https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fscl%2Ffo%2Fgffle6d9ppa47pkmes8gj%2Fh%3Frlkey%3D8swrsnlyiz61si5ycrxg5x9c2%26dl%3D0&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cd6ab124f41c940b268c408dc53c5214f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638477353349939790%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=%2Fz85DWhK31J4Shu5NPAYZm30ObapTTDSsIX6X0uF650%3D&reserved=0</a>>.<br>
I am first loading in the "info" structure, here is the code I am running:<br>
filename = "C:/Users/.../mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fifinfo = fiff_read_meas_info(filename);[raw] = fiff_setup_read_raw(filename);[data,times] = fiff_read_raw_segment(raw);<br>
<br>
I am able to read the "info" and "raw" objects, but when I run "fiff_read_raw_segment", I recieve the following error:<br>
Error using fseek. Invalid file identifier. Use fopen to generate a valid file identifier.<br>
Error in fiff_read_tag (line 83)<br>
fseek(fid,pos,'bof');<br>
Error in fiff_read_raw_segment (line 152)<br>
tag = fiff_read_tag(raw.fid,this.ent.pos);<br>
<br>
I also get this same error with other MEG "fif" files. Would you have any ideas as to what might be the issue?<br>
<br>
Thanks!<br>
Alexandria<br>
Physics PhD Student | I-LABS | University of Washington<br>
B.S. Engineering Physics | Colorado School of Mines<br>
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<br>
Message: 2<br>
Date: Thu, 4 Apr 2024 01:08:45 +0200<br>
From: MONALISA CHIKEZIE <<a href="mailto:chikeziemonalisa@gmail.com" target="_blank">chikeziemonalisa@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Plotting parametric cluster permutation<br>
Message-ID:<br>
<<a href="mailto:CAOJxHYLwEmZHExVMGBXCHOByOTyaKXnBLmMB%2B6xjYn7%2BQBQmCQ@mail.gmail.com" target="_blank">CAOJxHYLwEmZHExVMGBXCHOByOTyaKXnBLmMB+6xjYn7+QBQmCQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi All,<br>
I am relatively new to Fieldtrip and I want to plot source statistics<br>
results. How do I plot the results of my parametric cluster permutation.<br>
I used the following code to run the source statistics.<br>
<br>
cfg.stat = [];<br>
cfg.stat.method = 'analytic'; %<br>
cfg.stat.statistic = 'ft_statfun_depsamplesT';<br>
cfg.stat.correctm = 'fdr'; % Analytical methods with an FDR correction<br>
cfg.stat.parameter = 'pow';<br>
cfg.stat.clusteralpha = 0.05;<br>
cfg.stat.clustercritval = 0.05;<br>
cfg.stat.clusterstatistic = 'maxsum';<br>
cfg.stat.minnbchan = 2;<br>
cfg.stat.tail = 0;<br>
cfg.stat.clustertail = 0;<br>
cfg.stat.alpha = 0.025;<br>
cfg.stat.numrandomization = 500;<br>
cfg.stat.computecritval = 'yes' ; % calculates the critical values of the<br>
test statistics<br>
cfg.stat.computeprob = 'yes' ; %calculates the p-values<br>
cfg.stat.frequency = 'all';<br>
cfg.stat.ivar = 1; %conditions<br>
cfg.stat.uvar = 2; %Participnts<br>
<br>
I generated and saved the results as stats_results.mat.<br>
<br>
The output yielded the following fields:<br>
Field<br>
stat<br>
df<br>
critval<br>
prob<br>
mask<br>
dimord<br>
dim<br>
inside<br>
pos<br>
cfg<br>
<br>
Tutorials I saw on the ft website included fields like posclusters angled<br>
negclusters when using Montecarlo method.<br>
<br>
Thank you very much.<br>
<br>
Best,<br>
Monalisa<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 4 Apr 2024 06:09:49 +0000<br>
From: "Schoffelen, J.M. (Jan Mathijs)"<br>
<<a href="mailto:janmathijs.schoffelen@donders.ru.nl" target="_blank">janmathijs.schoffelen@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Plotting parametric cluster permutation<br>
Message-ID: <<a href="mailto:735242CD-4540-4293-8E99-C811CAE9A05C@donders.ru.nl" target="_blank">735242CD-4540-4293-8E99-C811CAE9A05C@donders.ru.nl</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Monalisa,<br>
<br>
The cfg that you used to instruct the statistics computation is somewhat ambiguous, and contains specification for options that are mutually exclusive.<br>
Specifically, when specifying cfg.correctm = ‘fdr’, all options that pertain to clustering have become non-functional (because the thing you fill in for correctm takes precedence in determining what’s going to happen). In other words, you either use ‘fdr’(=false discovery rate), or ‘cluster’(=for cluster-based inference + multiple comparison correction), not both. Thus, indeed, the output of the statistics computation by design will not have any information pertaining to clusters. The effect of the false discovery rate will be visible in the ‘mask’ field, which specifies for each channel/source-time-(frequency) point whether the null hypothesis of exchangeability between conditions can be rejected with sufficient confidence. The relationship between the p-values and mask are not so straightforward when using ‘fdr’ as a correction method. This is something that recently came up in another (unresolved, probably TLDR) thread: <a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2024-March/042417.html" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/pipermail/fieldtrip/2024-March/042417.html</a><<a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2024-March%2F042417.html&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C9c4ab2b947b347f889a008dc546dd5da%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638478077945050349%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fHqrXqfBaYWkJoGyr17Z496%2BuyCDk8gWHh31bqNDll4%3D&reserved=0" rel="noreferrer" target="_blank">https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2024-March%2F042417.html&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C9c4ab2b947b347f889a008dc546dd5da%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638478077945050349%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fHqrXqfBaYWkJoGyr17Z496%2BuyCDk8gWHh31bqNDll4%3D&reserved=0</a>><br>
<br>
So, long story short, if you want to make a visualization of the effect, I would display the statistics’ value (as present in the stat-field) and creatively think of a way of highlighting the data points that survive the statistical mask.<br>
<br>
One final point: when using ‘fdr’ typically it only makes sense if you use a very large number of randomizations, in your case I would go way beyond the listed 500. If your design admits (i.e. the maximum number of randomizations will be 2^#-of-participants) you should use at least 10000 or so. If that’s not possible, probably you’d need to consider another way of doing your inference.<br>
<br>
Good luck,<br>
Jan-Mathijs<br>
<br>
<br>
On 4 Apr 2024, at 01:08, MONALISA CHIKEZIE via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><mailto:<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>>> wrote:<br>
<br>
Hi All,<br>
I am relatively new to Fieldtrip and I want to plot source statistics results. How do I plot the results of my parametric cluster permutation.<br>
I used the following code to run the source statistics.<br>
<br>
cfg.stat = [];<br>
cfg.stat.method = 'analytic'; %<br>
cfg.stat.statistic = 'ft_statfun_depsamplesT';<br>
cfg.stat.correctm = 'fdr'; % Analytical methods with an FDR correction<br>
cfg.stat.parameter = 'pow';<br>
cfg.stat.clusteralpha = 0.05;<br>
cfg.stat.clustercritval = 0.05;<br>
cfg.stat.clusterstatistic = 'maxsum';<br>
cfg.stat.minnbchan = 2;<br>
cfg.stat.tail = 0;<br>
cfg.stat.clustertail = 0;<br>
cfg.stat.alpha = 0.025;<br>
cfg.stat.numrandomization = 500;<br>
cfg.stat.computecritval = 'yes' ; % calculates the critical values of the test statistics<br>
cfg.stat.computeprob = 'yes' ; %calculates the p-values<br>
cfg.stat.frequency = 'all';<br>
cfg.stat.ivar = 1; %conditions<br>
cfg.stat.uvar = 2; %Participnts<br>
<br>
I generated and saved the results as stats_results.mat.<br>
<br>
The output yielded the following fields:<br>
Field<br>
stat<br>
df<br>
critval<br>
prob<br>
mask<br>
dimord<br>
dim<br>
inside<br>
pos<br>
cfg<br>
<br>
Tutorials I saw on the ft website included fields like posclusters angled negclusters when using Montecarlo method.<br>
<br>
Thank you very much.<br>
<br>
Best,<br>
Monalisa<br>
<br>
<br>
<br>
<br>
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<a href="https://doi.org/10.1371/journal.pcbi.1002202" rel="noreferrer" target="_blank">https://doi.org/10.1371/journal.pcbi.1002202</a><br>
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------------------------------<br>
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End of fieldtrip Digest, Vol 161, Issue 4<br>
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