From bahman at neuromotor.org Sun Jul 1 19:43:00 2018 From: bahman at neuromotor.org (Bahman Nasseroleslami) Date: Sun, 1 Jul 2018 18:43:00 +0100 Subject: [FieldTrip] Research Assistant Position in Neural Engineering - Trinity College Dublin, the University of Dublin, Dublin, Ireland Message-ID: Dear all, There is a research assistant position available in Academic Unit of Neurology, Trinity College Dublin, the University of Dublin, Dublin, Ireland. The position is ideally suited to an individual with a BSc/MSc degree who is considering pursuing a PhD degree in longer term. --------------------------------------- Post Specification (033160) Post Title: Research Assistant in Neural Engineering Post Status: 12 month Fixed-term Contract, Full-time Research Group / Department / School: Academic Unit of Neurology, School of Medicine, Trinity College Dublin, the University of Dublin Location: Trinity Biomedical Sciences Institute, Trinity College Dublin, the University of Dublin College Green, Dublin D02 R590, Ireland Reports to: Professor Orla Hardiman/Dr Bahman Nasseroleslami Salary: Appointment will be made on the Research Assistant (Level 1) Salary Scale at a point in line with Government Pay Policy, €21,674 to €28,423 per annum (commensurate with qualifications and experience). Appointment will be made no higher than point 10. Hours of Work: 40 hours per week Closing Date: 12 Noon (Irish Standard Time), 24 July 2018 Please note that Garda vetting will be sought in respect of individuals who come under consideration for a post. Post Summary Applications are invited for a motivated and self-driven individual for the position of research assistant with the Irish ALS Research Group, hosted in the Trinity Biomedical Sciences Institute (TBSI)'s Academic Unit of Neurology. The ideal candidate will have an undergraduate or master's degree in engineering, bioengineering, mathematics, physics, computational biology, or a cognate area. Familiarity with and/or the ability to quickly acquire skills in electrophysiological recordings and analysis (e.g. EEG/EMG), would be highly desirable as would a knowledge of computer programming (MATLAB). --------------------------------------- The detailed job description file (PDF) and the application instructions can be found online at http://jobs.tcd.ie. or directly from https://drive.google.com/file/ d/14Q7DxqobPQCjgKpZ4UJS68xTIlRvnPcd/view?usp=sharing It would be really appreciated if you could share this with those that may be interested. Sincerely Bahman -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Sun Jul 1 20:10:06 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Sun, 1 Jul 2018 14:10:06 -0400 Subject: [FieldTrip] .avg field in GA structure for interaction test Message-ID: Hi Fieldtrip, I am following the tutorial 'How to test an interaction effect using cluster-based permutation tests?' for my own dataset. It says to compute the GA for each condition (my design is 2x2 so a total of 4 GA structures) with keepindividual set to 'yes'. However, when making the difference structures, it says the assignment to the difference structure should be made using the .avg field from 2 of the previous GA structures. But with the keepindividual set to 'yes', I am getting no .avg field in these GA structures to be used. Any advice as to how solve this issue? Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sun Jul 1 20:16:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sun, 1 Jul 2018 18:16:00 +0000 Subject: [FieldTrip] Concatenate different size of trials into single one trial In-Reply-To: References: Message-ID: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> Hi Yadwinder, Why would you want this? For this purpose, ft_appenddata is not your friend, if you want to ‘create a single data matrix’. It concatenate a bunch of matrices, you can use cat(2,data.trial{:}), but this will only be a meaningful operation in a very limited number of cases. Most of the time, the last time point of trial n-1 will not be temporally aligned with the first time point of trial n, and even if that were the case, trial specific filtering, baseline correction, or any trial-specific processing in general will lead to discontinuities in the signals. Best wishes, Jan-Mathijs On 30 Jun 2018, at 15:06, Yadwinder Kaur > wrote: Dear All I have pre-processed my EEG data cutting into different trials (35 trials total) using fieldtrip , now I wish to concatenate them into one single data matrix. The length of each trial varies form each other. ofcourse, ft_appenddata didn't work in this case. I would highly appreciate any help to solve this issue. Thanks in advance. Regards Yadwinder _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yadwinder.kaur at stud.uni-greifswald.de Sun Jul 1 23:00:55 2018 From: yadwinder.kaur at stud.uni-greifswald.de (Yadwinder Kaur) Date: Sun, 01 Jul 2018 23:00:55 +0200 Subject: [FieldTrip] Concatenate different size of trials into single one trial In-Reply-To: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> References: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> Message-ID: <3b876e61d0640121b93f7a60decaedd9@groupware.uni-greifswald.de> Hi Jan   Thanks for your reply.My idea was to extract trials (based on stimulus followed by response) , perform preprocessing and at the end concatenate them together, because my aim is to further divide the concatenated segment into four parts to perform latent variable analysis. Am I doing wrong in this way?  Thanks Regards Yadwinder On Sunday, 01-07-2018 at 20:16 Schoffelen, J.M. (Jan Mathijs) wrote: Hi Yadwinder, Why would you want this?  For this purpose, ft_appenddata is not your friend, if you want to ‘create a single data matrix’. It concatenate a bunch of matrices, you can use cat(2,data.trial{:}), but this will only be a meaningful operation in a very limited number of cases. Most of the time, the last time point of trial n-1 will not be temporally aligned with the first time point of trial n, and even if that were the case, trial specific filtering, baseline correction, or any trial-specific processing in general will lead to discontinuities in the signals. Best wishes, Jan-Mathijs On 30 Jun 2018, at 15:06, Yadwinder Kaur wrote: Dear All I have pre-processed my EEG data cutting into different trials (35 trials total) using fieldtrip , now I wish to concatenate them into one single data matrix. The length of each trial varies form each other. ofcourse, ft_appenddata didn't work in this case. I would highly appreciate any help to solve this issue. Thanks in advance. Regards Yadwinder _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alessandro.orticoni at gmail.com Mon Jul 2 00:21:53 2018 From: alessandro.orticoni at gmail.com (Alessandro Orticoni) Date: Mon, 2 Jul 2018 00:21:53 +0200 Subject: [FieldTrip] [Fieldtrip] Line noise Removal In-Reply-To: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> References: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Thanks a lot for your reply and your tips. Actually I've already segmented the data in 30 seconds epochs, and the reason why I did it is that these are sleep data: so I should keep this length because of the night scoring. I tried to enlarge the notch too, but it still doesn't work; the spectra before and after the filtering are exactly the same. Best, Alessandro Il giorno gio 28 giu 2018 alle ore 19:35 Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> ha scritto: > Dear Alessandro, > > Given the code you provided it looks as if you have one single very long > trial that you subject to dft-filtering. If the power line fluctuations > actually do vary a bit in amplitude, which is likely (particularly given > long sections of data), the pure 50 (or 60) Hz sinusoid will get some > ‘bandwidth’, so the removal won’t be perfect. I’d recommend to call > ft_redefinetrial first, and then do a second call to ft_preprocessing with > the dftfilter switched on. Yet, I’d expect that with 30 s segments it still > won’t work that well. In this case you could widen the notch a bit by > specifying cfg.dftfreq = 50+(-n:n)./30;, with n put to a small number, e.g. > <=3. However, unless you have good reasons to have the data chopped in > half-minute segments, I’d also consider to reduce this length, because you > probably do not need to have a 1/30 Hz frequency resolution in your > spectral decomposition. > > Best wishes, > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Associate PI, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 28 Jun 2018, at 16:22, Alessandro Orticoni < > alessandro.orticoni at gmail.com> wrote: > > Dear experts, > > I'm basically a beginner in coding with Fieldtrip, and I'm having a > problem with line noise filtering. > I would like to remove it from the heart rate signal, and I tried just > typing 'yes' at the option cfg.dftfilter. > But is doesn't seem to work, since the power spectrum contains the 50Hz > and her harmonics even after the filtering. > > You can find the code in the following lines: > > %% ===FREQUENCY Pre Filtering VERIFICATION=== > fs=data.fsample; > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'ECG 2'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.pad = 'nextpow2'; > cfg.foilim = [0.3 fs/2]; % teorema di Nyquist > freq_epoched_Cz = ft_freqanalysis(cfg, data_epoched_Cz); > > %% ===Plot Spectra=== > figure; > plot(freq_epoched_Cz.freq,mag2db(freq_epoched_Cz.powspctrm)); > > %% ===Filtering=== > cfg = []; > cfg.channel = {'ECG 2'}; > cfg.dftfilter = 'yes'; > ECG_Filtered = ft_preprocessing(cfg,data_Cz); > > cfg = []; > cfg.length = 30; % in seconds; > cfg.overlap = 0; > data_epoched_ECG_Filtered = ft_redefinetrial(cfg, ECG_Filtered); > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.pad = 'nextpow2'; > cfg.foilim = [0.3 fs/2]; % teorema di Nyquist > freq_epoched_Cz_Filtered = ft_freqanalysis(cfg, data_epoched_ECG_Filtered); > > %% ===Plot Spectra=== > > plot(freq_epoched_Cz_Filtered.freq,mag2db(freq_epoched_Cz_Filtered.powspctrm)); > > Thanks a lot. > > Kind regards, > Alessandro Orticoni > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Mon Jul 2 14:37:08 2018 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Mon, 2 Jul 2018 14:37:08 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel Message-ID: Dear Fieldtrippers, I have followed the Salzburg tutorial (http://www.fieldtriptoolbox. org/tutorial/salzburg) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. Best regards, Uri Ramirez University of Würzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From uwe.graichen at tu-ilmenau.de Mon Jul 2 14:46:06 2018 From: uwe.graichen at tu-ilmenau.de (Uwe Graichen) Date: Mon, 2 Jul 2018 14:46:06 +0200 Subject: [FieldTrip] =?utf-8?q?8th_International_Summer_School_=E2=80=9EMu?= =?utf-8?q?ltimodal_integration_of_brain_measurements_in_research_and_clin?= =?utf-8?q?ical_practice=E2=80=9C?= In-Reply-To: References: Message-ID: <0e7c5650-27bf-6225-9d8b-a651ec60c978@tu-ilmenau.de> Dear colleagues, we are pleased to announce the 8th International Summer School in Biomedical Engineering „Multimodal integration of brain measurements in research and clinical practice“, 1st – 12th October 2018 in Chengdu, China. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to EEG/MEG source reconstruction technologies in the frame work of multimodal integration of brain measurements in research and clinical practice. In particular, the 8th International Summer School on Biomedical Engineering will focus on methodological approaches and challenges, measurement devices and characteristics, types of underlying theoretic modeling, specifics of data analysis, ability to derive conclusions about neuroscientific meaning. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 8th International Summer School in Biomedical Engineering: www.bme-school.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Pedro Antonio Valdés-Sosa Dezhong Yao Jens Haueisen Thomas Knösche From tzvetan.popov at uni-konstanz.de Mon Jul 2 16:54:54 2018 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 2 Jul 2018 16:54:54 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: References: Message-ID: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Dear Uri, the solution to the problem (mesh inflation) is outlined in this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting?s[]=natmeg&s[]=headmodel#procedure Scroll down to the section "Construct the EEG volume conduction model" Good luck, tzvetan > Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos : > > Dear Fieldtrippers, > > I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.org/tutorial/salzburg ) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. > > What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? > > The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. > > Best regards, > > Uri Ramirez > University of Würzburg > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 2 17:47:48 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 2 Jul 2018 15:47:48 +0000 Subject: [FieldTrip] [Fieldtrip] Line noise Removal In-Reply-To: References: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> Message-ID: please have a look at the following piece of documentation: http://www.fieldtriptoolbox.org/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter?s[]=dftfilter Jan-Mathijs On 2 Jul 2018, at 00:21, Alessandro Orticoni > wrote: Dear Jan-Mathijs, Thanks a lot for your reply and your tips. Actually I've already segmented the data in 30 seconds epochs, and the reason why I did it is that these are sleep data: so I should keep this length because of the night scoring. I tried to enlarge the notch too, but it still doesn't work; the spectra before and after the filtering are exactly the same. Best, Alessandro Il giorno gio 28 giu 2018 alle ore 19:35 Schoffelen, J.M. (Jan Mathijs) > ha scritto: Dear Alessandro, Given the code you provided it looks as if you have one single very long trial that you subject to dft-filtering. If the power line fluctuations actually do vary a bit in amplitude, which is likely (particularly given long sections of data), the pure 50 (or 60) Hz sinusoid will get some ‘bandwidth’, so the removal won’t be perfect. I’d recommend to call ft_redefinetrial first, and then do a second call to ft_preprocessing with the dftfilter switched on. Yet, I’d expect that with 30 s segments it still won’t work that well. In this case you could widen the notch a bit by specifying cfg.dftfreq = 50+(-n:n)./30;, with n put to a small number, e.g. <=3. However, unless you have good reasons to have the data chopped in half-minute segments, I’d also consider to reduce this length, because you probably do not need to have a 1/30 Hz frequency resolution in your spectral decomposition. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Associate PI, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 28 Jun 2018, at 16:22, Alessandro Orticoni > wrote: Dear experts, I'm basically a beginner in coding with Fieldtrip, and I'm having a problem with line noise filtering. I would like to remove it from the heart rate signal, and I tried just typing 'yes' at the option cfg.dftfilter. But is doesn't seem to work, since the power spectrum contains the 50Hz and her harmonics even after the filtering. You can find the code in the following lines: %% ===FREQUENCY Pre Filtering VERIFICATION=== fs=data.fsample; cfg = []; cfg.output = 'pow'; cfg.channel = 'ECG 2'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.pad = 'nextpow2'; cfg.foilim = [0.3 fs/2]; % teorema di Nyquist freq_epoched_Cz = ft_freqanalysis(cfg, data_epoched_Cz); %% ===Plot Spectra=== figure; plot(freq_epoched_Cz.freq,mag2db(freq_epoched_Cz.powspctrm)); %% ===Filtering=== cfg = []; cfg.channel = {'ECG 2'}; cfg.dftfilter = 'yes'; ECG_Filtered = ft_preprocessing(cfg,data_Cz); cfg = []; cfg.length = 30; % in seconds; cfg.overlap = 0; data_epoched_ECG_Filtered = ft_redefinetrial(cfg, ECG_Filtered); cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.pad = 'nextpow2'; cfg.foilim = [0.3 fs/2]; % teorema di Nyquist freq_epoched_Cz_Filtered = ft_freqanalysis(cfg, data_epoched_ECG_Filtered); %% ===Plot Spectra=== plot(freq_epoched_Cz_Filtered.freq,mag2db(freq_epoched_Cz_Filtered.powspctrm)); Thanks a lot. Kind regards, Alessandro Orticoni _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maxime.ferez at gmail.com Tue Jul 3 09:57:19 2018 From: maxime.ferez at gmail.com (maxime ferez) Date: Tue, 3 Jul 2018 09:57:19 +0200 Subject: [FieldTrip] Problems with "filter_with_correction" Message-ID: Dear all, I have a question about Fieldtrip artifact-rejection. I find myself having a problem that I do not know how to solve. I am currently working on a pc a little old (~ 5 years) and my analyzes worked properly, or at least I had no bug. When I changed my pc the problem has arrived. I have an error message "Calculated filter coefficients have poles on or outside the unit circle and will not be stable. Try a higher cutoff frequency or a different type/order of filter" that appears in the "filter_with_correction" function .The problem seems to occur during the "roots" function of Matlab. I verified and the vector that is introduced is exactly the same in both cases, but after the function “roots” runs the result differs slightly and induces the error message above. Has anyone ever had this problem or know where the problem might come from? On both pcs I have exactly the same versions of Matlab (R2017a) and fieldtrip (fieldtrip-20171004 and fieldtrip-20180626). Scripts and data are also identical in all cases. I have tried several configurations but failed to find the solution: - Ubuntu 16.04 machine about 5 years -> OK - Ubuntu 16.04 machine about 2 years -> Not OK The two machines above are identical in all softwares (deployed with script in PXE) - Fedora 27 machine about 2 years -> Not OK - Ubuntu 16.04 about 2 years -> Not OK - Fedora 17 about 8 years old -> OK - Centos7 machine less than a year -> Not OK To conclude, the script only works on old hardware but this does not seem logical as an explanation. Best regards, Maxime Ferez -- Maxime Ferez, ingénieur d'étude Centre de Recherche en Neuroscience de Lyon (CRNL) Inserm équipe Dycog Bron, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Tue Jul 3 11:08:14 2018 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Tue, 3 Jul 2018 11:08:14 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> References: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Message-ID: Dear Tzvetan, That worked perfectly, thank you! Are there guidelines for use of mesh inflation? E.g., does dilation by two voxels greatly bias source reconstruction? If one inflates a subject's mesh, must one then inflate all other subjects' meshes to the same degree? Thank you again, Uri 2018-07-02 16:54 GMT+02:00 Tzvetan Popov : > Dear Uri, > > the solution to the problem (mesh inflation) is outlined in this tutorial: > http://www.fieldtriptoolbox.org/tutorial/natmeg/ > dipolefitting?s[]=natmeg&s[]=headmodel#procedure > > Scroll down to the section "Construct the EEG volume conduction model" > > Good luck, > tzvetan > > > Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos < > urieduardo at gmail.com>: > > Dear Fieldtrippers, > > I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.o > rg/tutorial/salzburg) to conduct EEG source reconstruction, but it > doesn't work with some subjects' segmented mri files (whether I use dipoli > or bemcp), due to intersections between surfaces. > > What are the typical trouble-shooting steps for this situation? I tried > using a lower number of vertices for the mesh ([800 800 600]), to no avail. > Are there any guidelines for the number of vertices? > > The number of subjects in my study is limited, so I would be loathe to > exclude any subject from the analysis. > > Best regards, > > Uri Ramirez > University of Würzburg > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.manahova at gmail.com Tue Jul 3 11:26:10 2018 From: m.manahova at gmail.com (Mariya Manahova) Date: Tue, 3 Jul 2018 11:26:10 +0200 Subject: [FieldTrip] .avg field in GA structure for interaction test In-Reply-To: References: Message-ID: Hi Paul, With keepindividual = 'yes', your parameter of interest is 'individual'. So try using cfg.parameter = 'individual' (instead of cfg.parameter = 'avg' which is probably the default) and that should work. All the best, Marisha On Sun, Jul 1, 2018 at 8:11 PM Paul Dhami wrote: > Hi Fieldtrip, > > I am following the tutorial 'How to test an interaction effect using > cluster-based permutation tests?' for my own dataset. It says to compute > the GA for each condition (my design is 2x2 so a total of 4 GA structures) > with keepindividual set to 'yes'. However, when making the difference > structures, it says the assignment to the difference structure should be > made using the .avg field from 2 of the previous GA structures. But with > the keepindividual set to 'yes', I am getting no .avg field in these GA > structures to be used. Any advice as to how solve this issue? > > Best, > Paul > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Tue Jul 3 11:36:54 2018 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Tue, 3 Jul 2018 11:36:54 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: References: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Message-ID: Dear Uri, > That worked perfectly, thank you! Are there guidelines for use of mesh inflation? no there aren’t any. > E.g., does dilation by two voxels greatly bias source reconstruction? no > If one inflates a subject's mesh, must one then inflate all other subjects' meshes to the same degree? I would do as minimum as possible and only there when needed. Best tzvetan > > Thank you again, > Uri > > 2018-07-02 16:54 GMT+02:00 Tzvetan Popov >: > Dear Uri, > > the solution to the problem (mesh inflation) is outlined in this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting?s[]=natmeg&s[]=headmodel#procedure > > Scroll down to the section "Construct the EEG volume conduction model" > > Good luck, > tzvetan > > >> Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos >: >> >> Dear Fieldtrippers, >> >> I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.org/tutorial/salzburg ) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. >> >> What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? >> >> The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. >> >> Best regards, >> >> Uri Ramirez >> University of Würzburg >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Wed Jul 4 02:54:37 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 3 Jul 2018 20:54:37 -0400 Subject: [FieldTrip] Submitting a correlation matrix for cluster-based permutation Message-ID: Hi FieldTripers, I was hoping to do a correlation between two sets of EEG datasets in a channel x time fashion. For each (channel,time), I ran a rho correlation between the two EEG datas, and stored the resulting coefficients in a matrix with the dimensions of channel and time. I was hoping to apply a cluster-based permutation testing to correct for multiple comparisons, but as the file I was hoping to submit is a raw matrix, I was hoping for some guidance as to 1) whether this is even an appropriate way of achieving a cluster-corrected correlation matrix and 2) how to implement this with the correlation matrix. Any help would be greatly appreciated. Thank you. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Jul 4 08:58:47 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 4 Jul 2018 06:58:47 +0000 Subject: [FieldTrip] Submitting a correlation matrix for cluster-based permutation In-Reply-To: References: Message-ID: <54A52603-0F1E-48F0-9141-C8C27A1656FC@donders.ru.nl> Do you have a null hypothesis? What is it you would want to permute? If you just have scalar value per channel/time point, there’s not much you can do. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 4 Jul 2018, at 02:54, Paul Dhami > wrote: Hi FieldTripers, I was hoping to do a correlation between two sets of EEG datasets in a channel x time fashion. For each (channel,time), I ran a rho correlation between the two EEG datas, and stored the resulting coefficients in a matrix with the dimensions of channel and time. I was hoping to apply a cluster-based permutation testing to correct for multiple comparisons, but as the file I was hoping to submit is a raw matrix, I was hoping for some guidance as to 1) whether this is even an appropriate way of achieving a cluster-corrected correlation matrix and 2) how to implement this with the correlation matrix. Any help would be greatly appreciated. Thank you. Paul _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From ablenkmann at gmail.com Fri Jul 6 21:38:15 2018 From: ablenkmann at gmail.com (Alejandro Blenkmann) Date: Fri, 6 Jul 2018 12:38:15 -0700 Subject: [FieldTrip] Neuroscience Lab Engineer Permanent position - University of Oslo, Norway Message-ID: Hi FieldTripers, There is a Lab Engineer Permanent position available in Oslo. https://www.jobbnorge.no/ledige-stillinger/stilling/154793 < https://www.jobbnorge.no/ledige-stillinger/stilling/154793> Best, Alejandro -- Alejandro Blenkmann, PhD Postdoctoral Fellow Front Neurolab Department of Psychology University of Oslo -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Jul 6 21:43:04 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 6 Jul 2018 21:43:04 +0200 Subject: [FieldTrip] Problems with "filter_with_correction" In-Reply-To: References: Message-ID: Hi Maxime, I wouldn't know why this would occur if everything else is the same, except that perhaps your current MATLAB in combination with your OS uses slightly different implementations of filter functions from e.g. another toolbox/other MATLAB versions. In any case, as the function suggests, these problems typically occur for me when the low-pass frequency that is requested is too low for what the data and filter allows. The artefact detection functions probably uses a low/bandpass filter so try increasing the low cutoff, changing the filter order, or the filter type. You might also try using longer trial-lengths. cheers, Stephen On 3 July 2018 at 09:57, maxime ferez wrote: > Dear all, > > I have a question about Fieldtrip artifact-rejection. I find myself having > a problem that I do not know how to solve. I am currently working on a pc a > little old (~ 5 years) and my analyzes worked properly, or at least I had > no bug. When I changed my pc the problem has arrived. I have an error > message "Calculated filter coefficients have poles on or outside the unit > circle and will not be stable. Try a higher cutoff frequency or a different > type/order of filter" that appears in the "filter_with_correction" function > .The problem seems to occur during the "roots" function of Matlab. I > verified and the vector that is introduced is exactly the same in both > cases, but after the function “roots” runs the result differs slightly > and induces the error message above. Has anyone ever had this problem or > know where the problem might come from? On both pcs I have exactly the same > versions of Matlab (R2017a) and fieldtrip (fieldtrip-20171004 and > fieldtrip-20180626). Scripts and data are also identical in all cases. I > have tried several configurations but failed to find the solution: > > - Ubuntu 16.04 machine about 5 years -> OK > > - Ubuntu 16.04 machine about 2 years -> Not OK > > The two machines above are identical in all softwares (deployed with > script in PXE) > > - Fedora 27 machine about 2 years -> Not OK > > - Ubuntu 16.04 about 2 years -> Not OK > > - Fedora 17 about 8 years old -> OK > > - Centos7 machine less than a year -> Not OK > > To conclude, the script only works on old hardware but this does not seem > logical as an explanation. > > Best regards, > > > > Maxime Ferez > > > -- > Maxime Ferez, ingénieur d'étude > Centre de Recherche en Neuroscience de Lyon (CRNL) > Inserm > équipe Dycog > Bron, France > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lindseyrtate at ou.edu Mon Jul 9 06:59:13 2018 From: lindseyrtate at ou.edu (Tate, Lindsey R.) Date: Mon, 9 Jul 2018 04:59:13 +0000 Subject: [FieldTrip] Adding MRI Overlay to ft_sourceplot Images Message-ID: Hello fieldtrip community, I have a project with a lot of source analysis of EEG data. I'm using ft_sourceanalysis and ft_sourceplot. I would like to add standard (e.g., Colin 27) MRI slices to these images as an overlay (underlay?) for reference. Is there a way to do this? How do I align the MRI with my source space? Example code for ft_sourceanalysis and ft_sourceplot are provided below my signature in case you need the reference. Thank you, Lindsey Tate PhD Candidate University of Oklahoma lindseyrtate at ou.edu /// %baseline period source analysis cfg = []; cfg.elec = elec ; cfg.method = 'dics'; cfg.frequency = 25 ; cfg.grid = grid; cfg.headmodel = headmodel; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = 0; cfg.latency = -0.7490 ; [presource25] = ft_sourceanalysis(cfg, prefreq25) %from ft_freqanalysis %same is done for a post-stimulus period, called pmsource25; code omitted for brevity %difference between pre- and post-stimulus periods source25diff = pmsource25 ; source25diff.avg.pow = (pmsource25.avg.pow - presource25.avg.pow) ./ presource25.avg.pow; %interpolate the difference between pre- and post-stimulus periods cfg = []; cfg.downsample = 2; cfg.parameter = 'avg.pow'; source25DiffInt = ft_sourceinterpolate(cfg, source25diff, grid); %plot cfg = []; cfg.method = 'slice'; cfg.funparameter = 'avg.pow'; cfg.maskparameter = cfg.funparameter; cfg.funcolorlim = [-1 2]; cfg.opacitylim = [-5 1]; cfg.opacitymap = 'rampup'; ft_sourceplot(cfg, source25DiffInt); -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon Jul 9 08:01:33 2018 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 9 Jul 2018 08:01:33 +0200 Subject: [FieldTrip] Adding MRI Overlay to ft_sourceplot Images In-Reply-To: References: Message-ID: Hi Lindsey, What is "grid" bases on? Is this the individual mri or a standard mri? In any case, you can use ft_sourceinterpolate to interpolate to a standard MRI. Then, you can set the anatomy parameter in ft_spurceplot. Check the details of both functions for the relevant cfg settings. Hope this helps, Cheers, Julian Tate, Lindsey R. schrieb am Mo. 9. Juli 2018 um 07:35: > Hello fieldtrip community, > > > I have a project with a lot of source analysis of EEG data. I'm using > ft_sourceanalysis and ft_sourceplot. I would like to add standard (e.g., > Colin 27) MRI slices to these images as an overlay (underlay?) for > reference. Is there a way to do this? How do I align the MRI with my source > space? > > > Example code for ft_sourceanalysis and ft_sourceplot are provided below my > signature in case you need the reference. > > > Thank you, > > > Lindsey Tate > PhD Candidate > University of Oklahoma > lindseyrtate at ou.edu > > > /// > > %baseline period source analysis > > cfg = []; > cfg.elec = elec ; > cfg.method = 'dics'; > cfg.frequency = 25 ; > cfg.grid = grid; > cfg.headmodel = headmodel; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = 0; > cfg.latency = -0.7490 ; > [presource25] = ft_sourceanalysis(cfg, prefreq25) %from ft_freqanalysis > > %same is done for a post-stimulus period, called pmsource25; code omitted > for brevity > > %difference between pre- and post-stimulus periods > source25diff = pmsource25 ; > source25diff.avg.pow = (pmsource25.avg.pow - presource25.avg.pow) ./ > presource25.avg.pow; > > %interpolate the difference between pre- and post-stimulus periods > cfg = []; > cfg.downsample = 2; > cfg.parameter = 'avg.pow'; > source25DiffInt = ft_sourceinterpolate(cfg, source25diff, grid); > > %plot > cfg = []; > cfg.method = 'slice'; > cfg.funparameter = 'avg.pow'; > cfg.maskparameter = cfg.funparameter; > cfg.funcolorlim = [-1 2]; > cfg.opacitylim = [-5 1]; > cfg.opacitymap = 'rampup'; > ft_sourceplot(cfg, source25DiffInt); > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.maye at uke.de Mon Jul 9 10:15:33 2018 From: a.maye at uke.de (Alexander Maye) Date: Mon, 9 Jul 2018 10:15:33 +0200 Subject: [FieldTrip] Call for Participation: summer school on 'mind reading technology' Message-ID: <7471317.dIuGlEM9So@mars> Dear colleagues, Below I forward an announcement for the above-mentioned summer school which readers of this list may find interesting. Best regards, Alexnder Maye. ---------- Weitergeleitete Nachricht ---------- Betreff: [CML] Call for Participation: summer school on 'mind reading technology' Datum: Donnerstag, 5. Juli 2018, 09:44:08 CEST Von: Dan Zhang An: cml at informatik.uni-hamburg.de Kopie: 洪波 Dear colleagues, Dr. Bo Hong and I are organizing a summer school during August 13-17 in Beijing. The topic of this summer school is ‘mind reading technology’ and we have invited the leading scientists in this field to give lectures. Please help us spread out the message and please contact us if you are interested. Many thanks in advance! Best, Dan -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- A non-text attachment was scrubbed... Name: Program of 2018 ISSNE.pdf Type: application/pdf Size: 115677 bytes Desc: Program of 2018 ISSNE.pdf URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ISSNE2018 Flyer.pdf Type: application/pdf Size: 474936 bytes Desc: ISSNE2018 Flyer.pdf URL: From krugliakova.es at gmail.com Tue Jul 10 21:36:19 2018 From: krugliakova.es at gmail.com (Elena Krugliakova) Date: Tue, 10 Jul 2018 21:36:19 +0200 Subject: [FieldTrip] phase-amplitude coupling measure Message-ID: Dear FieldTrip community, I have a question related to the ft_crossfrequencyanalysis: which phase - amplitude coupling measure for EEG is the least affected by the signal-to-noise ratio? If I have two conditions and in one of them the power of high frequency is much stronger (better signal-to-noise ratio), what would be the best measure to compare the coupling between the phase of slow frequency and the amplitude of high frequency? Thank you! Kind Regards, Elena Krugliakova -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Fri Jul 13 18:20:21 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Fri, 13 Jul 2018 18:20:21 +0200 Subject: [FieldTrip] git repo quite big. How to save space? Message-ID: Dear all, I have several copies of FieldTrip for several projects shared with others. Each has its own copy of FieldTrip, which is at the moment a 1.7GB folder, of which 1GB is taken by the .git directory. Would there be an easy way to prune the repository where needed? Best, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From christophe.grova at mcgill.ca Sun Jul 15 14:42:58 2018 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Sun, 15 Jul 2018 12:42:58 +0000 Subject: [FieldTrip] Postdoctoral Fellowship in Multimodal Neuroimaging of Sleep and Cognition at Concordia PERFORM centre In-Reply-To: References: , Message-ID: Dear colleagues, We are presently recruiting a Postdoctoral fellow in Multimodal Neuroimaging of Sleep and Cognition. This position consists in a prestigious Horizon Postdoctoral Fellowship at Concordia University, in Montréal (Québec, Canada). The fellow will have the opportunity to setup and conduct advanced neuroimaging studies in clinical and healthy samples, as well as to analyze and write up findings of previously collected human neuroimaging data. He/she will also have the opportunity to develop and evaluate new multimodal data analysis approaches, as for instance the study of sleep patterns combining high-density Electro-EncephaloGraphy (EEG) with functional Magnetic Resonance Imaging and for the very first time EEG with Near-Infra Red Spectroscopy (NIRS) during whole night recordings. These techniques will allow addressing links between bioelectrical neuronal activity and hemodynamic processes during sleep. He/she will be based at Concordia University (Montreal, Quebec), jointly supervised by Dr. Christophe Grova PhD and Dr. Thanh Dang-Vu MD-PhD, and will work in a highly multidisciplinary environment (neurosciences, kinesiology, physics, engineering, psychology) and in collaboration with multiple academic and hospital institutions in Montreal (PERFORM Center, Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal [CRIUGM], Montreal Neurological Institute [MNI]). The research themes that will be addressed by the Fellow will include: * The neural mechanisms of sleep, sleep deprivation and sleep disorders (chronic insomnia, central disorders of hypersomnolence), and their relationship with cognition. * Developing and evaluating methods dedicated to the analysis of multimodal neuroimaging data for sleep studies: (i) simultaneous EEG/fMRI, and (2) simultaneous EEG/NIRS, including the analysis of functional connectivity and brain network analysis The PERFORM Centre is a 8,000 m2 research facility including eight inter-related research platforms, such as a state of the art sleep laboratory (3 bedrooms with polysomnography and high-density EEG) and a fully equipped imaging suite (3T MRI, high-density EEG, NIRS, TMS, SPECT-CT, PET-CT, Ultrasound and Dexa) entirely dedicated to research (http://www.concordia.ca/research/perform.html ). Applicants must have a PhD (or close to completion) in a related field (e.g., neurosciences, computer science, (bio)medical engineering, physics). Experience in the analysis of hemodynamic signals from fMRI or NIRS is important. Applicants should have strong knowledge of Matlab and/or experience in analysis of neuroimaging, excellent organizational skills, an aptitude for teamwork, good writing skills and a productive publication record. Experience in one or more aspects of the research themes will constitute an asset. Salary will consist of 47,500 $/year (plus benefits) for 2 years. The position has a flexible start date. Interested applicants should submit their application as described in the following link, before September 1st 2018: http://www.concordia.ca/sgs/postdoctoral-fellows/funding/horizon/descriptions/5007.html Review of applications will begin as they are received and will continue until the position has been filled. All requests for additional information should also be directed to them. Only those candidates selected to interview will be contacted. Dr. Christophe Grova, Ph.D, Dr. Thanh Dang-Vu, M.D., Ph.D. Associate Professor Associate Professor, Neurologist, Department of Physics, Concordia U. Adjunct Professor in Biomedical Engineering, Concordia University Research Chair in Sleep, Neuroimaging and Cognitive Health, Neurology & Neurosurgery, McGill U. christophe.grova at concordia.ca Department of Health, Kinesiology and Applied Physiology, Concordia U. Assoc. Director for Clinical Research, CRIUGM tt.dangvu at concordia.ca For more information about our current research programs, please visit the lab websites: https://www.concordia.ca/artsci/physics/research/grova-research-group.html https://scnlab.com *************************** Christophe Grova, PhD Associate Professor, Physics Dpt, Concordia University PERFORM centre, Concordia University, Chair of PERFORM Applied Bio-Imaging Committee (ABC) Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute - epilepsy group Centre de Recherches en Mathématiques Physics Dpt Concordia University - Loyola Campus - Office SP 365.12 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Phone: (514) 848-2424 ext.4221 Biomedical Engineering Department McGill University - Room 304 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 Phone : (514) 398 2516 Fax : (514) 398 7461 email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca web: Explore Concordia: http://explore.concordia.ca/christophe-grova Physics, Concordia University: http://www.concordia.ca/artsci/physics/faculty.html?fpid=christophe-grova McGill University: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** [X] -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauppe.s at gmail.com Mon Jul 16 00:09:30 2018 From: sauppe.s at gmail.com (Sebastian Sauppe) Date: Mon, 16 Jul 2018 00:09:30 +0200 Subject: [FieldTrip] Error using ft_clusterplot: unsupported dimord unknown_freq_time Message-ID: Dear FieldTrip list users, I am trying to analyze a between-subjects experiment with cluster-based permutation tests. In setting up the tests, I followed the tutorial on the FieldTrip site (http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq#between-trial_experiments ). However, when I try to plot the results, I get the error „Error using ft_clusterplot (line 161) unsupported dimord unknown_freq_time“. I am very new to FieldTrip and its probably a rookie mistake that I am making but I’d be very grateful if someone who knows could point out what I might be doing wrong here. Here is the code: %% run cluster-based permutation test % set up cfg for ft_freqstatistics cfg = []; cfg.channel = 'all'; cfg.latency = 'all'; cfg.frequency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 20; % to make it quick % prepare_neighbours determines what electrodes may form clusters cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, freq_IPFV); cfg.spmversion = 'spm12'; design = zeros(1,size(freq_IPFV.powspctrm,1) + size(freq_PFV.powspctrm,1)); design(1,1:size(freq_IPFV.powspctrm,1)) = 1; design(1,(size(freq_IPFV.powspctrm,1)+1):(size(freq_IPFV.powspctrm,1)+... size(freq_PFV.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, freq_IPFV, freq_PFV); %% plot the results cfg = []; cfg.keeptrials = 'no'; freqdesc_IPFV = ft_freqdescriptives(cfg, freq_IPFV); freqdesc_PFV = ft_freqdescriptives(cfg, freq_PFV); stat.raweffect = freqdesc_IPFV.powspctrm - freqdesc_PFV.powspctrm; cfg = []; cfg.alpha = 0.025; cfg.parameter = 'raweffect'; cfg.zlim = [-1e-27 1e-27]; cfg.layout = 'GSN-HydroCel-129.sfp'; layout = ft_prepare_layout(cfg); cfg.layout = layout; ft_clusterplot(cfg, stat); Kind regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Phillip.Alday at mpi.nl Mon Jul 16 08:59:22 2018 From: Phillip.Alday at mpi.nl (Alday, Phillip) Date: Mon, 16 Jul 2018 06:59:22 +0000 Subject: [FieldTrip] git repo quite big. How to save space? In-Reply-To: References: Message-ID: <6002072a-9c62-bd54-34b0-fffc464db833@mpi.nl> There are a few things you can do: 1. Garbage collection and re-packing to get git to re-organize itself into a more compact layout : git gc --aggressive If that takes too long, do it without --aggressive : it will be much faster although potentially not as effective. 2. Use shallow clones (i.e. ones missing older history). 3. Clone from one local copy to another -- if the clones are on the same file system, then git will use hard links and git objects common to both repositories will be "shared" and only take up space equal to one instance. Note that garbage collection, re-packing, etc. can break this and lead to each clone having its own copies. 4. Don't keep a copy of FieldTrip in each project and start using paths, version management, etc. more effectively. You definitely should know which version of the software you used for a given analysis for reproducibility/replicability, but there are more efficient ways to do that than keeping a local copy. This is not meant to be harsh, but just trying to address a potential "XY problem" (https://meta.stackexchange.com/questions/66377/what-is-the-xy-problem). Best, Phillip Date: Fri, 13 Jul 2018 18:20:21 +0200 > From: Maximilien Chaumon > To: FieldTrip discussion list > Subject: [FieldTrip] git repo quite big. How to save space? > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I have several copies of FieldTrip for several projects shared with others. > Each has its own copy of FieldTrip, which is at the moment a 1.7GB folder, > of which 1GB is taken by the .git directory. Would there be an easy way to > prune the repository where needed? > > Best, > Max > From Amie.Fairs at mpi.nl Tue Jul 17 09:57:48 2018 From: Amie.Fairs at mpi.nl (Fairs, Amie) Date: Tue, 17 Jul 2018 07:57:48 +0000 Subject: [FieldTrip] Missing templates for planar gradients Message-ID: Dear FieldTrip list, Apologies for what seems like a silly question. I am calculating the planar gradient for my MEG data because it was recorded from axial gradiometers (on a CTF system with a 275 layout). I'm following the FieldTrip tutorial to calculate the planar gradient, and I would like to use the method 'template' to do so, and then specify a pre-existing template. From reading about which templates are shipped with FieldTrip (http://www.fieldtriptoolbox.org/template/neighbours) I think a bunch of templates should be found in FieldTrip, including the CTF 275 neighbourhood template. However, in my FieldTrip version there are no templates (the template folder is just empty). When I run ft_prepare_neighbours, specifying cfg.template = 'template' and cfg.template = 'CTF275_neighb.mat', I get an error message saying 'Template file could not be found'. Does anyone know where I can get hold of this template? I can't find a way to download other than downloading a new version of FieldTrip and seeing if it is there. The FieldTrip version I am using is fieldtrip-20170918 (so much after the 2011 template intro), on a Windows 7 computer, and matlab R2016a. I also calculated the planar gradient using the method 'triangulation' to check it isn't a data bug somehow, but that works perfectly fine (though I'd prefer the template option). Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Arana at donders.ru.nl Tue Jul 17 10:26:07 2018 From: S.Arana at donders.ru.nl (Arana, S.L. (Sophie)) Date: Tue, 17 Jul 2018 08:26:07 +0000 Subject: [FieldTrip] Missing templates for planar gradients In-Reply-To: References: Message-ID: Hi Amie, have you tried downloading the template file directly from the GitHub repo? https://github.com/fieldtrip/fieldtrip/tree/master/template/neighbours Best, Sophie ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Fairs, Amie [Amie.Fairs at mpi.nl] Sent: Tuesday, July 17, 2018 9:57 AM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Missing templates for planar gradients Dear FieldTrip list, Apologies for what seems like a silly question. I am calculating the planar gradient for my MEG data because it was recorded from axial gradiometers (on a CTF system with a 275 layout). I'm following the FieldTrip tutorial to calculate the planar gradient, and I would like to use the method 'template' to do so, and then specify a pre-existing template. From reading about which templates are shipped with FieldTrip (http://www.fieldtriptoolbox.org/template/neighbours) I think a bunch of templates should be found in FieldTrip, including the CTF 275 neighbourhood template. However, in my FieldTrip version there are no templates (the template folder is just empty). When I run ft_prepare_neighbours, specifying cfg.template = 'template' and cfg.template = 'CTF275_neighb.mat', I get an error message saying 'Template file could not be found'. Does anyone know where I can get hold of this template? I can't find a way to download other than downloading a new version of FieldTrip and seeing if it is there. The FieldTrip version I am using is fieldtrip-20170918 (so much after the 2011 template intro), on a Windows 7 computer, and matlab R2016a. I also calculated the planar gradient using the method 'triangulation' to check it isn't a data bug somehow, but that works perfectly fine (though I'd prefer the template option). Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauppe.s at gmail.com Thu Jul 19 09:01:59 2018 From: sauppe.s at gmail.com (Sebastian Sauppe) Date: Thu, 19 Jul 2018 09:01:59 +0200 Subject: [FieldTrip] Averaging over frequencies in ft_freqstatistics Message-ID: Dear FieldTrip list, I am testing different frequency bands with cluster-based permutation tests using ft_freqstatistics. For this, I use cfg.avgoverfreq = ‚yes‘ when setting up the test. However, I am unsure about how FieldTrip actually handles the frequency averaging. Does it take the mean power of the specified frequencies or does it take the power of the mean frequency? This is the relevant code I use: ... cfg.frequency = [3 8]; cfg.avgoverfreq = 'yes‘; ... [stat] = ft_freqstatistics(cfg, data_A, data_B); In my data, I have the following frequencies: [3.9062 4.8828 6.1035 7.0801 8.0566 9.0332 10.0098]. In the statistics output, after averaging over frequencies stat.freq returns only 6.0059. This is the mean of the frequencies between 3 and 8. But I can’t see whether somehow the power of that frequency was assessed in the test or whether the power of all frequencies in that band was first averaged and then tested. Regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From 007abhisheksamal at gmail.com Fri Jul 20 14:52:14 2018 From: 007abhisheksamal at gmail.com (Abhishek Samal) Date: Fri, 20 Jul 2018 18:22:14 +0530 Subject: [FieldTrip] Error in using EMG channel as trial definition Message-ID: Sir, This is Abhishek. I am trying to analyse Motor Evoked field MEG data. I have been trying to use the EMG channel as the trial definition for the triggers of epoch creation. But when I use the script that is given in tutorial definition I am getting the following error. The Input cfg = []; cfg.dataset = 'preetham_lt_motor_raw_tsss_mc.fif'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 0.5; cfg.trialfun = 'trialfun_emgdetect'; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); The Error 306 MEG channel locations transformed Reading preetham_lt_motor_raw_tsss_mc.fif ... Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... Range : 124000 ... 669999 = 62.000 ... 335.000 secs Ready. Reading 124000 ... 669999 = 62.000 ... 335.000 secs... [done] found 0 events created 210265 trials the call to "ft_definetrial" took 528 seconds 306 MEG channel locations transformed Reading preetham_lt_motor_raw_tsss_mc.fif ... Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... Range : 124000 ... 669999 = 62.000 ... 335.000 secs Ready. processing channel { 'EOG001' 'ECG002' 'EEG001' 'EEG002' 'EEG003' 'EEG004' 'EEG005' 'EEG006' 'EEG007' 'EEG008' 'EEG009' 'EEG010' 'EEG011' 'EEG012' 'EEG013' 'EEG014' 'EEG015' 'EEG016' 'EEG017' 'EEG018' 'EEG019' 'EEG020' 'EEG021' 'EEG022' 'EEG023' 'EEG024' 'EEG025' 'EXCI' 'IASX+' 'IASX-' 'IASY+' 'IASY-' 'IASZ+' 'IASZ-' 'IAS_DX' 'IAS_DY' 'IAS_X' 'IAS_Y' 'IAS_Z' 'MEG0111' 'MEG0112' 'MEG0113' 'MEG0121' 'MEG0122' 'MEG0123' 'MEG0131' 'MEG0132' 'MEG0133' 'MEG0141' 'MEG0142' 'MEG0143' 'MEG0211' 'MEG0212' 'MEG0213' 'MEG0221' 'MEG0222' 'MEG0223' 'MEG0231' 'MEG0232' 'MEG0233' 'MEG0241' 'MEG0242' 'MEG0243' 'MEG0311' 'MEG0312' 'MEG0313' 'MEG0321' 'MEG0322' 'MEG0323' 'MEG0331' 'MEG0332' 'MEG0333' 'MEG0341' 'MEG0342' 'MEG0343' 'MEG0411' 'MEG0412' 'MEG0413' 'MEG0421' 'MEG0422' 'MEG0423' 'MEG0431' 'MEG0432' 'MEG0433' 'MEG0441' 'MEG0442' 'MEG0443' 'MEG0511' 'MEG0512' 'MEG0513' 'MEG0521' 'MEG0522' 'MEG0523' 'MEG0531' 'MEG0532' 'MEG0533' 'MEG0541' 'MEG0542' 'MEG0543' 'MEG0611' 'MEG0612' 'MEG0613' 'MEG0621' 'MEG0622' 'MEG0623' 'MEG0631' 'MEG0632' 'MEG0633' 'MEG0641' 'MEG0642' 'MEG0643' 'MEG0711' 'MEG0712' 'MEG0713' 'MEG0721' 'MEG0722' 'MEG0723' 'MEG0731' 'MEG0732' 'MEG0733' 'MEG0741' 'MEG0742' 'MEG0743' 'MEG0811' 'MEG0812' 'MEG0813' 'MEG0821' 'MEG0822' 'MEG0823' 'MEG0911' 'MEG0912' 'MEG0913' 'MEG0921' 'MEG0922' 'MEG0923' 'MEG0931' 'MEG0932' 'MEG0933' 'MEG0941' 'MEG0942' 'MEG0943' 'MEG1011' 'MEG1012' 'MEG1013' 'MEG1021' 'MEG1022' 'MEG1023' 'MEG1031' 'MEG1032' 'MEG1033' 'MEG1041' 'MEG1042' 'MEG1043' 'MEG1111' 'MEG1112' 'MEG1113' 'MEG1121' 'MEG1122' 'MEG1123' 'MEG1131' 'MEG1132' 'MEG1133' 'MEG1141' 'MEG1142' 'MEG1143' 'MEG1211' 'MEG1212' 'MEG1213' 'MEG1221' 'MEG1222' 'MEG1223' 'MEG1231' 'MEG1232' 'MEG1233' 'MEG1241' 'MEG1242' 'MEG1243' 'MEG1311' 'MEG1312' 'MEG1313' 'MEG1321' 'MEG1322' 'MEG1323' 'MEG1331' 'MEG1332' 'MEG1333' 'MEG1341' 'MEG1342' 'MEG1343' 'MEG1411' 'MEG1412' 'MEG1413' 'MEG1421' 'MEG1422' 'MEG1423' 'MEG1431' 'MEG1432' 'MEG1433' 'MEG1441' 'MEG1442' 'MEG1443' 'MEG1511' 'MEG1512' 'MEG1513' 'MEG1521' 'MEG1522' 'MEG1523' 'MEG1531' 'MEG1532' 'MEG1533' 'MEG1541' 'MEG1542' 'MEG1543' 'MEG1611' 'MEG1612' 'MEG1613' 'MEG1621' 'MEG1622' 'MEG1623' 'MEG1631' 'MEG1632' 'MEG1633' 'MEG1641' 'MEG1642' 'MEG1643' 'MEG1711' 'MEG1712' 'MEG1713' 'MEG1721' 'MEG1722' 'MEG1723' 'MEG1731' 'MEG1732' 'MEG1733' 'MEG1741' 'MEG1742' 'MEG1743' 'MEG1811' 'MEG1812' 'MEG1813' 'MEG1821' 'MEG1822' 'MEG1823' 'MEG1831' 'MEG1832' 'MEG1833' 'MEG1841' 'MEG1842' 'MEG1843' 'MEG1911' 'MEG1912' 'MEG1913' 'MEG1921' 'MEG1922' 'MEG1923' 'MEG1931' 'MEG1932' 'MEG1933' 'MEG1941' 'MEG1942' 'MEG1943' 'MEG2011' 'MEG2012' 'MEG2013' 'MEG2021' 'MEG2022' 'MEG2023' 'MEG2031' 'MEG2032' 'MEG2033' 'MEG2041' 'MEG2042' 'MEG2043' 'MEG2111' 'MEG2112' 'MEG2113' 'MEG2121' 'MEG2122' 'MEG2123' 'MEG2131' 'MEG2132' 'MEG2133' 'MEG2141' 'MEG2142' 'MEG2143' 'MEG2211' 'MEG2212' 'MEG2213' 'MEG2221' 'MEG2222' 'MEG2223' 'MEG2231' 'MEG2232' 'MEG2233' 'MEG2241' 'MEG2242' 'MEG2243' 'MEG2311' 'MEG2312' 'MEG2313' 'MEG2321' 'MEG2322' 'MEG2323' 'MEG2331' 'MEG2332' 'MEG2333' 'MEG2341' 'MEG2342' 'MEG2343' 'MEG2411' 'MEG2412' 'MEG2413' 'MEG2421' 'MEG2422' 'MEG2423' 'MEG2431' 'MEG2432' 'MEG2433' 'MEG2441' 'MEG2442' 'MEG2443' 'MEG2511' 'MEG2512' 'MEG2513' 'MEG2521' 'MEG2522' 'MEG2523' 'MEG2531' 'MEG2532' 'MEG2533' 'MEG2541' 'MEG2542' 'MEG2543' 'MEG2611' 'MEG2612' 'MEG2613' 'MEG2621' 'MEG2622' 'MEG2623' 'MEG2631' 'MEG2632' 'MEG2633' 'MEG2641' 'MEG2642' 'MEG2643' 'STI101' 'SYS201' 'CHPI001' 'CHPI002' 'CHPI003' 'CHPI004' 'CHPI005' 'CHPI006' 'CHPI007' 'CHPI008' 'CHPI009' } reading and preprocessing reading and preprocessing trial 1 from 210265 Reading 264027 ... 4792reading and preprocessing trial 2 from 210265 Reading 327742 ... 4802reading and preprocessing trial 3 from 210265 . . . . . Reading 635443 ... 66reading and preprocessing trial 116 from 210265 Error using ft_read_data (line 225) cannot read data after the end of the file Error in ft_preprocessing (line 582) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); I am new to fieldtrip. Please help me with the above error. Regards, Abhishek. -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri Jul 20 15:00:04 2018 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 20 Jul 2018 15:00:04 +0200 Subject: [FieldTrip] Error in using EMG channel as trial definition In-Reply-To: References: Message-ID: <6B3105DE-53A4-4490-97A0-C7CC497B2B14@gmail.com> Dear Abhishek, this error occurs if less time than specified in cfg.trialdef.poststim is left after the last event code. In other words, you are trying to cut out more trials with a fixed latency than you have data. Please note that it appears as if your trial definition based on the EMG channel fails (see the „found 0 events“ notice and the rather large number of trials). I suggest going back to your trial function and checking whether everything works as intended there. Good luck, Julian ________________ Prof. Dr. Julian Keil Biological Psychology Olshausenstrasse 62 - R. 306 24118 Kiel, Germany +49 - 0431 - 880 - 4872 http://www.biopsych.uni-kiel.de/en Department of Psychiatry and Psychotherapy Charité at St. Hedwig-Hospital Große Hamburger Strasse 5-11 10115 Berlin, Germany +030 - 2311 - 1879 www.multisensorymind.com > Am 20.07.2018 um 14:52 schrieb Abhishek Samal <007abhisheksamal at gmail.com>: > > Sir, > This is Abhishek. I am trying to analyse Motor Evoked field MEG data. I have been trying to use the EMG channel as the trial definition for the triggers of epoch creation. But when I use the script that is given in tutorial definition I am getting the following error. > > The Input > > cfg = []; > cfg.dataset = 'preetham_lt_motor_raw_tsss_mc.fif'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 0.5; > cfg.trialfun = 'trialfun_emgdetect'; > cfg = ft_definetrial(cfg); > data = ft_preprocessing(cfg); > > The Error > > 306 MEG channel locations transformed > Reading preetham_lt_motor_raw_tsss_mc.fif ... > Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... > Range : 124000 ... 669999 = 62.000 ... 335.000 secs > Ready. > Reading 124000 ... 669999 = 62.000 ... 335.000 secs... [done] > found 0 events > created 210265 trials > the call to "ft_definetrial" took 528 seconds > 306 MEG channel locations transformed > Reading preetham_lt_motor_raw_tsss_mc.fif ... > Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... > Range : 124000 ... 669999 = 62.000 ... 335.000 secs > Ready. > processing channel { 'EOG001' 'ECG002' 'EEG001' 'EEG002' 'EEG003' 'EEG004' 'EEG005' 'EEG006' 'EEG007' 'EEG008' 'EEG009' 'EEG010' 'EEG011' 'EEG012' 'EEG013' 'EEG014' 'EEG015' 'EEG016' 'EEG017' 'EEG018' 'EEG019' 'EEG020' 'EEG021' 'EEG022' 'EEG023' 'EEG024' 'EEG025' 'EXCI' 'IASX+' 'IASX-' 'IASY+' 'IASY-' 'IASZ+' 'IASZ-' 'IAS_DX' 'IAS_DY' 'IAS_X' 'IAS_Y' 'IAS_Z' 'MEG0111' 'MEG0112' 'MEG0113' 'MEG0121' 'MEG0122' 'MEG0123' 'MEG0131' 'MEG0132' 'MEG0133' 'MEG0141' 'MEG0142' 'MEG0143' 'MEG0211' 'MEG0212' 'MEG0213' 'MEG0221' 'MEG0222' 'MEG0223' 'MEG0231' 'MEG0232' 'MEG0233' 'MEG0241' 'MEG0242' 'MEG0243' 'MEG0311' 'MEG0312' 'MEG0313' 'MEG0321' 'MEG0322' 'MEG0323' 'MEG0331' 'MEG0332' 'MEG0333' 'MEG0341' 'MEG0342' 'MEG0343' 'MEG0411' 'MEG0412' 'MEG0413' 'MEG0421' 'MEG0422' 'MEG0423' 'MEG0431' 'MEG0432' 'MEG0433' 'MEG0441' 'MEG0442' 'MEG0443' 'MEG0511' 'MEG0512' 'MEG0513' 'MEG0521' 'MEG0522' 'MEG0523' 'MEG0531' 'MEG0532' 'MEG0533' 'MEG0541' 'MEG0542' 'MEG0543' 'MEG0611' 'MEG0612' 'MEG0613' 'MEG0621' 'MEG0622' 'MEG0623' 'MEG0631' 'MEG0632' 'MEG0633' 'MEG0641' 'MEG0642' 'MEG0643' 'MEG0711' 'MEG0712' 'MEG0713' 'MEG0721' 'MEG0722' 'MEG0723' 'MEG0731' 'MEG0732' 'MEG0733' 'MEG0741' 'MEG0742' 'MEG0743' 'MEG0811' 'MEG0812' 'MEG0813' 'MEG0821' 'MEG0822' 'MEG0823' 'MEG0911' 'MEG0912' 'MEG0913' 'MEG0921' 'MEG0922' 'MEG0923' 'MEG0931' 'MEG0932' 'MEG0933' 'MEG0941' 'MEG0942' 'MEG0943' 'MEG1011' 'MEG1012' 'MEG1013' 'MEG1021' 'MEG1022' 'MEG1023' 'MEG1031' 'MEG1032' 'MEG1033' 'MEG1041' 'MEG1042' 'MEG1043' 'MEG1111' 'MEG1112' 'MEG1113' 'MEG1121' 'MEG1122' 'MEG1123' 'MEG1131' 'MEG1132' 'MEG1133' 'MEG1141' 'MEG1142' 'MEG1143' 'MEG1211' 'MEG1212' 'MEG1213' 'MEG1221' 'MEG1222' 'MEG1223' 'MEG1231' 'MEG1232' 'MEG1233' 'MEG1241' 'MEG1242' 'MEG1243' 'MEG1311' 'MEG1312' 'MEG1313' 'MEG1321' 'MEG1322' 'MEG1323' 'MEG1331' 'MEG1332' 'MEG1333' 'MEG1341' 'MEG1342' 'MEG1343' 'MEG1411' 'MEG1412' 'MEG1413' 'MEG1421' 'MEG1422' 'MEG1423' 'MEG1431' 'MEG1432' 'MEG1433' 'MEG1441' 'MEG1442' 'MEG1443' 'MEG1511' 'MEG1512' 'MEG1513' 'MEG1521' 'MEG1522' 'MEG1523' 'MEG1531' 'MEG1532' 'MEG1533' 'MEG1541' 'MEG1542' 'MEG1543' 'MEG1611' 'MEG1612' 'MEG1613' 'MEG1621' 'MEG1622' 'MEG1623' 'MEG1631' 'MEG1632' 'MEG1633' 'MEG1641' 'MEG1642' 'MEG1643' 'MEG1711' 'MEG1712' 'MEG1713' 'MEG1721' 'MEG1722' 'MEG1723' 'MEG1731' 'MEG1732' 'MEG1733' 'MEG1741' 'MEG1742' 'MEG1743' 'MEG1811' 'MEG1812' 'MEG1813' 'MEG1821' 'MEG1822' 'MEG1823' 'MEG1831' 'MEG1832' 'MEG1833' 'MEG1841' 'MEG1842' 'MEG1843' 'MEG1911' 'MEG1912' 'MEG1913' 'MEG1921' 'MEG1922' 'MEG1923' 'MEG1931' 'MEG1932' 'MEG1933' 'MEG1941' 'MEG1942' 'MEG1943' 'MEG2011' 'MEG2012' 'MEG2013' 'MEG2021' 'MEG2022' 'MEG2023' 'MEG2031' 'MEG2032' 'MEG2033' 'MEG2041' 'MEG2042' 'MEG2043' 'MEG2111' 'MEG2112' 'MEG2113' 'MEG2121' 'MEG2122' 'MEG2123' 'MEG2131' 'MEG2132' 'MEG2133' 'MEG2141' 'MEG2142' 'MEG2143' 'MEG2211' 'MEG2212' 'MEG2213' 'MEG2221' 'MEG2222' 'MEG2223' 'MEG2231' 'MEG2232' 'MEG2233' 'MEG2241' 'MEG2242' 'MEG2243' 'MEG2311' 'MEG2312' 'MEG2313' 'MEG2321' 'MEG2322' 'MEG2323' 'MEG2331' 'MEG2332' 'MEG2333' 'MEG2341' 'MEG2342' 'MEG2343' 'MEG2411' 'MEG2412' 'MEG2413' 'MEG2421' 'MEG2422' 'MEG2423' 'MEG2431' 'MEG2432' 'MEG2433' 'MEG2441' 'MEG2442' 'MEG2443' 'MEG2511' 'MEG2512' 'MEG2513' 'MEG2521' 'MEG2522' 'MEG2523' 'MEG2531' 'MEG2532' 'MEG2533' 'MEG2541' 'MEG2542' 'MEG2543' 'MEG2611' 'MEG2612' 'MEG2613' 'MEG2621' 'MEG2622' 'MEG2623' 'MEG2631' 'MEG2632' 'MEG2633' 'MEG2641' 'MEG2642' 'MEG2643' 'STI101' 'SYS201' 'CHPI001' 'CHPI002' 'CHPI003' 'CHPI004' 'CHPI005' 'CHPI006' 'CHPI007' 'CHPI008' 'CHPI009' } > reading and preprocessing > reading and preprocessing trial 1 from 210265 > Reading 264027 ... 4792reading and preprocessing trial 2 from 210265 > Reading 327742 ... 4802reading and preprocessing trial 3 from 210265 > . > . > . > . > . > Reading 635443 ... 66reading and preprocessing trial 116 from 210265 > Error using ft_read_data (line 225) > cannot read data after the end of the file > > Error in ft_preprocessing (line 582) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, > 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); > > > > I am new to fieldtrip. Please help me with the above error. > Regards, > Abhishek. > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: From apple.h99 at gmail.com Fri Jul 20 15:54:00 2018 From: apple.h99 at gmail.com (sara h) Date: Fri, 20 Jul 2018 18:24:00 +0430 Subject: [FieldTrip] Access to fieldtrip mailing list Message-ID: Dear all Hi I'm new with filedtrip and I'm going to search in fieldtrip mailing list but the list is not accessible and the webpage is not reachable. does any one have this issue?? how can I sove it? thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 23 10:55:24 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 23 Jul 2018 08:55:24 +0000 Subject: [FieldTrip] Access to fieldtrip mailing list In-Reply-To: References: Message-ID: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> Hi Sara, It works for me at the moment, so I don’t know what was/is causing your problem. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 20 Jul 2018, at 15:54, sara h > wrote: Dear all Hi I'm new with filedtrip and I'm going to search in fieldtrip mailing list but the list is not accessible and the webpage is not reachable. does any one have this issue?? how can I sove it? thanks _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 23 10:58:46 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 23 Jul 2018 08:58:46 +0000 Subject: [FieldTrip] Averaging over frequencies in ft_freqstatistics In-Reply-To: References: Message-ID: Hi Sebastian, ft_freqstatistics averages the power across the frequency bins, that have their bin-centre within the range specified by cfg.frequency. The output frequency in stat.freq represents the average of the bin-centres that went into the computation. No re-estimation of the power at this frequency is done. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 19 Jul 2018, at 09:01, Sebastian Sauppe > wrote: Dear FieldTrip list, I am testing different frequency bands with cluster-based permutation tests using ft_freqstatistics. For this, I use cfg.avgoverfreq = ‚yes‘ when setting up the test. However, I am unsure about how FieldTrip actually handles the frequency averaging. Does it take the mean power of the specified frequencies or does it take the power of the mean frequency? This is the relevant code I use: ... cfg.frequency = [3 8]; cfg.avgoverfreq = 'yes‘; ... [stat] = ft_freqstatistics(cfg, data_A, data_B); In my data, I have the following frequencies: [3.9062 4.8828 6.1035 7.0801 8.0566 9.0332 10.0098]. In the statistics output, after averaging over frequencies stat.freq returns only 6.0059. This is the mean of the frequencies between 3 and 8. But I can’t see whether somehow the power of that frequency was assessed in the test or whether the power of all frequencies in that band was first averaged and then tested. Regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rdm146 at newark.rutgers.edu Tue Jul 24 01:45:43 2018 From: rdm146 at newark.rutgers.edu (Ravi Mill) Date: Mon, 23 Jul 2018 23:45:43 +0000 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel Message-ID: Dear Fieldtrippers I've been scouring the FT documentation and mailing list but can't seem to find the answer to a fairly simple question (which seems to have remained unanswered previously https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010816.html): how does one know the size/'radius' of the individual source gridpoints modeled by Fieldtrip? I've been warping MNI template source models (with RO selected from a functional atlas of ~300 regions) to individual subject MRI headmodels to extract source timeseries via LCMV beamformer. In ft_prepare_sourcemodel there are seemingly options to control the *spacing* between gridpoints in a whole-brain source grid (cfg.grid.resolution), but nothing to control how large the individual sources are (either for whole-brain grids, or a priori cfg.grid.pos values that I've been using). Does this mean that the size of individual gridpoints cannot be changed within ft_prepare_sourcemodel? Are they also in absolute terms fairly small (e.g. ~1mm)? If so, is the only way to extract 'larger' sources to fit a whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), identify gridpoints after ft_sourceanalysis that fall within a specified Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and then e.g. average over all those gridpoints? I'm concerned that larger source gridpoints might have larger SNR... Thanks in advance! Ravi -- Ravi Mill, PhD Post-doctoral researcher Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers University -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Tue Jul 24 09:16:06 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 24 Jul 2018 09:16:06 +0200 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel In-Reply-To: References: Message-ID: Hi Ravi, Beamforming will estimate source activity at *point* sources; in other words, the grid points have no spatial extent (i.e., they are zero-dimensional). > If so, is the only way to extract 'larger' sources to fit a > whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), > identify gridpoints after ft_sourceanalysis that fall within a specified > Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and > then e.g. average over all those gridpoints? Yes, that is definitely a valid approach. You will probably not need to use such a finely spaced grid if you end up averaging over grid points anyway. Typically, the spatial filters for neighbouring grid points will be highly correlated. Best, Eelke > > > Thanks in advance! > > Ravi > > > -- > Ravi Mill, PhD > Post-doctoral researcher > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers University > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > From apple.h99 at gmail.com Tue Jul 24 12:07:30 2018 From: apple.h99 at gmail.com (sara h) Date: Tue, 24 Jul 2018 14:37:30 +0430 Subject: [FieldTrip] Access to fieldtrip mailing list In-Reply-To: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> References: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> Message-ID: Hi Jan yes it is ok for me now too. thank you regards Sara On Mon, Jul 23, 2018 at 1:43 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Sara, > It works for me at the moment, so I don’t know what was/is causing your > problem. > Best wishes, > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > On 20 Jul 2018, at 15:54, sara h wrote: > > Dear all > Hi > > I'm new with filedtrip and I'm going to search in fieldtrip mailing list > but the list is not accessible and the webpage is not reachable. does any > one have this issue?? how can I sove it? > > thanks > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunnypitt1965 at gmail.com Tue Jul 24 21:24:19 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Tue, 24 Jul 2018 15:24:19 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Message-ID: Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From rdm146 at newark.rutgers.edu Tue Jul 24 23:59:02 2018 From: rdm146 at newark.rutgers.edu (Ravi Mill) Date: Tue, 24 Jul 2018 21:59:02 +0000 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel In-Reply-To: References: , Message-ID: Many thanks for clarifying that Eelke! ________________________________ From: fieldtrip on behalf of Eelke Spaak Sent: Tuesday, July 24, 2018 3:16:06 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel Hi Ravi, Beamforming will estimate source activity at *point* sources; in other words, the grid points have no spatial extent (i.e., they are zero-dimensional). > If so, is the only way to extract 'larger' sources to fit a > whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), > identify gridpoints after ft_sourceanalysis that fall within a specified > Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and > then e.g. average over all those gridpoints? Yes, that is definitely a valid approach. You will probably not need to use such a finely spaced grid if you end up averaging over grid points anyway. Typically, the spatial filters for neighbouring grid points will be highly correlated. Best, Eelke > > > Thanks in advance! > > Ravi > > > -- > Ravi Mill, PhD > Post-doctoral researcher > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers University > > > _______________________________________________ > fieldtrip mailing list > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=tqWRL8OWLPKt73S8XFXfPIoyeYVV60WTJuZVW3Vil%2Fs%3D&reserved=0 > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=nx%2B1yhLpHm1tXwX1KjTK6qwhvnWyk%2FWZMTAm5xp9Qbg%3D&reserved=0 > _______________________________________________ fieldtrip mailing list https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=tqWRL8OWLPKt73S8XFXfPIoyeYVV60WTJuZVW3Vil%2Fs%3D&reserved=0 https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=nx%2B1yhLpHm1tXwX1KjTK6qwhvnWyk%2FWZMTAm5xp9Qbg%3D&reserved=0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Arana at donders.ru.nl Wed Jul 25 13:49:56 2018 From: S.Arana at donders.ru.nl (Arana, S.L. (Sophie)) Date: Wed, 25 Jul 2018 11:49:56 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:ii_jk039gcg0_164cdbfadfb3de10] Thanks for your understanding and support Best Regards, Sunny -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: image.png URL: From sunnypitt1965 at gmail.com Wed Jul 25 14:22:33 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Wed, 25 Jul 2018 08:22:33 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) wrote: > Dear Sunny, > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > Best, > > Sophie > > ------------------------------ > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > Hope you are doing fine, > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > Thanks for your understanding and support > > Best Regards, > Sunny > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From Silvia.Formica at UGent.be Thu Jul 26 09:57:32 2018 From: Silvia.Formica at UGent.be (Silvia Formica) Date: Thu, 26 Jul 2018 07:57:32 +0000 Subject: [FieldTrip] ft_freqanalysis wavelet problem Message-ID: <1532591852846.46333@UGent.be> Dear all, I am new to fieldtrip so I apologize in advance if my question is trivial. I am trying to run a time frequency analysis with Morlet wavelets. Here is the code I am using: cfg = []; cfg.channel = 1:64; cfg.method = 'wavelet'; cfg.pad = 10; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 4:1:30; cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz TFRwave = ft_freqanalysis(cfg, data_clean); Where data_clean is the struct containing my trials. All my trials are the same length. When I run this code, I get the following warning: Warning: output time-bins are different from input time-bins trial 1, frequency 26 (29.00 Hz) Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) [...] I have no idea what this means. Any suggestion? Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot: cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.zlim = [-3e-27 3e-27]; cfg.showlabels = 'yes'; cfg.layout = 'biosemi64.lay'; figure ft_multiplotTFR(cfg, TFRwave) When I check the content of my TFRwave I can see it is not made of NaNs. Is the problem due to the setting cfg.zlim? It is not clear to me how to set it. Thanks in advance for any help! Silvia -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Jul 26 11:32:36 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 26 Jul 2018 11:32:36 +0200 Subject: [FieldTrip] ft_freqanalysis wavelet problem In-Reply-To: <1532591852846.46333@UGent.be> References: <1532591852846.46333@UGent.be> Message-ID: Dear Silvia, The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information, speeding it up as well) Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options. Best wishes, Stephen On 26 July 2018 at 09:57, Silvia Formica wrote: > Dear all, > > > I am new to fieldtrip so I apologize in advance if my question is trivial. > > I am trying to run a time frequency analysis with Morlet wavelets. > > Here is the code I am using: > > > cfg = []; > cfg.channel = 1:64; > cfg.method = 'wavelet'; > cfg.pad = 10; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 4:1:30; > cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz > TFRwave = ft_freqanalysis(cfg, data_clean); > > > Where data_clean is the struct containing my trials. All my trials are > the same length. > > When I run this code, I get the following warning: > > Warning: output time-bins are different from input time-bins > trial 1, frequency 26 (29.00 Hz) > Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) > Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) > Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) > Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) > [...] > > I have no idea what this means. Any suggestion? > > Despite the warning, the TRFwave is computed, but when I try to plot it I > get a completely blue output. Here is the code I am using for the plot: > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.zlim = [-3e-27 3e-27]; > cfg.showlabels = 'yes'; > cfg.layout = 'biosemi64.lay'; > figure > ft_multiplotTFR(cfg, TFRwave) > > > When I check the content of my TFRwave I can see it is not made of NaNs. > Is the problem due to the setting cfg.zlim? It is not clear to me how to > set it. > > Thanks in advance for any help! > > Silvia > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Silvia.Formica at UGent.be Thu Jul 26 12:45:26 2018 From: Silvia.Formica at UGent.be (Silvia Formica) Date: Thu, 26 Jul 2018 10:45:26 +0000 Subject: [FieldTrip] ft_freqanalysis wavelet problem In-Reply-To: References: <1532591852846.46333@UGent.be>, Message-ID: <1532601927049.21531@UGent.be> Dear Stephen, thanks a lot for your reply. I actually figured out the baseline was the issue, as I was computing the Morlet on a shorter time-window and I was trying to baseline-correct with an interval that was outside of my TFR. With this adjustment I do see the plot as I expected it. Concerning the warning on the cfg.toi, I chose on purpose the step according to my sampling rate, but I will consider increasing it. My concern is that I might somehow be losing information due to this mismatch between input and output time-bins. Thanks! Best, Silvia ________________________________ From: fieldtrip on behalf of Stephen Whitmarsh Sent: 26 July 2018 11:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_freqanalysis wavelet problem Dear Silvia, The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information, speeding it up as well) Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options. Best wishes, Stephen On 26 July 2018 at 09:57, Silvia Formica > wrote: Dear all, I am new to fieldtrip so I apologize in advance if my question is trivial. I am trying to run a time frequency analysis with Morlet wavelets. Here is the code I am using: cfg = []; cfg.channel = 1:64; cfg.method = 'wavelet'; cfg.pad = 10; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 4:1:30; cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz TFRwave = ft_freqanalysis(cfg, data_clean); Where data_clean is the struct containing my trials. All my trials are the same length. When I run this code, I get the following warning: Warning: output time-bins are different from input time-bins trial 1, frequency 26 (29.00 Hz) Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) [...] I have no idea what this means. Any suggestion? Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot: cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.zlim = [-3e-27 3e-27]; cfg.showlabels = 'yes'; cfg.layout = 'biosemi64.lay'; figure ft_multiplotTFR(cfg, TFRwave) When I check the content of my TFRwave I can see it is not made of NaNs. Is the problem due to the setting cfg.zlim? It is not clear to me how to set it. Thanks in advance for any help! Silvia _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brooks.jl at gmail.com Thu Jul 26 19:22:44 2018 From: brooks.jl at gmail.com (Joseph Brooks) Date: Thu, 26 Jul 2018 18:22:44 +0100 Subject: [FieldTrip] Lecturer (Assistant Prof Equivalent) in Psychology @ Keele University, UK Message-ID: Job Link: https://www.jobs.ac.uk/job/BLE960/lecturer-in-psychology/ Deadline: 9 Aug 2018 Psychology at Keele University (UK) is looking for an excellent researcher to join one or more of our growing research groups in Cognitive & Biological Psych, Social & Developmental, or Health & Wellbeing. We welcome applicants from across psychology but particularly those using quantitative methods. For Cognitive/Cog Neuro applicants, we have a new 64 channel Biosemi EEG laboratory, Eyelink eyetracking lab, Virtual Reality lab, Biopac psychophysiology labs, an MRI access agreement with Liverpool, and good links with Stoke University Hospital and Keele Medical School for neuropsych patient recruitment. More on facilities at https://www.keele.ac.uk/psychology/equipmentandfacilities/ . Applicants should have a strong track record of peer-reviewed publications and be able to contribute teaching to our undergraduate and post-graduate programmes. Note: This is a permanent academic position (subject to usual probationary period) which is equivalent to a tenure-track assistant professor position in North America. Keele has a beautiful campus in the West Midlands of England only 40 minutes from Manchester and Birmingham and 1.5 hours by train from London. We are a friendly community of academics and students (UG, MSc, and PhD) with a diverse range of interests across Psychology including both quantitative and qualitative methods. We are situated in the Dorothy Hodgkin Building which houses our laboratories For full details of the position, please see the advertisement at: https://www.jobs.ac.uk/job/BLE960/lecturer-in-psychology/ -------------------------------------------- Dr Joseph Brooks Senior Lecturer in Psychology Research Lead, Cognitive & Biological Research Group Programme Lead, MSc Cognitive Psychology School of Psychology, Keele University Office: Dorothy Hodgkin Building 1.74 Lab Website: https://sites.google.com/view/brookslab -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.herrero66 at gmail.com Fri Jul 27 15:29:47 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Fri, 27 Jul 2018 09:29:47 -0400 Subject: [FieldTrip] iEEG cluster statistics Message-ID: Hi FT, quick question on how to perform cluster statistics multiple comparisons correction with cfg.correctm = cluster' on iEEG data. I'm preparing neighbors with the two nearest contacts to the contact in question but the code gives an error (the 'fdr' method works fine). Is this method exclusive to standard montages or can be done manually. I've tried to do it manually so that neighbors format is similar to one of the examples MEG montage but still not working. Thoughts? JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Jul 27 15:35:49 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 27 Jul 2018 13:35:49 +0000 Subject: [FieldTrip] iEEG cluster statistics In-Reply-To: References: Message-ID: What’s the error? In principle, if your neighbourhood-structure is well-defined it should work. Best, JM On 27 Jul 2018, at 15:29, Jose Herrero > wrote: Hi FT, quick question on how to perform cluster statistics multiple comparisons correction with cfg.correctm = cluster' on iEEG data. I'm preparing neighbors with the two nearest contacts to the contact in question but the code gives an error (the 'fdr' method works fine). Is this method exclusive to standard montages or can be done manually. I've tried to do it manually so that neighbors format is similar to one of the examples MEG montage but still not working. Thoughts? JHerr _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabriel.delara at med.uni-goettingen.de Fri Jul 27 17:04:33 2018 From: gabriel.delara at med.uni-goettingen.de (Amador, Gabriel) Date: Fri, 27 Jul 2018 15:04:33 +0000 Subject: [FieldTrip] scalp EEG resting-state analysis Message-ID: Dear Field trippers, My first e-mail to this list. Thanks for paying attention to this, whoever took time to read it. I am currently doing my PhD in Göttingen, at the moment running a scalp-EEG (26-channels) analysis with Fieldtrip for a dataset of healthy participants. I have a repeated-measures design, where each participant undergoes 4 sessions, with n = 20. For each session, I performed two 5' eyes-open resting-state recordings per participant: one before and one after intervention (pre-, post-). The goal is to simply detect power changes in the pre X post comparison. Recordings were segmented into 2s trials with 50% overlap followed by other pre-processing steps. I am having some doubts on the feasibility/correctness of the steps after the pre-processing. My main critical question is the procedures sequence to correctly run the Monte Carlo stats in the end (if and when to keep trials, to average trials, to average across participants, and so on). Some options available: 1. First running TFA (mtmfft, dpss,) keeping the trials. Then, appending participants with ft_appendfreq. Afterwards, stats: parameters (Montecarlo, depsamplesT, cluster correction, 5.000 iterations). First problem arises in the design matrix: Since trials are kept in the FA, they are uneven for every session (appending leads to different trials between pre X post), and also the appended data does not keep the participant as UO, so design matrix has to be design as trials in the first row. To make it work, trials have to be shortened from one condition, so they are paired (which seems obvious for depsamplesT, since it does would not accept different values in the uvar). Statistics run after doing all this, but I am not sure, since having a uvar with ~10.000 points, that were the individual trials of every session (there are 20 participants) sounds strange (there were no 10.000 participants). This option was run for one condition, significant difference happened, clusters were formed, etc. Is this reasonable? 2. First running TFA (mtmfft, dpss,) keeping the trials. After, apply ft_freqdescriptives to every subject, in oder to be able to use ft_freq_grandaverage. Apply ft_freqgrandaverage across participants, but keeping individuals (for the design matrix).After ft_ freqgrandaverage, stats as described above, with design matrix with 1:20 in the first row (uvar) and the two conditions (pre X post) at the second. This works, but leads to no clusters found (ran it on more than one condition). Doubt here is: using ft_freqdescriptives and then ft_freq_grandaverage compromises the monte carlo procedure, having just one value for each channel (the grand-averaged trials power)? Any suggestions? Thanks! Gabriel Amador de Lara wissenschaftlicher Mitarbeiter / PhD candidate Klinik für klinische Neurophysiologie / Department of Clinical Neurophysiology Universitätsmedizin / Medical Center Georg-August-Universität Göttingen Robert-Koch-Str. 40, 37075 +49 0551 3919265 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunnypitt1965 at gmail.com Fri Jul 27 20:41:12 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Fri, 27 Jul 2018 14:41:12 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON ( https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > Hello Sophie, > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > Thanks for your understanding and support. > > Best Regards, > Sunny > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > >> Hello Sophie, >> >> Thanks a lot for your clarification. This is very useful. >> >> Sunny >> >> >> On Wednesday, July 25, 2018, Arana, S.L. (Sophie) >> wrote: >> >>> Dear Sunny, >>> >>> the multi-channel NIRS data tutorial is currently under construction and >>> will hopefully be fully available in a couple of weeks. Until then, there >>> might still be some inconsistencies such as the one you have encountered. >>> >>> The variable you refer to is indeed missing. It refers to a filtered >>> version of the data, and you can created it by running the following code >>> before the epoching. >>> >>> cfg = []; >>> >>> cfg.hpfilter = 'yes'; >>> >>> cfg.hpfreq = 0.01; >>> >>> data_flt = ft_preprocessing(cfg,data_down); >>> >>> >>> This should help you to continue with the tutorial, but please do keep >>> in mind that we are currently working on it and you might encounter some >>> other inconsistencies still later on. >>> >>> >>> Best, >>> >>> Sophie >>> >>> ------------------------------ >>> *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny >>> p [sunnypitt1965 at gmail.com] >>> *Sent:* Tuesday, July 24, 2018 9:24 PM >>> *To:* fieldtrip at science.ru.nl >>> *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging >>> of multi-channel NIRS data >>> >>> Hello All Good Day, >>> >>> Hope you are doing fine, >>> >>> Thanks a lot for providing with fieldtrip which is really useful to >>> analyze fNIRS data. I have an issue in the "Preprocessing and averaging of >>> multi-channel NIRS data" tutorial. Can you please help me with this issue? >>> >>> Issue: In the "Preprocessing and averaging of multi-channel NIRS data" >>> tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel >>> >>> The "Epoch" section consists of a variable "data_flt.fsample" where >>> "data_flt" variable is not defined. Can you please inform what is this >>> variable related to? as this is needed to complete my analysis. >>> >>> >>> >>> >>> Thanks for your understanding and support >>> >>> Best Regards, >>> Sunny >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From lizhipeng3924 at gmail.com Sun Jul 29 04:55:37 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Sun, 29 Jul 2018 10:55:37 +0800 Subject: [FieldTrip] A question about MEG source reconstruction Message-ID: Dear all, When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. I would appreciate it if you could help me. Yours, zhipeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 5933 bytes Desc: not available URL: From alexandre.gramfort at inria.fr Sun Jul 29 10:03:59 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 29 Jul 2018 10:03:59 +0200 Subject: [FieldTrip] A question about MEG source reconstruction In-Reply-To: References: Message-ID: hi, indeed there is a typo: $ cd $MNE_ROOT $ ls bin/mne_setup* bin/mne_setup bin/mne_setup_matlab_csh bin/mne_setup_mri bin/mne_setup_source_space bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh depending on your shell it can be source $MNE_ROOT/bin/mne_setup_sh HTH Alex On Sun, Jul 29, 2018 at 4:58 AM zhipeng li wrote: > > External Email - Use Caution > > Dear all, > When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. > I would appreciate it if you could help me. > Yours, > zhipeng > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From lizhipeng3924 at gmail.com Mon Jul 30 03:49:11 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Mon, 30 Jul 2018 09:49:11 +0800 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 In-Reply-To: References: Message-ID: - First of all, thank you very much for your reply @ Alexandre Gramfort . - But none of the files you listed were found in bin - - This is all the files contained in bin, - I need your further help. - Yours, zhipeng 2018-07-29 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. A question about MEG source reconstruction (zhipeng li) > 2. Re: A question about MEG source reconstruction > (Alexandre Gramfort) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 29 Jul 2018 10:55:37 +0800 > From: zhipeng li > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] A question about MEG source reconstruction > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > I would appreciate it if you could help me. > Yours, > zhipeng > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180729/9711b38d/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 5933 bytes > Desc: not available > URL: attachments/20180729/9711b38d/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Sun, 29 Jul 2018 10:03:59 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] A question about MEG source reconstruction > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > hi, > > indeed there is a typo: > > $ cd $MNE_ROOT > $ ls bin/mne_setup* > bin/mne_setup bin/mne_setup_matlab_csh > bin/mne_setup_mri bin/mne_setup_source_space > bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > > depending on your shell it can be > > source $MNE_ROOT/bin/mne_setup_sh > > HTH > Alex > > On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > Dear all, > > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > > I would appreciate it if you could help me. > > Yours, > > zhipeng > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 19 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 159116 bytes Desc: not available URL: From jorn at artinis.com Mon Jul 30 08:47:25 2018 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Mon, 30 Jul 2018 08:47:25 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) Cc: FieldTrip discussion list Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From alexandre.gramfort at inria.fr Mon Jul 30 08:49:46 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Mon, 30 Jul 2018 08:49:46 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 In-Reply-To: References: Message-ID: it's the $MNE_ROOT/bin folder after setting the MNE_ROOT env variable to the folder that contains the MNE command line tools. HTH Alex On Mon, Jul 30, 2018 at 3:52 AM zhipeng li wrote: > > External Email - Use Caution > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > But none of the files you listed were found in bin > > > This is all the files contained in bin, > > I need your further help. > > Yours, > zhipeng > > > 2018-07-29 18:00 GMT+08:00 : >> >> Send fieldtrip mailing list submissions to >> fieldtrip at science.ru.nl >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> or, via email, send a message with subject or body 'help' to >> fieldtrip-request at science.ru.nl >> >> You can reach the person managing the list at >> fieldtrip-owner at science.ru.nl >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of fieldtrip digest..." >> >> >> Today's Topics: >> >> 1. A question about MEG source reconstruction (zhipeng li) >> 2. Re: A question about MEG source reconstruction >> (Alexandre Gramfort) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 29 Jul 2018 10:55:37 +0800 >> From: zhipeng li >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] A question about MEG source reconstruction >> Message-ID: >> >> Content-Type: text/plain; charset="utf-8" >> >> Dear all, >> When I was about to create a sourcemodel, I ran into a problem.The >> documentary which I refers to is Tutorial documentation>Source >> reconstruction of event-related fields using minimum-norm >> estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG >> data.When I installed MNE as their description, I found that the.sh file >> doesn't exist.The command I am using is posted below as a >> picture.Therefore, the following steps cannot be carried out. >> I would appreciate it if you could help me. >> Yours, >> zhipeng >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: image.png >> Type: image/png >> Size: 5933 bytes >> Desc: not available >> URL: >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 29 Jul 2018 10:03:59 +0200 >> From: Alexandre Gramfort >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] A question about MEG source reconstruction >> Message-ID: >> >> Content-Type: text/plain; charset="UTF-8" >> >> hi, >> >> indeed there is a typo: >> >> $ cd $MNE_ROOT >> $ ls bin/mne_setup* >> bin/mne_setup bin/mne_setup_matlab_csh >> bin/mne_setup_mri bin/mne_setup_source_space >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh >> >> depending on your shell it can be >> >> source $MNE_ROOT/bin/mne_setup_sh >> >> HTH >> Alex >> >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li wrote: >> > >> > External Email - Use Caution >> > >> > Dear all, >> > When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. >> > I would appreciate it if you could help me. >> > Yours, >> > zhipeng >> > >> > >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > https://doi.org/10.1371/journal.pcbi.1002202 >> > >> > >> > The information in this e-mail is intended only for the person to whom it is >> > addressed. If you believe this e-mail was sent to you in error and the e-mail >> > contains patient information, please contact the Partners Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you in error >> > but does not contain patient information, please contact the sender and properly >> > dispose of the e-mail. >> >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> https://doi.org/10.1371/journal.pcbi.1002202 >> >> >> ------------------------------ >> >> End of fieldtrip Digest, Vol 92, Issue 19 >> ***************************************** > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From S.Hanslmayr at bham.ac.uk Mon Jul 30 11:23:31 2018 From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr) Date: Mon, 30 Jul 2018 09:23:31 +0000 Subject: [FieldTrip] Postdoc position to work with human single neurons and LFPs, 9 days left to apply! Message-ID: <257F6C65A372A04CA41056EACC0DE7CED8783389@EX12.adf.bham.ac.uk> Dear Fieldtrippers, We are pleased to announce an open postdoc position in our group to work with human single neurons and LFP recordings in an exciting memory project funded by the ERC. The position is initially for 2 years with an option for 1 year extension. The negotiable start date is 1st Oct. Preliminary data has been collected and is waiting to be analysed. If you have strong electrophysiological analytical skills and are interested then please do not hesitate to apply here: http://www.memorybham.com/open-positions/ If you have any questions then please do not hesitate to contact me. Best wishes, Dr. Simon Hanslmayr Reader in Cognitive Neuroscience Royal Society Wolfson Research Merit Award Holder School of Psychology Hills Building 2.37 University of Birmingham Edgbaston Birmingham B15 2TT UK Tel +44 121 4146203 http://www.memorybham.com/people/#/simon-hanslmayr/ [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 8560 bytes Desc: image001.gif URL: From sunnypitt1965 at gmail.com Mon Jul 30 15:29:19 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Mon, 30 Jul 2018 09:29:19 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <007201d427d1$2d7d9500$8878bf00$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Message-ID: Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig wrote: > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* fieldtrip *On Behalf Of *Sunny p > *Sent:* Friday, July 27, 2018 20:41 > *To:* Arana, S.L. (Sophie) > *Cc:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > ------------------------------ > > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > > > Virus-free. www.avg.com > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jorn at artinis.com Mon Jul 30 15:41:40 2018 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Mon, 30 Jul 2018 15:41:40 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Message-ID: <012001d4280b$0c17baa0$24472fe0$@artinis.com> Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list ; jorn at artinis.com Cc: Arana, S.L. (Sophie) Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From sunnypitt1965 at gmail.com Mon Jul 30 16:44:40 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Mon, 30 Jul 2018 10:44:40 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <012001d4280b$0c17baa0$24472fe0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> Message-ID: Hello Jorn, Thanks a lot for your response. Yes, I just collected the data samples, My primary aim is to visualize this data on a head model using field trip. so that it will be easy to understand. Please find attached data set collected using Octamon in this email. I also created layout for this. I attached data, layout and image in this email. Thanks a lot for your support. Its very useful for my research. Best Regards, Sunny On Mon, Jul 30, 2018 at 9:41 AM, Jörn M. Horschig wrote: > Hi Sunny, > > > > The ADC channels in the tutorial are used as a trigger-channel. I am not > sure how you insert the triggers in your experiment, but the Octamon has no > direct trigger input (you could add triggers either wirelessly using a > PortaSync or directly from within Oxysoft). The ADC of the Octamon is the > battery level and not a trigger input. Depending on what you did, you have > to follow different processing steps. If you let me know more about the > events and triggers, I can let you know what to do (you could also send me > some example data and I will send you an example script back that reads in > the data in FieldTrip). > > > > With best regards, > > Jörn > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* Sunny p > *Sent:* Monday, July 30, 2018 15:29 > *To:* FieldTrip discussion list ; > jorn at artinis.com > *Cc:* Arana, S.L. (Sophie) > > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Jorn, > > > > Thanks a lot for your response. I am working with Octamon data (4*2 > Channel). I am trying to visualize the data using topo plot on head based > image following http://www.fieldtriptoolbox.org/tutorial/ > nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon > which has 48 channel). I am wondering what parameter changes should I make > to get the data for OCTAMON visualization as my data has only ADC001 and > there is no ADC002 in data for epoch section. As I am not an NIRS expert, > its difficult to figure out which parameters gives me the visualization as > its throwing errors when following the tutorial. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* fieldtrip *On Behalf Of *Sunny p > *Sent:* Friday, July 27, 2018 20:41 > *To:* Arana, S.L. (Sophie) > *Cc:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > ------------------------------ > > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > > > Virus-free. www.avg.com > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OCTAMON.oxy3 Type: application/octet-stream Size: 417156 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OCTA_layout_MAIN.mat Type: application/octet-stream Size: 1493 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Brain_PreFrontal_Cortex.PNG Type: image/png Size: 88327 bytes Desc: not available URL: From jorn at artinis.com Tue Jul 31 09:16:24 2018 From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=) Date: Tue, 31 Jul 2018 09:16:24 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <012001d4280b$0c17baa0$24472fe0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> Message-ID: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jorn at artinis.com Tue Jul 31 09:34:55 2018 From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=) Date: Tue, 31 Jul 2018 09:34:55 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Message-ID: <004d01d428a0$fae2e840$f0a8b8c0$@artinis.com> Small typo, it should of course say >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.poststim = 35; >> cfg = ft_definetrial(cfg); -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Tuesday, July 31, 2018 9:16 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Tue Jul 31 09:38:53 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 31 Jul 2018 07:38:53 +0000 Subject: [FieldTrip] field trip loreta error References: Message-ID: Dear list, See forwarded message below for a question by Tyler. Tyler, could you send your e-mails to fieldtrip at science.ru.nl? Thanks. Jan-Mathijs Begin forwarded message: From: Tyler Durden > Subject: field trip loreta error Date: 31 July 2018 at 09:20:05 GMT+2 To: > Hi all, I am brand new to fieldtrip and still fairly new to Matlab (R2014a) . I downloaded the fieldtrip toolbox (20180722) and set up paths as instructed. Now I tried to convert some loreta files I have into fieldtrip files but I keep getting this error: "Error using ft_preamble (line 82) Could not run ft_preamble_callinfo - does not seem to exist Error in loreta2fieldtrip (line 48) ft_preamble callinfo I searched the net but I could not find any satisfying answers. I then found the ft_preamble callinfo script on github and just copied and saved it in my directory as a .m file. Now that error is gone but when I want to execute loreta2fieldtrip I get another error: Error using ft_notification (line 340) unsupported LORETA format Error in ft_error (line 39) ft_notification(varargin{:}); Error in loreta2fieldtrip (line 82) ft_error('unsupported LORETA format'); I tried some stuff but as far as I can judge I converted the slor-files appropriately and I have no idea what to do with this error...Since I really want to use your tool box, it would be super if you could help me out! Best -------------- next part -------------- An HTML attachment was scrubbed... URL: From hgould at memphis.edu Tue Jul 31 15:37:06 2018 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 31 Jul 2018 13:37:06 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com>, <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:image001.png at 01D428AE.213F63D0] Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: image001.png URL: From lizhipeng3924 at gmail.com Tue Jul 31 15:52:11 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Tue, 31 Jul 2018 21:52:11 +0800 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21 In-Reply-To: References: Message-ID: - Thank you very much for your reply.@ Alexandre Gramfort But with your answer, my question remains unsolved . On my computer, I can't find any files on mne setup, including any of your list. Following the instructions on the site, I made this step - But the setup file can't be found,I hope you can give me further guidance. - Yours, - zhipeng 2018-07-30 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) > 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort) > 3. Postdoc position to work with human single neurons and LFPs, > 9 days left to apply! (Simon Hanslmayr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2018 08:47:25 +0200 > From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" > To: "'FieldTrip discussion list'" , "'Arana, > S.L. \(Sophie\)'" > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> > Content-Type: text/plain; charset="utf-8" > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > -- > Jörn M. Horschig, PhD, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> > > > > From: fieldtrip On Behalf Of Sunny p > Sent: Friday, July 27, 2018 20:41 > To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging > of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p sunnypitt1965 at gmail.com> > wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > > > _____ > > > From: fieldtrip [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [ > sunnypitt1965 at gmail.com ] > Sent: Tuesday, July 24, 2018 9:24 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " > http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > > Virus-free. utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > www.avg.com > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/577081f5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 4228 bytes > Desc: not available > URL: attachments/20180730/577081f5/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jul 2018 08:49:46 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > it's the $MNE_ROOT/bin folder > after setting the MNE_ROOT env variable to the folder that contains > the MNE command line tools. > > HTH > Alex > On Mon, Jul 30, 2018 at 3:52 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > > > But none of the files you listed were found in bin > > > > > > This is all the files contained in bin, > > > > I need your further help. > > > > Yours, > > zhipeng > > > > > > 2018-07-29 18:00 GMT+08:00 : > >> > >> Send fieldtrip mailing list submissions to > >> fieldtrip at science.ru.nl > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> or, via email, send a message with subject or body 'help' to > >> fieldtrip-request at science.ru.nl > >> > >> You can reach the person managing the list at > >> fieldtrip-owner at science.ru.nl > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of fieldtrip digest..." > >> > >> > >> Today's Topics: > >> > >> 1. A question about MEG source reconstruction (zhipeng li) > >> 2. Re: A question about MEG source reconstruction > >> (Alexandre Gramfort) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 29 Jul 2018 10:55:37 +0800 > >> From: zhipeng li > >> To: fieldtrip at science.ru.nl > >> Subject: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all, > >> When I was about to create a sourcemodel, I ran into a problem.The > >> documentary which I refers to is Tutorial documentation>Source > >> reconstruction of event-related fields using minimum-norm > >> estimation>Creating a sourcemodel for source-reconstruction of MEG or > EEG > >> data.When I installed MNE as their description, I found that the.sh file > >> doesn't exist.The command I am using is posted below as a > >> picture.Therefore, the following steps cannot be carried out. > >> I would appreciate it if you could help me. > >> Yours, > >> zhipeng > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: attachments/20180729/9711b38d/attachment-0001.html> > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: image.png > >> Type: image/png > >> Size: 5933 bytes > >> Desc: not available > >> URL: attachments/20180729/9711b38d/attachment-0001.png> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 29 Jul 2018 10:03:59 +0200 > >> From: Alexandre Gramfort > >> To: FieldTrip discussion list > >> Subject: Re: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> hi, > >> > >> indeed there is a typo: > >> > >> $ cd $MNE_ROOT > >> $ ls bin/mne_setup* > >> bin/mne_setup bin/mne_setup_matlab_csh > >> bin/mne_setup_mri bin/mne_setup_source_space > >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > >> > >> depending on your shell it can be > >> > >> source $MNE_ROOT/bin/mne_setup_sh > >> > >> HTH > >> Alex > >> > >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Dear all, > >> > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > >> > I would appreciate it if you could help me. > >> > Yours, > >> > zhipeng > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > https://doi.org/10.1371/journal.pcbi.1002202 > >> > > >> > > >> > The information in this e-mail is intended only for the person to > whom it is > >> > addressed. If you believe this e-mail was sent to you in error and > the e-mail > >> > contains patient information, please contact the Partners Compliance > HelpLine at > >> > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > >> > but does not contain patient information, please contact the sender > and properly > >> > dispose of the e-mail. > >> > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> https://doi.org/10.1371/journal.pcbi.1002202 > >> > >> > >> ------------------------------ > >> > >> End of fieldtrip Digest, Vol 92, Issue 19 > >> ***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jul 2018 09:23:31 +0000 > From: Simon Hanslmayr > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Postdoc position to work with human single > neurons and LFPs, 9 days left to apply! > Message-ID: > <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > We are pleased to announce an open postdoc position in our group to work > with human single neurons and LFP recordings in an exciting memory project > funded by the ERC. The position is initially for 2 years with an option for > 1 year extension. The negotiable start date is 1st Oct. Preliminary data > has been collected and is waiting to be analysed. If you have strong > electrophysiological analytical skills and are interested then please do > not hesitate to apply here: http://www.memorybham.com/open-positions/ > > If you have any questions then please do not hesitate to contact me. > > Best wishes, > Dr. Simon Hanslmayr > Reader in Cognitive Neuroscience > Royal Society Wolfson Research Merit Award Holder > School of Psychology > Hills Building 2.37 > University of Birmingham > Edgbaston > Birmingham > B15 2TT > UK > > Tel +44 121 4146203 > http://www.memorybham.com/people/#/simon-hanslmayr/ > [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/c066a17a/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.gif > Type: image/gif > Size: 8560 bytes > Desc: image001.gif > URL: attachments/20180730/c066a17a/attachment-0001.gif> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 21 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11167 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 171819 bytes Desc: not available URL: From Amie.Fairs at mpi.nl Tue Jul 31 16:11:15 2018 From: Amie.Fairs at mpi.nl (Fairs, Amie) Date: Tue, 31 Jul 2018 14:11:15 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 24 In-Reply-To: References: Message-ID: Hi Zhipeng, I am quite sure of your issue because any images you send in your email are scrubbed and I can't see them, but I might be able to help. I recently also had some issues following this tutorial. For me, MNE for python was accidentally downloaded at first. For instance, when I first did a 'which mne' search in my system it said [this is my specific path]: /usr/local/apps/python-2.7.11/bin/mne And this mne is not the same MNE suite that is discussed in the tutorial. This mne is 'in' python, so it contains: ls /usr/local/apps/python-2.7.11/bin/ 2to3 folia2html foliatree python rst2html.pyc rst2xetex.pyc alpino2folia folia2rst foliavalidator python2 rst2latex.py rst2xml.py build folia2txt idle python2.7 rst2latex.pyc rst2xml.pyc csv2rdf foliacat mne python2.7-config rst2man.py rstpep2html.py cygdb foliacorrect nosetests python2-config rst2man.pyc rstpep2html.pyc cython foliacount nosetests-2.7 python-config rst2odt_prepstyles.py smtpd.py cythonize foliafreqlist pip rdf2dot rst2odt_prepstyles.pyc tclsh8.5 dcoi2folia foliamerge pip2 rdfgraphisomorphism rst2odt.py virtualenv easy_install foliaquery pip2.7 rdfpipe rst2odt.pyc wish8.5 easy_install-2.7 foliaquery1 pt2to3 rdfs2dot rst2pseudoxml.py f2py foliasetdefinition ptdump rst2folia rst2pseudoxml.pyc folia2annotatedtxt foliaspec ptrepack rst2html5.py rst2s5.py folia2columns foliaspec2json pttree rst2html5.pyc rst2s5.pyc folia2dcoi foliatextcontent pydoc rst2html.py rst2xetex.py [sorry for the formatting] Maybe your system looks something like this? MNE suite actually looks something like this [with the path on my system]: ls /usr/local/apps/MNE/MNE-2.7.0-3106-Linux-x86_64/bin mne_add_patch_info mne_copy_processing_history mne_list_bem mne_redo_file_nocwd mne_add_to_meas_info mne_cov2proj mne_list_coil_def mne_remove_platform mne_add_triggers mne_create_comp_data mne_list_proj mne_rename_channels mne_analyze mne_ctf2fiff mne_list_source_space mne_sensitivity_map mne_annot2labels mne_ctf_dig2fiff mne_list_versions mne_sensor_locations mne_anonymize mne_dacq_annotator mne_make_cor_set mne_setup mne_average_estimates mne_dicom_essentials mne_make_derivations mne_setup_forward_model mne_average_forward_solutions mne_dipole_fit mne_make_eeg_layout mne_setup_mri mne_brain_vision2fiff mne_do_forward_solution mne_make_morph_maps mne_setup_sh mne_browse_raw mne_do_inverse_operator mne_make_movie mne_setup_source_space mne_change_baselines mne_edf2fiff mne_make_scalp_surfaces mne_show_environment mne_change_nave mne_epochs2mat mne_make_source_space mne_show_fiff mne_check_eeg_locations mne_epochs2mat.bin mne_make_sphere_bem mne_simu mne_check_surface mne_evoked_data_summary mne_make_uniform_stc mne_simu.bin mne_collect_transforms mne_eximia2fiff mne_map_data mne_smooth mne_compensate_data mne_fit_sphere_to_surf mne_mark_bad_channels mne_surf2bem mne_compute_mne mne_fix_mag_coil_types mne_morph_labels mne_toggle_skips mne_compute_raw_inverse mne_fix_stim14 mne_opengl_test mne_transform_points mne_convert_ctf_markers mne_flash_bem mne_organize_dicom mne_tufts2fiff mne_convert_dig_data mne_forward_solution mne_prepare_bem_model mne_version_test mne_convert_lspcov mne_insert_4D_comp mne_process_raw mne_view_manual mne_convert_mne_data mne_install_packages mne_process_stc mne_volume_data2mri mne_convert_mne_data.bin mne_inverse_operator mne_raw2mat mne_volume_source_space mne_convert_ncov mne_kit2fiff mne_raw2mat.bin mne_watershed_bem mne_convert_surface mne_launcher mne_redo_file Then you can see mne_setup_sh, and mne_setup_source_space - the two things you need. I hope maybe this is helpful? Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -----Original Message----- From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of fieldtrip-request at science.ru.nl Sent: dinsdag 31 juli 2018 15:52 To: fieldtrip at science.ru.nl Subject: fieldtrip Digest, Vol 92, Issue 24 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit https://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. Re: Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data (Herbert J Gould (hgould)) 2. Re: fieldtrip Digest, Vol 92, Issue 21 (zhipeng li) ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 Jul 2018 13:37:06 +0000 From: "Herbert J Gould (hgould)" To: FieldTrip discussion list Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861 at email.android.com> Content-Type: text/plain; charset="windows-1252" Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:image001.png at 01D428AE.213F63D0] Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: image001.png URL: ------------------------------ Message: 2 Date: Tue, 31 Jul 2018 21:52:11 +0800 From: zhipeng li To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21 Message-ID: Content-Type: text/plain; charset="utf-8" - Thank you very much for your reply.@ Alexandre Gramfort But with your answer, my question remains unsolved . On my computer, I can't find any files on mne setup, including any of your list. Following the instructions on the site, I made this step - But the setup file can't be found,I hope you can give me further guidance. - Yours, - zhipeng 2018-07-30 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) > 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort) > 3. Postdoc position to work with human single neurons and LFPs, > 9 days left to apply! (Simon Hanslmayr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2018 08:47:25 +0200 > From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" > To: "'FieldTrip discussion list'" , "'Arana, > S.L. \(Sophie\)'" > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> > Content-Type: text/plain; charset="utf-8" > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > -- > Jörn M. Horschig, PhD, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> > > > > From: fieldtrip On Behalf Of Sunny p > Sent: Friday, July 27, 2018 20:41 > To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging > of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p sunnypitt1965 at gmail.com> > wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > > > _____ > > > From: fieldtrip [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [ > sunnypitt1965 at gmail.com ] > Sent: Tuesday, July 24, 2018 9:24 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " > http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > > Virus-free. utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > www.avg.com > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/577081f5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 4228 bytes > Desc: not available > URL: attachments/20180730/577081f5/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jul 2018 08:49:46 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > it's the $MNE_ROOT/bin folder > after setting the MNE_ROOT env variable to the folder that contains > the MNE command line tools. > > HTH > Alex > On Mon, Jul 30, 2018 at 3:52 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > > > But none of the files you listed were found in bin > > > > > > This is all the files contained in bin, > > > > I need your further help. > > > > Yours, > > zhipeng > > > > > > 2018-07-29 18:00 GMT+08:00 : > >> > >> Send fieldtrip mailing list submissions to > >> fieldtrip at science.ru.nl > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> or, via email, send a message with subject or body 'help' to > >> fieldtrip-request at science.ru.nl > >> > >> You can reach the person managing the list at > >> fieldtrip-owner at science.ru.nl > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of fieldtrip digest..." > >> > >> > >> Today's Topics: > >> > >> 1. A question about MEG source reconstruction (zhipeng li) > >> 2. Re: A question about MEG source reconstruction > >> (Alexandre Gramfort) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 29 Jul 2018 10:55:37 +0800 > >> From: zhipeng li > >> To: fieldtrip at science.ru.nl > >> Subject: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all, > >> When I was about to create a sourcemodel, I ran into a problem.The > >> documentary which I refers to is Tutorial documentation>Source > >> reconstruction of event-related fields using minimum-norm > >> estimation>Creating a sourcemodel for source-reconstruction of MEG or > EEG > >> data.When I installed MNE as their description, I found that the.sh file > >> doesn't exist.The command I am using is posted below as a > >> picture.Therefore, the following steps cannot be carried out. > >> I would appreciate it if you could help me. > >> Yours, > >> zhipeng > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: attachments/20180729/9711b38d/attachment-0001.html> > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: image.png > >> Type: image/png > >> Size: 5933 bytes > >> Desc: not available > >> URL: attachments/20180729/9711b38d/attachment-0001.png> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 29 Jul 2018 10:03:59 +0200 > >> From: Alexandre Gramfort > >> To: FieldTrip discussion list > >> Subject: Re: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> hi, > >> > >> indeed there is a typo: > >> > >> $ cd $MNE_ROOT > >> $ ls bin/mne_setup* > >> bin/mne_setup bin/mne_setup_matlab_csh > >> bin/mne_setup_mri bin/mne_setup_source_space > >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > >> > >> depending on your shell it can be > >> > >> source $MNE_ROOT/bin/mne_setup_sh > >> > >> HTH > >> Alex > >> > >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Dear all, > >> > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > >> > I would appreciate it if you could help me. > >> > Yours, > >> > zhipeng > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > https://doi.org/10.1371/journal.pcbi.1002202 > >> > > >> > > >> > The information in this e-mail is intended only for the person to > whom it is > >> > addressed. If you believe this e-mail was sent to you in error and > the e-mail > >> > contains patient information, please contact the Partners Compliance > HelpLine at > >> > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > >> > but does not contain patient information, please contact the sender > and properly > >> > dispose of the e-mail. > >> > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> https://doi.org/10.1371/journal.pcbi.1002202 > >> > >> > >> ------------------------------ > >> > >> End of fieldtrip Digest, Vol 92, Issue 19 > >> ***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jul 2018 09:23:31 +0000 > From: Simon Hanslmayr > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Postdoc position to work with human single > neurons and LFPs, 9 days left to apply! > Message-ID: > <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > We are pleased to announce an open postdoc position in our group to work > with human single neurons and LFP recordings in an exciting memory project > funded by the ERC. The position is initially for 2 years with an option for > 1 year extension. The negotiable start date is 1st Oct. Preliminary data > has been collected and is waiting to be analysed. If you have strong > electrophysiological analytical skills and are interested then please do > not hesitate to apply here: http://www.memorybham.com/open-positions/ > > If you have any questions then please do not hesitate to contact me. > > Best wishes, > Dr. Simon Hanslmayr > Reader in Cognitive Neuroscience > Royal Society Wolfson Research Merit Award Holder > School of Psychology > Hills Building 2.37 > University of Birmingham > Edgbaston > Birmingham > B15 2TT > UK > > Tel +44 121 4146203 > http://www.memorybham.com/people/#/simon-hanslmayr/ > [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/c066a17a/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.gif > Type: image/gif > Size: 8560 bytes > Desc: image001.gif > URL: attachments/20180730/c066a17a/attachment-0001.gif> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 21 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11167 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 171819 bytes Desc: not available URL: ------------------------------ Subject: Digest Footer _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 ------------------------------ End of fieldtrip Digest, Vol 92, Issue 24 ***************************************** From Pranish.Kantak at UTSouthwestern.edu Tue Jul 31 18:05:38 2018 From: Pranish.Kantak at UTSouthwestern.edu (Pranish Kantak) Date: Tue, 31 Jul 2018 16:05:38 +0000 Subject: [FieldTrip] Blackrock Data Message-ID: <5E4FC234-9787-415B-8126-5A5064FCB061@utsouthwestern.edu> Hi All, I was just wondering if the functionality of using Blackrock data has been implemented into the toolbox yet? Thanks! Pranish Kantak ________________________________ UT Southwestern Medical Center The future of medicine, today. From jan.schoffelen at donders.ru.nl Tue Jul 31 20:49:38 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 31 Jul 2018 18:49:38 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> Message-ID: Dear Herbert, I have unsubscribed you. To all, note that you can manage your subscription yourself on the listservers interface, which can be reached through http://www.fieldtriptoolbox.org/discussion_list (following the first link therein). Best wishes, Jan-Mathijs Schoffelen On 31 Jul 2018, at 15:37, Herbert J Gould (hgould) > wrote: Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bahman at neuromotor.org Sun Jul 1 19:43:00 2018 From: bahman at neuromotor.org (Bahman Nasseroleslami) Date: Sun, 1 Jul 2018 18:43:00 +0100 Subject: [FieldTrip] Research Assistant Position in Neural Engineering - Trinity College Dublin, the University of Dublin, Dublin, Ireland Message-ID: Dear all, There is a research assistant position available in Academic Unit of Neurology, Trinity College Dublin, the University of Dublin, Dublin, Ireland. The position is ideally suited to an individual with a BSc/MSc degree who is considering pursuing a PhD degree in longer term. --------------------------------------- Post Specification (033160) Post Title: Research Assistant in Neural Engineering Post Status: 12 month Fixed-term Contract, Full-time Research Group / Department / School: Academic Unit of Neurology, School of Medicine, Trinity College Dublin, the University of Dublin Location: Trinity Biomedical Sciences Institute, Trinity College Dublin, the University of Dublin College Green, Dublin D02 R590, Ireland Reports to: Professor Orla Hardiman/Dr Bahman Nasseroleslami Salary: Appointment will be made on the Research Assistant (Level 1) Salary Scale at a point in line with Government Pay Policy, €21,674 to €28,423 per annum (commensurate with qualifications and experience). Appointment will be made no higher than point 10. Hours of Work: 40 hours per week Closing Date: 12 Noon (Irish Standard Time), 24 July 2018 Please note that Garda vetting will be sought in respect of individuals who come under consideration for a post. Post Summary Applications are invited for a motivated and self-driven individual for the position of research assistant with the Irish ALS Research Group, hosted in the Trinity Biomedical Sciences Institute (TBSI)'s Academic Unit of Neurology. The ideal candidate will have an undergraduate or master's degree in engineering, bioengineering, mathematics, physics, computational biology, or a cognate area. Familiarity with and/or the ability to quickly acquire skills in electrophysiological recordings and analysis (e.g. EEG/EMG), would be highly desirable as would a knowledge of computer programming (MATLAB). --------------------------------------- The detailed job description file (PDF) and the application instructions can be found online at http://jobs.tcd.ie. or directly from https://drive.google.com/file/ d/14Q7DxqobPQCjgKpZ4UJS68xTIlRvnPcd/view?usp=sharing It would be really appreciated if you could share this with those that may be interested. Sincerely Bahman -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Sun Jul 1 20:10:06 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Sun, 1 Jul 2018 14:10:06 -0400 Subject: [FieldTrip] .avg field in GA structure for interaction test Message-ID: Hi Fieldtrip, I am following the tutorial 'How to test an interaction effect using cluster-based permutation tests?' for my own dataset. It says to compute the GA for each condition (my design is 2x2 so a total of 4 GA structures) with keepindividual set to 'yes'. However, when making the difference structures, it says the assignment to the difference structure should be made using the .avg field from 2 of the previous GA structures. But with the keepindividual set to 'yes', I am getting no .avg field in these GA structures to be used. Any advice as to how solve this issue? Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sun Jul 1 20:16:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sun, 1 Jul 2018 18:16:00 +0000 Subject: [FieldTrip] Concatenate different size of trials into single one trial In-Reply-To: References: Message-ID: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> Hi Yadwinder, Why would you want this? For this purpose, ft_appenddata is not your friend, if you want to ‘create a single data matrix’. It concatenate a bunch of matrices, you can use cat(2,data.trial{:}), but this will only be a meaningful operation in a very limited number of cases. Most of the time, the last time point of trial n-1 will not be temporally aligned with the first time point of trial n, and even if that were the case, trial specific filtering, baseline correction, or any trial-specific processing in general will lead to discontinuities in the signals. Best wishes, Jan-Mathijs On 30 Jun 2018, at 15:06, Yadwinder Kaur > wrote: Dear All I have pre-processed my EEG data cutting into different trials (35 trials total) using fieldtrip , now I wish to concatenate them into one single data matrix. The length of each trial varies form each other. ofcourse, ft_appenddata didn't work in this case. I would highly appreciate any help to solve this issue. Thanks in advance. Regards Yadwinder _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yadwinder.kaur at stud.uni-greifswald.de Sun Jul 1 23:00:55 2018 From: yadwinder.kaur at stud.uni-greifswald.de (Yadwinder Kaur) Date: Sun, 01 Jul 2018 23:00:55 +0200 Subject: [FieldTrip] Concatenate different size of trials into single one trial In-Reply-To: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> References: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> Message-ID: <3b876e61d0640121b93f7a60decaedd9@groupware.uni-greifswald.de> Hi Jan   Thanks for your reply.My idea was to extract trials (based on stimulus followed by response) , perform preprocessing and at the end concatenate them together, because my aim is to further divide the concatenated segment into four parts to perform latent variable analysis. Am I doing wrong in this way?  Thanks Regards Yadwinder On Sunday, 01-07-2018 at 20:16 Schoffelen, J.M. (Jan Mathijs) wrote: Hi Yadwinder, Why would you want this?  For this purpose, ft_appenddata is not your friend, if you want to ‘create a single data matrix’. It concatenate a bunch of matrices, you can use cat(2,data.trial{:}), but this will only be a meaningful operation in a very limited number of cases. Most of the time, the last time point of trial n-1 will not be temporally aligned with the first time point of trial n, and even if that were the case, trial specific filtering, baseline correction, or any trial-specific processing in general will lead to discontinuities in the signals. Best wishes, Jan-Mathijs On 30 Jun 2018, at 15:06, Yadwinder Kaur wrote: Dear All I have pre-processed my EEG data cutting into different trials (35 trials total) using fieldtrip , now I wish to concatenate them into one single data matrix. The length of each trial varies form each other. ofcourse, ft_appenddata didn't work in this case. I would highly appreciate any help to solve this issue. Thanks in advance. Regards Yadwinder _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alessandro.orticoni at gmail.com Mon Jul 2 00:21:53 2018 From: alessandro.orticoni at gmail.com (Alessandro Orticoni) Date: Mon, 2 Jul 2018 00:21:53 +0200 Subject: [FieldTrip] [Fieldtrip] Line noise Removal In-Reply-To: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> References: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Thanks a lot for your reply and your tips. Actually I've already segmented the data in 30 seconds epochs, and the reason why I did it is that these are sleep data: so I should keep this length because of the night scoring. I tried to enlarge the notch too, but it still doesn't work; the spectra before and after the filtering are exactly the same. Best, Alessandro Il giorno gio 28 giu 2018 alle ore 19:35 Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> ha scritto: > Dear Alessandro, > > Given the code you provided it looks as if you have one single very long > trial that you subject to dft-filtering. If the power line fluctuations > actually do vary a bit in amplitude, which is likely (particularly given > long sections of data), the pure 50 (or 60) Hz sinusoid will get some > ‘bandwidth’, so the removal won’t be perfect. I’d recommend to call > ft_redefinetrial first, and then do a second call to ft_preprocessing with > the dftfilter switched on. Yet, I’d expect that with 30 s segments it still > won’t work that well. In this case you could widen the notch a bit by > specifying cfg.dftfreq = 50+(-n:n)./30;, with n put to a small number, e.g. > <=3. However, unless you have good reasons to have the data chopped in > half-minute segments, I’d also consider to reduce this length, because you > probably do not need to have a 1/30 Hz frequency resolution in your > spectral decomposition. > > Best wishes, > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Associate PI, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 28 Jun 2018, at 16:22, Alessandro Orticoni < > alessandro.orticoni at gmail.com> wrote: > > Dear experts, > > I'm basically a beginner in coding with Fieldtrip, and I'm having a > problem with line noise filtering. > I would like to remove it from the heart rate signal, and I tried just > typing 'yes' at the option cfg.dftfilter. > But is doesn't seem to work, since the power spectrum contains the 50Hz > and her harmonics even after the filtering. > > You can find the code in the following lines: > > %% ===FREQUENCY Pre Filtering VERIFICATION=== > fs=data.fsample; > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'ECG 2'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.pad = 'nextpow2'; > cfg.foilim = [0.3 fs/2]; % teorema di Nyquist > freq_epoched_Cz = ft_freqanalysis(cfg, data_epoched_Cz); > > %% ===Plot Spectra=== > figure; > plot(freq_epoched_Cz.freq,mag2db(freq_epoched_Cz.powspctrm)); > > %% ===Filtering=== > cfg = []; > cfg.channel = {'ECG 2'}; > cfg.dftfilter = 'yes'; > ECG_Filtered = ft_preprocessing(cfg,data_Cz); > > cfg = []; > cfg.length = 30; % in seconds; > cfg.overlap = 0; > data_epoched_ECG_Filtered = ft_redefinetrial(cfg, ECG_Filtered); > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.pad = 'nextpow2'; > cfg.foilim = [0.3 fs/2]; % teorema di Nyquist > freq_epoched_Cz_Filtered = ft_freqanalysis(cfg, data_epoched_ECG_Filtered); > > %% ===Plot Spectra=== > > plot(freq_epoched_Cz_Filtered.freq,mag2db(freq_epoched_Cz_Filtered.powspctrm)); > > Thanks a lot. > > Kind regards, > Alessandro Orticoni > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Mon Jul 2 14:37:08 2018 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Mon, 2 Jul 2018 14:37:08 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel Message-ID: Dear Fieldtrippers, I have followed the Salzburg tutorial (http://www.fieldtriptoolbox. org/tutorial/salzburg) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. Best regards, Uri Ramirez University of Würzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From uwe.graichen at tu-ilmenau.de Mon Jul 2 14:46:06 2018 From: uwe.graichen at tu-ilmenau.de (Uwe Graichen) Date: Mon, 2 Jul 2018 14:46:06 +0200 Subject: [FieldTrip] =?utf-8?q?8th_International_Summer_School_=E2=80=9EMu?= =?utf-8?q?ltimodal_integration_of_brain_measurements_in_research_and_clin?= =?utf-8?q?ical_practice=E2=80=9C?= In-Reply-To: References: Message-ID: <0e7c5650-27bf-6225-9d8b-a651ec60c978@tu-ilmenau.de> Dear colleagues, we are pleased to announce the 8th International Summer School in Biomedical Engineering „Multimodal integration of brain measurements in research and clinical practice“, 1st – 12th October 2018 in Chengdu, China. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to EEG/MEG source reconstruction technologies in the frame work of multimodal integration of brain measurements in research and clinical practice. In particular, the 8th International Summer School on Biomedical Engineering will focus on methodological approaches and challenges, measurement devices and characteristics, types of underlying theoretic modeling, specifics of data analysis, ability to derive conclusions about neuroscientific meaning. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 8th International Summer School in Biomedical Engineering: www.bme-school.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Pedro Antonio Valdés-Sosa Dezhong Yao Jens Haueisen Thomas Knösche From tzvetan.popov at uni-konstanz.de Mon Jul 2 16:54:54 2018 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 2 Jul 2018 16:54:54 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: References: Message-ID: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Dear Uri, the solution to the problem (mesh inflation) is outlined in this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting?s[]=natmeg&s[]=headmodel#procedure Scroll down to the section "Construct the EEG volume conduction model" Good luck, tzvetan > Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos : > > Dear Fieldtrippers, > > I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.org/tutorial/salzburg ) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. > > What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? > > The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. > > Best regards, > > Uri Ramirez > University of Würzburg > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 2 17:47:48 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 2 Jul 2018 15:47:48 +0000 Subject: [FieldTrip] [Fieldtrip] Line noise Removal In-Reply-To: References: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> Message-ID: please have a look at the following piece of documentation: http://www.fieldtriptoolbox.org/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter?s[]=dftfilter Jan-Mathijs On 2 Jul 2018, at 00:21, Alessandro Orticoni > wrote: Dear Jan-Mathijs, Thanks a lot for your reply and your tips. Actually I've already segmented the data in 30 seconds epochs, and the reason why I did it is that these are sleep data: so I should keep this length because of the night scoring. I tried to enlarge the notch too, but it still doesn't work; the spectra before and after the filtering are exactly the same. Best, Alessandro Il giorno gio 28 giu 2018 alle ore 19:35 Schoffelen, J.M. (Jan Mathijs) > ha scritto: Dear Alessandro, Given the code you provided it looks as if you have one single very long trial that you subject to dft-filtering. If the power line fluctuations actually do vary a bit in amplitude, which is likely (particularly given long sections of data), the pure 50 (or 60) Hz sinusoid will get some ‘bandwidth’, so the removal won’t be perfect. I’d recommend to call ft_redefinetrial first, and then do a second call to ft_preprocessing with the dftfilter switched on. Yet, I’d expect that with 30 s segments it still won’t work that well. In this case you could widen the notch a bit by specifying cfg.dftfreq = 50+(-n:n)./30;, with n put to a small number, e.g. <=3. However, unless you have good reasons to have the data chopped in half-minute segments, I’d also consider to reduce this length, because you probably do not need to have a 1/30 Hz frequency resolution in your spectral decomposition. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Associate PI, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 28 Jun 2018, at 16:22, Alessandro Orticoni > wrote: Dear experts, I'm basically a beginner in coding with Fieldtrip, and I'm having a problem with line noise filtering. I would like to remove it from the heart rate signal, and I tried just typing 'yes' at the option cfg.dftfilter. But is doesn't seem to work, since the power spectrum contains the 50Hz and her harmonics even after the filtering. You can find the code in the following lines: %% ===FREQUENCY Pre Filtering VERIFICATION=== fs=data.fsample; cfg = []; cfg.output = 'pow'; cfg.channel = 'ECG 2'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.pad = 'nextpow2'; cfg.foilim = [0.3 fs/2]; % teorema di Nyquist freq_epoched_Cz = ft_freqanalysis(cfg, data_epoched_Cz); %% ===Plot Spectra=== figure; plot(freq_epoched_Cz.freq,mag2db(freq_epoched_Cz.powspctrm)); %% ===Filtering=== cfg = []; cfg.channel = {'ECG 2'}; cfg.dftfilter = 'yes'; ECG_Filtered = ft_preprocessing(cfg,data_Cz); cfg = []; cfg.length = 30; % in seconds; cfg.overlap = 0; data_epoched_ECG_Filtered = ft_redefinetrial(cfg, ECG_Filtered); cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.pad = 'nextpow2'; cfg.foilim = [0.3 fs/2]; % teorema di Nyquist freq_epoched_Cz_Filtered = ft_freqanalysis(cfg, data_epoched_ECG_Filtered); %% ===Plot Spectra=== plot(freq_epoched_Cz_Filtered.freq,mag2db(freq_epoched_Cz_Filtered.powspctrm)); Thanks a lot. Kind regards, Alessandro Orticoni _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maxime.ferez at gmail.com Tue Jul 3 09:57:19 2018 From: maxime.ferez at gmail.com (maxime ferez) Date: Tue, 3 Jul 2018 09:57:19 +0200 Subject: [FieldTrip] Problems with "filter_with_correction" Message-ID: Dear all, I have a question about Fieldtrip artifact-rejection. I find myself having a problem that I do not know how to solve. I am currently working on a pc a little old (~ 5 years) and my analyzes worked properly, or at least I had no bug. When I changed my pc the problem has arrived. I have an error message "Calculated filter coefficients have poles on or outside the unit circle and will not be stable. Try a higher cutoff frequency or a different type/order of filter" that appears in the "filter_with_correction" function .The problem seems to occur during the "roots" function of Matlab. I verified and the vector that is introduced is exactly the same in both cases, but after the function “roots” runs the result differs slightly and induces the error message above. Has anyone ever had this problem or know where the problem might come from? On both pcs I have exactly the same versions of Matlab (R2017a) and fieldtrip (fieldtrip-20171004 and fieldtrip-20180626). Scripts and data are also identical in all cases. I have tried several configurations but failed to find the solution: - Ubuntu 16.04 machine about 5 years -> OK - Ubuntu 16.04 machine about 2 years -> Not OK The two machines above are identical in all softwares (deployed with script in PXE) - Fedora 27 machine about 2 years -> Not OK - Ubuntu 16.04 about 2 years -> Not OK - Fedora 17 about 8 years old -> OK - Centos7 machine less than a year -> Not OK To conclude, the script only works on old hardware but this does not seem logical as an explanation. Best regards, Maxime Ferez -- Maxime Ferez, ingénieur d'étude Centre de Recherche en Neuroscience de Lyon (CRNL) Inserm équipe Dycog Bron, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Tue Jul 3 11:08:14 2018 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Tue, 3 Jul 2018 11:08:14 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> References: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Message-ID: Dear Tzvetan, That worked perfectly, thank you! Are there guidelines for use of mesh inflation? E.g., does dilation by two voxels greatly bias source reconstruction? If one inflates a subject's mesh, must one then inflate all other subjects' meshes to the same degree? Thank you again, Uri 2018-07-02 16:54 GMT+02:00 Tzvetan Popov : > Dear Uri, > > the solution to the problem (mesh inflation) is outlined in this tutorial: > http://www.fieldtriptoolbox.org/tutorial/natmeg/ > dipolefitting?s[]=natmeg&s[]=headmodel#procedure > > Scroll down to the section "Construct the EEG volume conduction model" > > Good luck, > tzvetan > > > Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos < > urieduardo at gmail.com>: > > Dear Fieldtrippers, > > I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.o > rg/tutorial/salzburg) to conduct EEG source reconstruction, but it > doesn't work with some subjects' segmented mri files (whether I use dipoli > or bemcp), due to intersections between surfaces. > > What are the typical trouble-shooting steps for this situation? I tried > using a lower number of vertices for the mesh ([800 800 600]), to no avail. > Are there any guidelines for the number of vertices? > > The number of subjects in my study is limited, so I would be loathe to > exclude any subject from the analysis. > > Best regards, > > Uri Ramirez > University of Würzburg > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.manahova at gmail.com Tue Jul 3 11:26:10 2018 From: m.manahova at gmail.com (Mariya Manahova) Date: Tue, 3 Jul 2018 11:26:10 +0200 Subject: [FieldTrip] .avg field in GA structure for interaction test In-Reply-To: References: Message-ID: Hi Paul, With keepindividual = 'yes', your parameter of interest is 'individual'. So try using cfg.parameter = 'individual' (instead of cfg.parameter = 'avg' which is probably the default) and that should work. All the best, Marisha On Sun, Jul 1, 2018 at 8:11 PM Paul Dhami wrote: > Hi Fieldtrip, > > I am following the tutorial 'How to test an interaction effect using > cluster-based permutation tests?' for my own dataset. It says to compute > the GA for each condition (my design is 2x2 so a total of 4 GA structures) > with keepindividual set to 'yes'. However, when making the difference > structures, it says the assignment to the difference structure should be > made using the .avg field from 2 of the previous GA structures. But with > the keepindividual set to 'yes', I am getting no .avg field in these GA > structures to be used. Any advice as to how solve this issue? > > Best, > Paul > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Tue Jul 3 11:36:54 2018 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Tue, 3 Jul 2018 11:36:54 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: References: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Message-ID: Dear Uri, > That worked perfectly, thank you! Are there guidelines for use of mesh inflation? no there aren’t any. > E.g., does dilation by two voxels greatly bias source reconstruction? no > If one inflates a subject's mesh, must one then inflate all other subjects' meshes to the same degree? I would do as minimum as possible and only there when needed. Best tzvetan > > Thank you again, > Uri > > 2018-07-02 16:54 GMT+02:00 Tzvetan Popov >: > Dear Uri, > > the solution to the problem (mesh inflation) is outlined in this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting?s[]=natmeg&s[]=headmodel#procedure > > Scroll down to the section "Construct the EEG volume conduction model" > > Good luck, > tzvetan > > >> Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos >: >> >> Dear Fieldtrippers, >> >> I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.org/tutorial/salzburg ) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. >> >> What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? >> >> The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. >> >> Best regards, >> >> Uri Ramirez >> University of Würzburg >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Wed Jul 4 02:54:37 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 3 Jul 2018 20:54:37 -0400 Subject: [FieldTrip] Submitting a correlation matrix for cluster-based permutation Message-ID: Hi FieldTripers, I was hoping to do a correlation between two sets of EEG datasets in a channel x time fashion. For each (channel,time), I ran a rho correlation between the two EEG datas, and stored the resulting coefficients in a matrix with the dimensions of channel and time. I was hoping to apply a cluster-based permutation testing to correct for multiple comparisons, but as the file I was hoping to submit is a raw matrix, I was hoping for some guidance as to 1) whether this is even an appropriate way of achieving a cluster-corrected correlation matrix and 2) how to implement this with the correlation matrix. Any help would be greatly appreciated. Thank you. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Jul 4 08:58:47 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 4 Jul 2018 06:58:47 +0000 Subject: [FieldTrip] Submitting a correlation matrix for cluster-based permutation In-Reply-To: References: Message-ID: <54A52603-0F1E-48F0-9141-C8C27A1656FC@donders.ru.nl> Do you have a null hypothesis? What is it you would want to permute? If you just have scalar value per channel/time point, there’s not much you can do. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 4 Jul 2018, at 02:54, Paul Dhami > wrote: Hi FieldTripers, I was hoping to do a correlation between two sets of EEG datasets in a channel x time fashion. For each (channel,time), I ran a rho correlation between the two EEG datas, and stored the resulting coefficients in a matrix with the dimensions of channel and time. I was hoping to apply a cluster-based permutation testing to correct for multiple comparisons, but as the file I was hoping to submit is a raw matrix, I was hoping for some guidance as to 1) whether this is even an appropriate way of achieving a cluster-corrected correlation matrix and 2) how to implement this with the correlation matrix. Any help would be greatly appreciated. Thank you. Paul _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From ablenkmann at gmail.com Fri Jul 6 21:38:15 2018 From: ablenkmann at gmail.com (Alejandro Blenkmann) Date: Fri, 6 Jul 2018 12:38:15 -0700 Subject: [FieldTrip] Neuroscience Lab Engineer Permanent position - University of Oslo, Norway Message-ID: Hi FieldTripers, There is a Lab Engineer Permanent position available in Oslo. https://www.jobbnorge.no/ledige-stillinger/stilling/154793 < https://www.jobbnorge.no/ledige-stillinger/stilling/154793> Best, Alejandro -- Alejandro Blenkmann, PhD Postdoctoral Fellow Front Neurolab Department of Psychology University of Oslo -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Jul 6 21:43:04 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 6 Jul 2018 21:43:04 +0200 Subject: [FieldTrip] Problems with "filter_with_correction" In-Reply-To: References: Message-ID: Hi Maxime, I wouldn't know why this would occur if everything else is the same, except that perhaps your current MATLAB in combination with your OS uses slightly different implementations of filter functions from e.g. another toolbox/other MATLAB versions. In any case, as the function suggests, these problems typically occur for me when the low-pass frequency that is requested is too low for what the data and filter allows. The artefact detection functions probably uses a low/bandpass filter so try increasing the low cutoff, changing the filter order, or the filter type. You might also try using longer trial-lengths. cheers, Stephen On 3 July 2018 at 09:57, maxime ferez wrote: > Dear all, > > I have a question about Fieldtrip artifact-rejection. I find myself having > a problem that I do not know how to solve. I am currently working on a pc a > little old (~ 5 years) and my analyzes worked properly, or at least I had > no bug. When I changed my pc the problem has arrived. I have an error > message "Calculated filter coefficients have poles on or outside the unit > circle and will not be stable. Try a higher cutoff frequency or a different > type/order of filter" that appears in the "filter_with_correction" function > .The problem seems to occur during the "roots" function of Matlab. I > verified and the vector that is introduced is exactly the same in both > cases, but after the function “roots” runs the result differs slightly > and induces the error message above. Has anyone ever had this problem or > know where the problem might come from? On both pcs I have exactly the same > versions of Matlab (R2017a) and fieldtrip (fieldtrip-20171004 and > fieldtrip-20180626). Scripts and data are also identical in all cases. I > have tried several configurations but failed to find the solution: > > - Ubuntu 16.04 machine about 5 years -> OK > > - Ubuntu 16.04 machine about 2 years -> Not OK > > The two machines above are identical in all softwares (deployed with > script in PXE) > > - Fedora 27 machine about 2 years -> Not OK > > - Ubuntu 16.04 about 2 years -> Not OK > > - Fedora 17 about 8 years old -> OK > > - Centos7 machine less than a year -> Not OK > > To conclude, the script only works on old hardware but this does not seem > logical as an explanation. > > Best regards, > > > > Maxime Ferez > > > -- > Maxime Ferez, ingénieur d'étude > Centre de Recherche en Neuroscience de Lyon (CRNL) > Inserm > équipe Dycog > Bron, France > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lindseyrtate at ou.edu Mon Jul 9 06:59:13 2018 From: lindseyrtate at ou.edu (Tate, Lindsey R.) Date: Mon, 9 Jul 2018 04:59:13 +0000 Subject: [FieldTrip] Adding MRI Overlay to ft_sourceplot Images Message-ID: Hello fieldtrip community, I have a project with a lot of source analysis of EEG data. I'm using ft_sourceanalysis and ft_sourceplot. I would like to add standard (e.g., Colin 27) MRI slices to these images as an overlay (underlay?) for reference. Is there a way to do this? How do I align the MRI with my source space? Example code for ft_sourceanalysis and ft_sourceplot are provided below my signature in case you need the reference. Thank you, Lindsey Tate PhD Candidate University of Oklahoma lindseyrtate at ou.edu /// %baseline period source analysis cfg = []; cfg.elec = elec ; cfg.method = 'dics'; cfg.frequency = 25 ; cfg.grid = grid; cfg.headmodel = headmodel; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = 0; cfg.latency = -0.7490 ; [presource25] = ft_sourceanalysis(cfg, prefreq25) %from ft_freqanalysis %same is done for a post-stimulus period, called pmsource25; code omitted for brevity %difference between pre- and post-stimulus periods source25diff = pmsource25 ; source25diff.avg.pow = (pmsource25.avg.pow - presource25.avg.pow) ./ presource25.avg.pow; %interpolate the difference between pre- and post-stimulus periods cfg = []; cfg.downsample = 2; cfg.parameter = 'avg.pow'; source25DiffInt = ft_sourceinterpolate(cfg, source25diff, grid); %plot cfg = []; cfg.method = 'slice'; cfg.funparameter = 'avg.pow'; cfg.maskparameter = cfg.funparameter; cfg.funcolorlim = [-1 2]; cfg.opacitylim = [-5 1]; cfg.opacitymap = 'rampup'; ft_sourceplot(cfg, source25DiffInt); -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon Jul 9 08:01:33 2018 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 9 Jul 2018 08:01:33 +0200 Subject: [FieldTrip] Adding MRI Overlay to ft_sourceplot Images In-Reply-To: References: Message-ID: Hi Lindsey, What is "grid" bases on? Is this the individual mri or a standard mri? In any case, you can use ft_sourceinterpolate to interpolate to a standard MRI. Then, you can set the anatomy parameter in ft_spurceplot. Check the details of both functions for the relevant cfg settings. Hope this helps, Cheers, Julian Tate, Lindsey R. schrieb am Mo. 9. Juli 2018 um 07:35: > Hello fieldtrip community, > > > I have a project with a lot of source analysis of EEG data. I'm using > ft_sourceanalysis and ft_sourceplot. I would like to add standard (e.g., > Colin 27) MRI slices to these images as an overlay (underlay?) for > reference. Is there a way to do this? How do I align the MRI with my source > space? > > > Example code for ft_sourceanalysis and ft_sourceplot are provided below my > signature in case you need the reference. > > > Thank you, > > > Lindsey Tate > PhD Candidate > University of Oklahoma > lindseyrtate at ou.edu > > > /// > > %baseline period source analysis > > cfg = []; > cfg.elec = elec ; > cfg.method = 'dics'; > cfg.frequency = 25 ; > cfg.grid = grid; > cfg.headmodel = headmodel; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = 0; > cfg.latency = -0.7490 ; > [presource25] = ft_sourceanalysis(cfg, prefreq25) %from ft_freqanalysis > > %same is done for a post-stimulus period, called pmsource25; code omitted > for brevity > > %difference between pre- and post-stimulus periods > source25diff = pmsource25 ; > source25diff.avg.pow = (pmsource25.avg.pow - presource25.avg.pow) ./ > presource25.avg.pow; > > %interpolate the difference between pre- and post-stimulus periods > cfg = []; > cfg.downsample = 2; > cfg.parameter = 'avg.pow'; > source25DiffInt = ft_sourceinterpolate(cfg, source25diff, grid); > > %plot > cfg = []; > cfg.method = 'slice'; > cfg.funparameter = 'avg.pow'; > cfg.maskparameter = cfg.funparameter; > cfg.funcolorlim = [-1 2]; > cfg.opacitylim = [-5 1]; > cfg.opacitymap = 'rampup'; > ft_sourceplot(cfg, source25DiffInt); > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.maye at uke.de Mon Jul 9 10:15:33 2018 From: a.maye at uke.de (Alexander Maye) Date: Mon, 9 Jul 2018 10:15:33 +0200 Subject: [FieldTrip] Call for Participation: summer school on 'mind reading technology' Message-ID: <7471317.dIuGlEM9So@mars> Dear colleagues, Below I forward an announcement for the above-mentioned summer school which readers of this list may find interesting. Best regards, Alexnder Maye. ---------- Weitergeleitete Nachricht ---------- Betreff: [CML] Call for Participation: summer school on 'mind reading technology' Datum: Donnerstag, 5. Juli 2018, 09:44:08 CEST Von: Dan Zhang An: cml at informatik.uni-hamburg.de Kopie: 洪波 Dear colleagues, Dr. Bo Hong and I are organizing a summer school during August 13-17 in Beijing. The topic of this summer school is ‘mind reading technology’ and we have invited the leading scientists in this field to give lectures. Please help us spread out the message and please contact us if you are interested. Many thanks in advance! Best, Dan -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- A non-text attachment was scrubbed... Name: Program of 2018 ISSNE.pdf Type: application/pdf Size: 115677 bytes Desc: Program of 2018 ISSNE.pdf URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ISSNE2018 Flyer.pdf Type: application/pdf Size: 474936 bytes Desc: ISSNE2018 Flyer.pdf URL: From krugliakova.es at gmail.com Tue Jul 10 21:36:19 2018 From: krugliakova.es at gmail.com (Elena Krugliakova) Date: Tue, 10 Jul 2018 21:36:19 +0200 Subject: [FieldTrip] phase-amplitude coupling measure Message-ID: Dear FieldTrip community, I have a question related to the ft_crossfrequencyanalysis: which phase - amplitude coupling measure for EEG is the least affected by the signal-to-noise ratio? If I have two conditions and in one of them the power of high frequency is much stronger (better signal-to-noise ratio), what would be the best measure to compare the coupling between the phase of slow frequency and the amplitude of high frequency? Thank you! Kind Regards, Elena Krugliakova -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Fri Jul 13 18:20:21 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Fri, 13 Jul 2018 18:20:21 +0200 Subject: [FieldTrip] git repo quite big. How to save space? Message-ID: Dear all, I have several copies of FieldTrip for several projects shared with others. Each has its own copy of FieldTrip, which is at the moment a 1.7GB folder, of which 1GB is taken by the .git directory. Would there be an easy way to prune the repository where needed? Best, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From christophe.grova at mcgill.ca Sun Jul 15 14:42:58 2018 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Sun, 15 Jul 2018 12:42:58 +0000 Subject: [FieldTrip] Postdoctoral Fellowship in Multimodal Neuroimaging of Sleep and Cognition at Concordia PERFORM centre In-Reply-To: References: , Message-ID: Dear colleagues, We are presently recruiting a Postdoctoral fellow in Multimodal Neuroimaging of Sleep and Cognition. This position consists in a prestigious Horizon Postdoctoral Fellowship at Concordia University, in Montréal (Québec, Canada). The fellow will have the opportunity to setup and conduct advanced neuroimaging studies in clinical and healthy samples, as well as to analyze and write up findings of previously collected human neuroimaging data. He/she will also have the opportunity to develop and evaluate new multimodal data analysis approaches, as for instance the study of sleep patterns combining high-density Electro-EncephaloGraphy (EEG) with functional Magnetic Resonance Imaging and for the very first time EEG with Near-Infra Red Spectroscopy (NIRS) during whole night recordings. These techniques will allow addressing links between bioelectrical neuronal activity and hemodynamic processes during sleep. He/she will be based at Concordia University (Montreal, Quebec), jointly supervised by Dr. Christophe Grova PhD and Dr. Thanh Dang-Vu MD-PhD, and will work in a highly multidisciplinary environment (neurosciences, kinesiology, physics, engineering, psychology) and in collaboration with multiple academic and hospital institutions in Montreal (PERFORM Center, Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal [CRIUGM], Montreal Neurological Institute [MNI]). The research themes that will be addressed by the Fellow will include: * The neural mechanisms of sleep, sleep deprivation and sleep disorders (chronic insomnia, central disorders of hypersomnolence), and their relationship with cognition. * Developing and evaluating methods dedicated to the analysis of multimodal neuroimaging data for sleep studies: (i) simultaneous EEG/fMRI, and (2) simultaneous EEG/NIRS, including the analysis of functional connectivity and brain network analysis The PERFORM Centre is a 8,000 m2 research facility including eight inter-related research platforms, such as a state of the art sleep laboratory (3 bedrooms with polysomnography and high-density EEG) and a fully equipped imaging suite (3T MRI, high-density EEG, NIRS, TMS, SPECT-CT, PET-CT, Ultrasound and Dexa) entirely dedicated to research (http://www.concordia.ca/research/perform.html ). Applicants must have a PhD (or close to completion) in a related field (e.g., neurosciences, computer science, (bio)medical engineering, physics). Experience in the analysis of hemodynamic signals from fMRI or NIRS is important. Applicants should have strong knowledge of Matlab and/or experience in analysis of neuroimaging, excellent organizational skills, an aptitude for teamwork, good writing skills and a productive publication record. Experience in one or more aspects of the research themes will constitute an asset. Salary will consist of 47,500 $/year (plus benefits) for 2 years. The position has a flexible start date. Interested applicants should submit their application as described in the following link, before September 1st 2018: http://www.concordia.ca/sgs/postdoctoral-fellows/funding/horizon/descriptions/5007.html Review of applications will begin as they are received and will continue until the position has been filled. All requests for additional information should also be directed to them. Only those candidates selected to interview will be contacted. Dr. Christophe Grova, Ph.D, Dr. Thanh Dang-Vu, M.D., Ph.D. Associate Professor Associate Professor, Neurologist, Department of Physics, Concordia U. Adjunct Professor in Biomedical Engineering, Concordia University Research Chair in Sleep, Neuroimaging and Cognitive Health, Neurology & Neurosurgery, McGill U. christophe.grova at concordia.ca Department of Health, Kinesiology and Applied Physiology, Concordia U. Assoc. Director for Clinical Research, CRIUGM tt.dangvu at concordia.ca For more information about our current research programs, please visit the lab websites: https://www.concordia.ca/artsci/physics/research/grova-research-group.html https://scnlab.com *************************** Christophe Grova, PhD Associate Professor, Physics Dpt, Concordia University PERFORM centre, Concordia University, Chair of PERFORM Applied Bio-Imaging Committee (ABC) Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute - epilepsy group Centre de Recherches en Mathématiques Physics Dpt Concordia University - Loyola Campus - Office SP 365.12 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Phone: (514) 848-2424 ext.4221 Biomedical Engineering Department McGill University - Room 304 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 Phone : (514) 398 2516 Fax : (514) 398 7461 email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca web: Explore Concordia: http://explore.concordia.ca/christophe-grova Physics, Concordia University: http://www.concordia.ca/artsci/physics/faculty.html?fpid=christophe-grova McGill University: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** [X] -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauppe.s at gmail.com Mon Jul 16 00:09:30 2018 From: sauppe.s at gmail.com (Sebastian Sauppe) Date: Mon, 16 Jul 2018 00:09:30 +0200 Subject: [FieldTrip] Error using ft_clusterplot: unsupported dimord unknown_freq_time Message-ID: Dear FieldTrip list users, I am trying to analyze a between-subjects experiment with cluster-based permutation tests. In setting up the tests, I followed the tutorial on the FieldTrip site (http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq#between-trial_experiments ). However, when I try to plot the results, I get the error „Error using ft_clusterplot (line 161) unsupported dimord unknown_freq_time“. I am very new to FieldTrip and its probably a rookie mistake that I am making but I’d be very grateful if someone who knows could point out what I might be doing wrong here. Here is the code: %% run cluster-based permutation test % set up cfg for ft_freqstatistics cfg = []; cfg.channel = 'all'; cfg.latency = 'all'; cfg.frequency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 20; % to make it quick % prepare_neighbours determines what electrodes may form clusters cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, freq_IPFV); cfg.spmversion = 'spm12'; design = zeros(1,size(freq_IPFV.powspctrm,1) + size(freq_PFV.powspctrm,1)); design(1,1:size(freq_IPFV.powspctrm,1)) = 1; design(1,(size(freq_IPFV.powspctrm,1)+1):(size(freq_IPFV.powspctrm,1)+... size(freq_PFV.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, freq_IPFV, freq_PFV); %% plot the results cfg = []; cfg.keeptrials = 'no'; freqdesc_IPFV = ft_freqdescriptives(cfg, freq_IPFV); freqdesc_PFV = ft_freqdescriptives(cfg, freq_PFV); stat.raweffect = freqdesc_IPFV.powspctrm - freqdesc_PFV.powspctrm; cfg = []; cfg.alpha = 0.025; cfg.parameter = 'raweffect'; cfg.zlim = [-1e-27 1e-27]; cfg.layout = 'GSN-HydroCel-129.sfp'; layout = ft_prepare_layout(cfg); cfg.layout = layout; ft_clusterplot(cfg, stat); Kind regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Phillip.Alday at mpi.nl Mon Jul 16 08:59:22 2018 From: Phillip.Alday at mpi.nl (Alday, Phillip) Date: Mon, 16 Jul 2018 06:59:22 +0000 Subject: [FieldTrip] git repo quite big. How to save space? In-Reply-To: References: Message-ID: <6002072a-9c62-bd54-34b0-fffc464db833@mpi.nl> There are a few things you can do: 1. Garbage collection and re-packing to get git to re-organize itself into a more compact layout : git gc --aggressive If that takes too long, do it without --aggressive : it will be much faster although potentially not as effective. 2. Use shallow clones (i.e. ones missing older history). 3. Clone from one local copy to another -- if the clones are on the same file system, then git will use hard links and git objects common to both repositories will be "shared" and only take up space equal to one instance. Note that garbage collection, re-packing, etc. can break this and lead to each clone having its own copies. 4. Don't keep a copy of FieldTrip in each project and start using paths, version management, etc. more effectively. You definitely should know which version of the software you used for a given analysis for reproducibility/replicability, but there are more efficient ways to do that than keeping a local copy. This is not meant to be harsh, but just trying to address a potential "XY problem" (https://meta.stackexchange.com/questions/66377/what-is-the-xy-problem). Best, Phillip Date: Fri, 13 Jul 2018 18:20:21 +0200 > From: Maximilien Chaumon > To: FieldTrip discussion list > Subject: [FieldTrip] git repo quite big. How to save space? > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I have several copies of FieldTrip for several projects shared with others. > Each has its own copy of FieldTrip, which is at the moment a 1.7GB folder, > of which 1GB is taken by the .git directory. Would there be an easy way to > prune the repository where needed? > > Best, > Max > From Amie.Fairs at mpi.nl Tue Jul 17 09:57:48 2018 From: Amie.Fairs at mpi.nl (Fairs, Amie) Date: Tue, 17 Jul 2018 07:57:48 +0000 Subject: [FieldTrip] Missing templates for planar gradients Message-ID: Dear FieldTrip list, Apologies for what seems like a silly question. I am calculating the planar gradient for my MEG data because it was recorded from axial gradiometers (on a CTF system with a 275 layout). I'm following the FieldTrip tutorial to calculate the planar gradient, and I would like to use the method 'template' to do so, and then specify a pre-existing template. From reading about which templates are shipped with FieldTrip (http://www.fieldtriptoolbox.org/template/neighbours) I think a bunch of templates should be found in FieldTrip, including the CTF 275 neighbourhood template. However, in my FieldTrip version there are no templates (the template folder is just empty). When I run ft_prepare_neighbours, specifying cfg.template = 'template' and cfg.template = 'CTF275_neighb.mat', I get an error message saying 'Template file could not be found'. Does anyone know where I can get hold of this template? I can't find a way to download other than downloading a new version of FieldTrip and seeing if it is there. The FieldTrip version I am using is fieldtrip-20170918 (so much after the 2011 template intro), on a Windows 7 computer, and matlab R2016a. I also calculated the planar gradient using the method 'triangulation' to check it isn't a data bug somehow, but that works perfectly fine (though I'd prefer the template option). Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Arana at donders.ru.nl Tue Jul 17 10:26:07 2018 From: S.Arana at donders.ru.nl (Arana, S.L. (Sophie)) Date: Tue, 17 Jul 2018 08:26:07 +0000 Subject: [FieldTrip] Missing templates for planar gradients In-Reply-To: References: Message-ID: Hi Amie, have you tried downloading the template file directly from the GitHub repo? https://github.com/fieldtrip/fieldtrip/tree/master/template/neighbours Best, Sophie ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Fairs, Amie [Amie.Fairs at mpi.nl] Sent: Tuesday, July 17, 2018 9:57 AM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Missing templates for planar gradients Dear FieldTrip list, Apologies for what seems like a silly question. I am calculating the planar gradient for my MEG data because it was recorded from axial gradiometers (on a CTF system with a 275 layout). I'm following the FieldTrip tutorial to calculate the planar gradient, and I would like to use the method 'template' to do so, and then specify a pre-existing template. From reading about which templates are shipped with FieldTrip (http://www.fieldtriptoolbox.org/template/neighbours) I think a bunch of templates should be found in FieldTrip, including the CTF 275 neighbourhood template. However, in my FieldTrip version there are no templates (the template folder is just empty). When I run ft_prepare_neighbours, specifying cfg.template = 'template' and cfg.template = 'CTF275_neighb.mat', I get an error message saying 'Template file could not be found'. Does anyone know where I can get hold of this template? I can't find a way to download other than downloading a new version of FieldTrip and seeing if it is there. The FieldTrip version I am using is fieldtrip-20170918 (so much after the 2011 template intro), on a Windows 7 computer, and matlab R2016a. I also calculated the planar gradient using the method 'triangulation' to check it isn't a data bug somehow, but that works perfectly fine (though I'd prefer the template option). Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauppe.s at gmail.com Thu Jul 19 09:01:59 2018 From: sauppe.s at gmail.com (Sebastian Sauppe) Date: Thu, 19 Jul 2018 09:01:59 +0200 Subject: [FieldTrip] Averaging over frequencies in ft_freqstatistics Message-ID: Dear FieldTrip list, I am testing different frequency bands with cluster-based permutation tests using ft_freqstatistics. For this, I use cfg.avgoverfreq = ‚yes‘ when setting up the test. However, I am unsure about how FieldTrip actually handles the frequency averaging. Does it take the mean power of the specified frequencies or does it take the power of the mean frequency? This is the relevant code I use: ... cfg.frequency = [3 8]; cfg.avgoverfreq = 'yes‘; ... [stat] = ft_freqstatistics(cfg, data_A, data_B); In my data, I have the following frequencies: [3.9062 4.8828 6.1035 7.0801 8.0566 9.0332 10.0098]. In the statistics output, after averaging over frequencies stat.freq returns only 6.0059. This is the mean of the frequencies between 3 and 8. But I can’t see whether somehow the power of that frequency was assessed in the test or whether the power of all frequencies in that band was first averaged and then tested. Regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From 007abhisheksamal at gmail.com Fri Jul 20 14:52:14 2018 From: 007abhisheksamal at gmail.com (Abhishek Samal) Date: Fri, 20 Jul 2018 18:22:14 +0530 Subject: [FieldTrip] Error in using EMG channel as trial definition Message-ID: Sir, This is Abhishek. I am trying to analyse Motor Evoked field MEG data. I have been trying to use the EMG channel as the trial definition for the triggers of epoch creation. But when I use the script that is given in tutorial definition I am getting the following error. The Input cfg = []; cfg.dataset = 'preetham_lt_motor_raw_tsss_mc.fif'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 0.5; cfg.trialfun = 'trialfun_emgdetect'; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); The Error 306 MEG channel locations transformed Reading preetham_lt_motor_raw_tsss_mc.fif ... Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... Range : 124000 ... 669999 = 62.000 ... 335.000 secs Ready. Reading 124000 ... 669999 = 62.000 ... 335.000 secs... [done] found 0 events created 210265 trials the call to "ft_definetrial" took 528 seconds 306 MEG channel locations transformed Reading preetham_lt_motor_raw_tsss_mc.fif ... Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... Range : 124000 ... 669999 = 62.000 ... 335.000 secs Ready. processing channel { 'EOG001' 'ECG002' 'EEG001' 'EEG002' 'EEG003' 'EEG004' 'EEG005' 'EEG006' 'EEG007' 'EEG008' 'EEG009' 'EEG010' 'EEG011' 'EEG012' 'EEG013' 'EEG014' 'EEG015' 'EEG016' 'EEG017' 'EEG018' 'EEG019' 'EEG020' 'EEG021' 'EEG022' 'EEG023' 'EEG024' 'EEG025' 'EXCI' 'IASX+' 'IASX-' 'IASY+' 'IASY-' 'IASZ+' 'IASZ-' 'IAS_DX' 'IAS_DY' 'IAS_X' 'IAS_Y' 'IAS_Z' 'MEG0111' 'MEG0112' 'MEG0113' 'MEG0121' 'MEG0122' 'MEG0123' 'MEG0131' 'MEG0132' 'MEG0133' 'MEG0141' 'MEG0142' 'MEG0143' 'MEG0211' 'MEG0212' 'MEG0213' 'MEG0221' 'MEG0222' 'MEG0223' 'MEG0231' 'MEG0232' 'MEG0233' 'MEG0241' 'MEG0242' 'MEG0243' 'MEG0311' 'MEG0312' 'MEG0313' 'MEG0321' 'MEG0322' 'MEG0323' 'MEG0331' 'MEG0332' 'MEG0333' 'MEG0341' 'MEG0342' 'MEG0343' 'MEG0411' 'MEG0412' 'MEG0413' 'MEG0421' 'MEG0422' 'MEG0423' 'MEG0431' 'MEG0432' 'MEG0433' 'MEG0441' 'MEG0442' 'MEG0443' 'MEG0511' 'MEG0512' 'MEG0513' 'MEG0521' 'MEG0522' 'MEG0523' 'MEG0531' 'MEG0532' 'MEG0533' 'MEG0541' 'MEG0542' 'MEG0543' 'MEG0611' 'MEG0612' 'MEG0613' 'MEG0621' 'MEG0622' 'MEG0623' 'MEG0631' 'MEG0632' 'MEG0633' 'MEG0641' 'MEG0642' 'MEG0643' 'MEG0711' 'MEG0712' 'MEG0713' 'MEG0721' 'MEG0722' 'MEG0723' 'MEG0731' 'MEG0732' 'MEG0733' 'MEG0741' 'MEG0742' 'MEG0743' 'MEG0811' 'MEG0812' 'MEG0813' 'MEG0821' 'MEG0822' 'MEG0823' 'MEG0911' 'MEG0912' 'MEG0913' 'MEG0921' 'MEG0922' 'MEG0923' 'MEG0931' 'MEG0932' 'MEG0933' 'MEG0941' 'MEG0942' 'MEG0943' 'MEG1011' 'MEG1012' 'MEG1013' 'MEG1021' 'MEG1022' 'MEG1023' 'MEG1031' 'MEG1032' 'MEG1033' 'MEG1041' 'MEG1042' 'MEG1043' 'MEG1111' 'MEG1112' 'MEG1113' 'MEG1121' 'MEG1122' 'MEG1123' 'MEG1131' 'MEG1132' 'MEG1133' 'MEG1141' 'MEG1142' 'MEG1143' 'MEG1211' 'MEG1212' 'MEG1213' 'MEG1221' 'MEG1222' 'MEG1223' 'MEG1231' 'MEG1232' 'MEG1233' 'MEG1241' 'MEG1242' 'MEG1243' 'MEG1311' 'MEG1312' 'MEG1313' 'MEG1321' 'MEG1322' 'MEG1323' 'MEG1331' 'MEG1332' 'MEG1333' 'MEG1341' 'MEG1342' 'MEG1343' 'MEG1411' 'MEG1412' 'MEG1413' 'MEG1421' 'MEG1422' 'MEG1423' 'MEG1431' 'MEG1432' 'MEG1433' 'MEG1441' 'MEG1442' 'MEG1443' 'MEG1511' 'MEG1512' 'MEG1513' 'MEG1521' 'MEG1522' 'MEG1523' 'MEG1531' 'MEG1532' 'MEG1533' 'MEG1541' 'MEG1542' 'MEG1543' 'MEG1611' 'MEG1612' 'MEG1613' 'MEG1621' 'MEG1622' 'MEG1623' 'MEG1631' 'MEG1632' 'MEG1633' 'MEG1641' 'MEG1642' 'MEG1643' 'MEG1711' 'MEG1712' 'MEG1713' 'MEG1721' 'MEG1722' 'MEG1723' 'MEG1731' 'MEG1732' 'MEG1733' 'MEG1741' 'MEG1742' 'MEG1743' 'MEG1811' 'MEG1812' 'MEG1813' 'MEG1821' 'MEG1822' 'MEG1823' 'MEG1831' 'MEG1832' 'MEG1833' 'MEG1841' 'MEG1842' 'MEG1843' 'MEG1911' 'MEG1912' 'MEG1913' 'MEG1921' 'MEG1922' 'MEG1923' 'MEG1931' 'MEG1932' 'MEG1933' 'MEG1941' 'MEG1942' 'MEG1943' 'MEG2011' 'MEG2012' 'MEG2013' 'MEG2021' 'MEG2022' 'MEG2023' 'MEG2031' 'MEG2032' 'MEG2033' 'MEG2041' 'MEG2042' 'MEG2043' 'MEG2111' 'MEG2112' 'MEG2113' 'MEG2121' 'MEG2122' 'MEG2123' 'MEG2131' 'MEG2132' 'MEG2133' 'MEG2141' 'MEG2142' 'MEG2143' 'MEG2211' 'MEG2212' 'MEG2213' 'MEG2221' 'MEG2222' 'MEG2223' 'MEG2231' 'MEG2232' 'MEG2233' 'MEG2241' 'MEG2242' 'MEG2243' 'MEG2311' 'MEG2312' 'MEG2313' 'MEG2321' 'MEG2322' 'MEG2323' 'MEG2331' 'MEG2332' 'MEG2333' 'MEG2341' 'MEG2342' 'MEG2343' 'MEG2411' 'MEG2412' 'MEG2413' 'MEG2421' 'MEG2422' 'MEG2423' 'MEG2431' 'MEG2432' 'MEG2433' 'MEG2441' 'MEG2442' 'MEG2443' 'MEG2511' 'MEG2512' 'MEG2513' 'MEG2521' 'MEG2522' 'MEG2523' 'MEG2531' 'MEG2532' 'MEG2533' 'MEG2541' 'MEG2542' 'MEG2543' 'MEG2611' 'MEG2612' 'MEG2613' 'MEG2621' 'MEG2622' 'MEG2623' 'MEG2631' 'MEG2632' 'MEG2633' 'MEG2641' 'MEG2642' 'MEG2643' 'STI101' 'SYS201' 'CHPI001' 'CHPI002' 'CHPI003' 'CHPI004' 'CHPI005' 'CHPI006' 'CHPI007' 'CHPI008' 'CHPI009' } reading and preprocessing reading and preprocessing trial 1 from 210265 Reading 264027 ... 4792reading and preprocessing trial 2 from 210265 Reading 327742 ... 4802reading and preprocessing trial 3 from 210265 . . . . . Reading 635443 ... 66reading and preprocessing trial 116 from 210265 Error using ft_read_data (line 225) cannot read data after the end of the file Error in ft_preprocessing (line 582) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); I am new to fieldtrip. Please help me with the above error. Regards, Abhishek. -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri Jul 20 15:00:04 2018 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 20 Jul 2018 15:00:04 +0200 Subject: [FieldTrip] Error in using EMG channel as trial definition In-Reply-To: References: Message-ID: <6B3105DE-53A4-4490-97A0-C7CC497B2B14@gmail.com> Dear Abhishek, this error occurs if less time than specified in cfg.trialdef.poststim is left after the last event code. In other words, you are trying to cut out more trials with a fixed latency than you have data. Please note that it appears as if your trial definition based on the EMG channel fails (see the „found 0 events“ notice and the rather large number of trials). I suggest going back to your trial function and checking whether everything works as intended there. Good luck, Julian ________________ Prof. Dr. Julian Keil Biological Psychology Olshausenstrasse 62 - R. 306 24118 Kiel, Germany +49 - 0431 - 880 - 4872 http://www.biopsych.uni-kiel.de/en Department of Psychiatry and Psychotherapy Charité at St. Hedwig-Hospital Große Hamburger Strasse 5-11 10115 Berlin, Germany +030 - 2311 - 1879 www.multisensorymind.com > Am 20.07.2018 um 14:52 schrieb Abhishek Samal <007abhisheksamal at gmail.com>: > > Sir, > This is Abhishek. I am trying to analyse Motor Evoked field MEG data. I have been trying to use the EMG channel as the trial definition for the triggers of epoch creation. But when I use the script that is given in tutorial definition I am getting the following error. > > The Input > > cfg = []; > cfg.dataset = 'preetham_lt_motor_raw_tsss_mc.fif'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 0.5; > cfg.trialfun = 'trialfun_emgdetect'; > cfg = ft_definetrial(cfg); > data = ft_preprocessing(cfg); > > The Error > > 306 MEG channel locations transformed > Reading preetham_lt_motor_raw_tsss_mc.fif ... > Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... > Range : 124000 ... 669999 = 62.000 ... 335.000 secs > Ready. > Reading 124000 ... 669999 = 62.000 ... 335.000 secs... [done] > found 0 events > created 210265 trials > the call to "ft_definetrial" took 528 seconds > 306 MEG channel locations transformed > Reading preetham_lt_motor_raw_tsss_mc.fif ... > Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... > Range : 124000 ... 669999 = 62.000 ... 335.000 secs > Ready. > processing channel { 'EOG001' 'ECG002' 'EEG001' 'EEG002' 'EEG003' 'EEG004' 'EEG005' 'EEG006' 'EEG007' 'EEG008' 'EEG009' 'EEG010' 'EEG011' 'EEG012' 'EEG013' 'EEG014' 'EEG015' 'EEG016' 'EEG017' 'EEG018' 'EEG019' 'EEG020' 'EEG021' 'EEG022' 'EEG023' 'EEG024' 'EEG025' 'EXCI' 'IASX+' 'IASX-' 'IASY+' 'IASY-' 'IASZ+' 'IASZ-' 'IAS_DX' 'IAS_DY' 'IAS_X' 'IAS_Y' 'IAS_Z' 'MEG0111' 'MEG0112' 'MEG0113' 'MEG0121' 'MEG0122' 'MEG0123' 'MEG0131' 'MEG0132' 'MEG0133' 'MEG0141' 'MEG0142' 'MEG0143' 'MEG0211' 'MEG0212' 'MEG0213' 'MEG0221' 'MEG0222' 'MEG0223' 'MEG0231' 'MEG0232' 'MEG0233' 'MEG0241' 'MEG0242' 'MEG0243' 'MEG0311' 'MEG0312' 'MEG0313' 'MEG0321' 'MEG0322' 'MEG0323' 'MEG0331' 'MEG0332' 'MEG0333' 'MEG0341' 'MEG0342' 'MEG0343' 'MEG0411' 'MEG0412' 'MEG0413' 'MEG0421' 'MEG0422' 'MEG0423' 'MEG0431' 'MEG0432' 'MEG0433' 'MEG0441' 'MEG0442' 'MEG0443' 'MEG0511' 'MEG0512' 'MEG0513' 'MEG0521' 'MEG0522' 'MEG0523' 'MEG0531' 'MEG0532' 'MEG0533' 'MEG0541' 'MEG0542' 'MEG0543' 'MEG0611' 'MEG0612' 'MEG0613' 'MEG0621' 'MEG0622' 'MEG0623' 'MEG0631' 'MEG0632' 'MEG0633' 'MEG0641' 'MEG0642' 'MEG0643' 'MEG0711' 'MEG0712' 'MEG0713' 'MEG0721' 'MEG0722' 'MEG0723' 'MEG0731' 'MEG0732' 'MEG0733' 'MEG0741' 'MEG0742' 'MEG0743' 'MEG0811' 'MEG0812' 'MEG0813' 'MEG0821' 'MEG0822' 'MEG0823' 'MEG0911' 'MEG0912' 'MEG0913' 'MEG0921' 'MEG0922' 'MEG0923' 'MEG0931' 'MEG0932' 'MEG0933' 'MEG0941' 'MEG0942' 'MEG0943' 'MEG1011' 'MEG1012' 'MEG1013' 'MEG1021' 'MEG1022' 'MEG1023' 'MEG1031' 'MEG1032' 'MEG1033' 'MEG1041' 'MEG1042' 'MEG1043' 'MEG1111' 'MEG1112' 'MEG1113' 'MEG1121' 'MEG1122' 'MEG1123' 'MEG1131' 'MEG1132' 'MEG1133' 'MEG1141' 'MEG1142' 'MEG1143' 'MEG1211' 'MEG1212' 'MEG1213' 'MEG1221' 'MEG1222' 'MEG1223' 'MEG1231' 'MEG1232' 'MEG1233' 'MEG1241' 'MEG1242' 'MEG1243' 'MEG1311' 'MEG1312' 'MEG1313' 'MEG1321' 'MEG1322' 'MEG1323' 'MEG1331' 'MEG1332' 'MEG1333' 'MEG1341' 'MEG1342' 'MEG1343' 'MEG1411' 'MEG1412' 'MEG1413' 'MEG1421' 'MEG1422' 'MEG1423' 'MEG1431' 'MEG1432' 'MEG1433' 'MEG1441' 'MEG1442' 'MEG1443' 'MEG1511' 'MEG1512' 'MEG1513' 'MEG1521' 'MEG1522' 'MEG1523' 'MEG1531' 'MEG1532' 'MEG1533' 'MEG1541' 'MEG1542' 'MEG1543' 'MEG1611' 'MEG1612' 'MEG1613' 'MEG1621' 'MEG1622' 'MEG1623' 'MEG1631' 'MEG1632' 'MEG1633' 'MEG1641' 'MEG1642' 'MEG1643' 'MEG1711' 'MEG1712' 'MEG1713' 'MEG1721' 'MEG1722' 'MEG1723' 'MEG1731' 'MEG1732' 'MEG1733' 'MEG1741' 'MEG1742' 'MEG1743' 'MEG1811' 'MEG1812' 'MEG1813' 'MEG1821' 'MEG1822' 'MEG1823' 'MEG1831' 'MEG1832' 'MEG1833' 'MEG1841' 'MEG1842' 'MEG1843' 'MEG1911' 'MEG1912' 'MEG1913' 'MEG1921' 'MEG1922' 'MEG1923' 'MEG1931' 'MEG1932' 'MEG1933' 'MEG1941' 'MEG1942' 'MEG1943' 'MEG2011' 'MEG2012' 'MEG2013' 'MEG2021' 'MEG2022' 'MEG2023' 'MEG2031' 'MEG2032' 'MEG2033' 'MEG2041' 'MEG2042' 'MEG2043' 'MEG2111' 'MEG2112' 'MEG2113' 'MEG2121' 'MEG2122' 'MEG2123' 'MEG2131' 'MEG2132' 'MEG2133' 'MEG2141' 'MEG2142' 'MEG2143' 'MEG2211' 'MEG2212' 'MEG2213' 'MEG2221' 'MEG2222' 'MEG2223' 'MEG2231' 'MEG2232' 'MEG2233' 'MEG2241' 'MEG2242' 'MEG2243' 'MEG2311' 'MEG2312' 'MEG2313' 'MEG2321' 'MEG2322' 'MEG2323' 'MEG2331' 'MEG2332' 'MEG2333' 'MEG2341' 'MEG2342' 'MEG2343' 'MEG2411' 'MEG2412' 'MEG2413' 'MEG2421' 'MEG2422' 'MEG2423' 'MEG2431' 'MEG2432' 'MEG2433' 'MEG2441' 'MEG2442' 'MEG2443' 'MEG2511' 'MEG2512' 'MEG2513' 'MEG2521' 'MEG2522' 'MEG2523' 'MEG2531' 'MEG2532' 'MEG2533' 'MEG2541' 'MEG2542' 'MEG2543' 'MEG2611' 'MEG2612' 'MEG2613' 'MEG2621' 'MEG2622' 'MEG2623' 'MEG2631' 'MEG2632' 'MEG2633' 'MEG2641' 'MEG2642' 'MEG2643' 'STI101' 'SYS201' 'CHPI001' 'CHPI002' 'CHPI003' 'CHPI004' 'CHPI005' 'CHPI006' 'CHPI007' 'CHPI008' 'CHPI009' } > reading and preprocessing > reading and preprocessing trial 1 from 210265 > Reading 264027 ... 4792reading and preprocessing trial 2 from 210265 > Reading 327742 ... 4802reading and preprocessing trial 3 from 210265 > . > . > . > . > . > Reading 635443 ... 66reading and preprocessing trial 116 from 210265 > Error using ft_read_data (line 225) > cannot read data after the end of the file > > Error in ft_preprocessing (line 582) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, > 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); > > > > I am new to fieldtrip. Please help me with the above error. > Regards, > Abhishek. > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: From apple.h99 at gmail.com Fri Jul 20 15:54:00 2018 From: apple.h99 at gmail.com (sara h) Date: Fri, 20 Jul 2018 18:24:00 +0430 Subject: [FieldTrip] Access to fieldtrip mailing list Message-ID: Dear all Hi I'm new with filedtrip and I'm going to search in fieldtrip mailing list but the list is not accessible and the webpage is not reachable. does any one have this issue?? how can I sove it? thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 23 10:55:24 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 23 Jul 2018 08:55:24 +0000 Subject: [FieldTrip] Access to fieldtrip mailing list In-Reply-To: References: Message-ID: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> Hi Sara, It works for me at the moment, so I don’t know what was/is causing your problem. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 20 Jul 2018, at 15:54, sara h > wrote: Dear all Hi I'm new with filedtrip and I'm going to search in fieldtrip mailing list but the list is not accessible and the webpage is not reachable. does any one have this issue?? how can I sove it? thanks _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 23 10:58:46 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 23 Jul 2018 08:58:46 +0000 Subject: [FieldTrip] Averaging over frequencies in ft_freqstatistics In-Reply-To: References: Message-ID: Hi Sebastian, ft_freqstatistics averages the power across the frequency bins, that have their bin-centre within the range specified by cfg.frequency. The output frequency in stat.freq represents the average of the bin-centres that went into the computation. No re-estimation of the power at this frequency is done. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 19 Jul 2018, at 09:01, Sebastian Sauppe > wrote: Dear FieldTrip list, I am testing different frequency bands with cluster-based permutation tests using ft_freqstatistics. For this, I use cfg.avgoverfreq = ‚yes‘ when setting up the test. However, I am unsure about how FieldTrip actually handles the frequency averaging. Does it take the mean power of the specified frequencies or does it take the power of the mean frequency? This is the relevant code I use: ... cfg.frequency = [3 8]; cfg.avgoverfreq = 'yes‘; ... [stat] = ft_freqstatistics(cfg, data_A, data_B); In my data, I have the following frequencies: [3.9062 4.8828 6.1035 7.0801 8.0566 9.0332 10.0098]. In the statistics output, after averaging over frequencies stat.freq returns only 6.0059. This is the mean of the frequencies between 3 and 8. But I can’t see whether somehow the power of that frequency was assessed in the test or whether the power of all frequencies in that band was first averaged and then tested. Regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rdm146 at newark.rutgers.edu Tue Jul 24 01:45:43 2018 From: rdm146 at newark.rutgers.edu (Ravi Mill) Date: Mon, 23 Jul 2018 23:45:43 +0000 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel Message-ID: Dear Fieldtrippers I've been scouring the FT documentation and mailing list but can't seem to find the answer to a fairly simple question (which seems to have remained unanswered previously https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010816.html): how does one know the size/'radius' of the individual source gridpoints modeled by Fieldtrip? I've been warping MNI template source models (with RO selected from a functional atlas of ~300 regions) to individual subject MRI headmodels to extract source timeseries via LCMV beamformer. In ft_prepare_sourcemodel there are seemingly options to control the *spacing* between gridpoints in a whole-brain source grid (cfg.grid.resolution), but nothing to control how large the individual sources are (either for whole-brain grids, or a priori cfg.grid.pos values that I've been using). Does this mean that the size of individual gridpoints cannot be changed within ft_prepare_sourcemodel? Are they also in absolute terms fairly small (e.g. ~1mm)? If so, is the only way to extract 'larger' sources to fit a whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), identify gridpoints after ft_sourceanalysis that fall within a specified Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and then e.g. average over all those gridpoints? I'm concerned that larger source gridpoints might have larger SNR... Thanks in advance! Ravi -- Ravi Mill, PhD Post-doctoral researcher Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers University -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Tue Jul 24 09:16:06 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 24 Jul 2018 09:16:06 +0200 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel In-Reply-To: References: Message-ID: Hi Ravi, Beamforming will estimate source activity at *point* sources; in other words, the grid points have no spatial extent (i.e., they are zero-dimensional). > If so, is the only way to extract 'larger' sources to fit a > whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), > identify gridpoints after ft_sourceanalysis that fall within a specified > Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and > then e.g. average over all those gridpoints? Yes, that is definitely a valid approach. You will probably not need to use such a finely spaced grid if you end up averaging over grid points anyway. Typically, the spatial filters for neighbouring grid points will be highly correlated. Best, Eelke > > > Thanks in advance! > > Ravi > > > -- > Ravi Mill, PhD > Post-doctoral researcher > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers University > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > From apple.h99 at gmail.com Tue Jul 24 12:07:30 2018 From: apple.h99 at gmail.com (sara h) Date: Tue, 24 Jul 2018 14:37:30 +0430 Subject: [FieldTrip] Access to fieldtrip mailing list In-Reply-To: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> References: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> Message-ID: Hi Jan yes it is ok for me now too. thank you regards Sara On Mon, Jul 23, 2018 at 1:43 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Sara, > It works for me at the moment, so I don’t know what was/is causing your > problem. > Best wishes, > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > On 20 Jul 2018, at 15:54, sara h wrote: > > Dear all > Hi > > I'm new with filedtrip and I'm going to search in fieldtrip mailing list > but the list is not accessible and the webpage is not reachable. does any > one have this issue?? how can I sove it? > > thanks > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunnypitt1965 at gmail.com Tue Jul 24 21:24:19 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Tue, 24 Jul 2018 15:24:19 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Message-ID: Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From rdm146 at newark.rutgers.edu Tue Jul 24 23:59:02 2018 From: rdm146 at newark.rutgers.edu (Ravi Mill) Date: Tue, 24 Jul 2018 21:59:02 +0000 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel In-Reply-To: References: , Message-ID: Many thanks for clarifying that Eelke! ________________________________ From: fieldtrip on behalf of Eelke Spaak Sent: Tuesday, July 24, 2018 3:16:06 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel Hi Ravi, Beamforming will estimate source activity at *point* sources; in other words, the grid points have no spatial extent (i.e., they are zero-dimensional). > If so, is the only way to extract 'larger' sources to fit a > whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), > identify gridpoints after ft_sourceanalysis that fall within a specified > Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and > then e.g. average over all those gridpoints? Yes, that is definitely a valid approach. You will probably not need to use such a finely spaced grid if you end up averaging over grid points anyway. Typically, the spatial filters for neighbouring grid points will be highly correlated. Best, Eelke > > > Thanks in advance! > > Ravi > > > -- > Ravi Mill, PhD > Post-doctoral researcher > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers University > > > _______________________________________________ > fieldtrip mailing list > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=tqWRL8OWLPKt73S8XFXfPIoyeYVV60WTJuZVW3Vil%2Fs%3D&reserved=0 > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=nx%2B1yhLpHm1tXwX1KjTK6qwhvnWyk%2FWZMTAm5xp9Qbg%3D&reserved=0 > _______________________________________________ fieldtrip mailing list https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=tqWRL8OWLPKt73S8XFXfPIoyeYVV60WTJuZVW3Vil%2Fs%3D&reserved=0 https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=nx%2B1yhLpHm1tXwX1KjTK6qwhvnWyk%2FWZMTAm5xp9Qbg%3D&reserved=0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Arana at donders.ru.nl Wed Jul 25 13:49:56 2018 From: S.Arana at donders.ru.nl (Arana, S.L. (Sophie)) Date: Wed, 25 Jul 2018 11:49:56 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:ii_jk039gcg0_164cdbfadfb3de10] Thanks for your understanding and support Best Regards, Sunny -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: image.png URL: From sunnypitt1965 at gmail.com Wed Jul 25 14:22:33 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Wed, 25 Jul 2018 08:22:33 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) wrote: > Dear Sunny, > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > Best, > > Sophie > > ------------------------------ > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > Hope you are doing fine, > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > Thanks for your understanding and support > > Best Regards, > Sunny > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From Silvia.Formica at UGent.be Thu Jul 26 09:57:32 2018 From: Silvia.Formica at UGent.be (Silvia Formica) Date: Thu, 26 Jul 2018 07:57:32 +0000 Subject: [FieldTrip] ft_freqanalysis wavelet problem Message-ID: <1532591852846.46333@UGent.be> Dear all, I am new to fieldtrip so I apologize in advance if my question is trivial. I am trying to run a time frequency analysis with Morlet wavelets. Here is the code I am using: cfg = []; cfg.channel = 1:64; cfg.method = 'wavelet'; cfg.pad = 10; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 4:1:30; cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz TFRwave = ft_freqanalysis(cfg, data_clean); Where data_clean is the struct containing my trials. All my trials are the same length. When I run this code, I get the following warning: Warning: output time-bins are different from input time-bins trial 1, frequency 26 (29.00 Hz) Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) [...] I have no idea what this means. Any suggestion? Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot: cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.zlim = [-3e-27 3e-27]; cfg.showlabels = 'yes'; cfg.layout = 'biosemi64.lay'; figure ft_multiplotTFR(cfg, TFRwave) When I check the content of my TFRwave I can see it is not made of NaNs. Is the problem due to the setting cfg.zlim? It is not clear to me how to set it. Thanks in advance for any help! Silvia -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Jul 26 11:32:36 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 26 Jul 2018 11:32:36 +0200 Subject: [FieldTrip] ft_freqanalysis wavelet problem In-Reply-To: <1532591852846.46333@UGent.be> References: <1532591852846.46333@UGent.be> Message-ID: Dear Silvia, The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information, speeding it up as well) Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options. Best wishes, Stephen On 26 July 2018 at 09:57, Silvia Formica wrote: > Dear all, > > > I am new to fieldtrip so I apologize in advance if my question is trivial. > > I am trying to run a time frequency analysis with Morlet wavelets. > > Here is the code I am using: > > > cfg = []; > cfg.channel = 1:64; > cfg.method = 'wavelet'; > cfg.pad = 10; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 4:1:30; > cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz > TFRwave = ft_freqanalysis(cfg, data_clean); > > > Where data_clean is the struct containing my trials. All my trials are > the same length. > > When I run this code, I get the following warning: > > Warning: output time-bins are different from input time-bins > trial 1, frequency 26 (29.00 Hz) > Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) > Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) > Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) > Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) > [...] > > I have no idea what this means. Any suggestion? > > Despite the warning, the TRFwave is computed, but when I try to plot it I > get a completely blue output. Here is the code I am using for the plot: > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.zlim = [-3e-27 3e-27]; > cfg.showlabels = 'yes'; > cfg.layout = 'biosemi64.lay'; > figure > ft_multiplotTFR(cfg, TFRwave) > > > When I check the content of my TFRwave I can see it is not made of NaNs. > Is the problem due to the setting cfg.zlim? It is not clear to me how to > set it. > > Thanks in advance for any help! > > Silvia > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Silvia.Formica at UGent.be Thu Jul 26 12:45:26 2018 From: Silvia.Formica at UGent.be (Silvia Formica) Date: Thu, 26 Jul 2018 10:45:26 +0000 Subject: [FieldTrip] ft_freqanalysis wavelet problem In-Reply-To: References: <1532591852846.46333@UGent.be>, Message-ID: <1532601927049.21531@UGent.be> Dear Stephen, thanks a lot for your reply. I actually figured out the baseline was the issue, as I was computing the Morlet on a shorter time-window and I was trying to baseline-correct with an interval that was outside of my TFR. With this adjustment I do see the plot as I expected it. Concerning the warning on the cfg.toi, I chose on purpose the step according to my sampling rate, but I will consider increasing it. My concern is that I might somehow be losing information due to this mismatch between input and output time-bins. Thanks! Best, Silvia ________________________________ From: fieldtrip on behalf of Stephen Whitmarsh Sent: 26 July 2018 11:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_freqanalysis wavelet problem Dear Silvia, The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information, speeding it up as well) Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options. Best wishes, Stephen On 26 July 2018 at 09:57, Silvia Formica > wrote: Dear all, I am new to fieldtrip so I apologize in advance if my question is trivial. I am trying to run a time frequency analysis with Morlet wavelets. Here is the code I am using: cfg = []; cfg.channel = 1:64; cfg.method = 'wavelet'; cfg.pad = 10; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 4:1:30; cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz TFRwave = ft_freqanalysis(cfg, data_clean); Where data_clean is the struct containing my trials. All my trials are the same length. When I run this code, I get the following warning: Warning: output time-bins are different from input time-bins trial 1, frequency 26 (29.00 Hz) Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) [...] I have no idea what this means. Any suggestion? Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot: cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.zlim = [-3e-27 3e-27]; cfg.showlabels = 'yes'; cfg.layout = 'biosemi64.lay'; figure ft_multiplotTFR(cfg, TFRwave) When I check the content of my TFRwave I can see it is not made of NaNs. Is the problem due to the setting cfg.zlim? It is not clear to me how to set it. Thanks in advance for any help! Silvia _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brooks.jl at gmail.com Thu Jul 26 19:22:44 2018 From: brooks.jl at gmail.com (Joseph Brooks) Date: Thu, 26 Jul 2018 18:22:44 +0100 Subject: [FieldTrip] Lecturer (Assistant Prof Equivalent) in Psychology @ Keele University, UK Message-ID: Job Link: https://www.jobs.ac.uk/job/BLE960/lecturer-in-psychology/ Deadline: 9 Aug 2018 Psychology at Keele University (UK) is looking for an excellent researcher to join one or more of our growing research groups in Cognitive & Biological Psych, Social & Developmental, or Health & Wellbeing. We welcome applicants from across psychology but particularly those using quantitative methods. For Cognitive/Cog Neuro applicants, we have a new 64 channel Biosemi EEG laboratory, Eyelink eyetracking lab, Virtual Reality lab, Biopac psychophysiology labs, an MRI access agreement with Liverpool, and good links with Stoke University Hospital and Keele Medical School for neuropsych patient recruitment. More on facilities at https://www.keele.ac.uk/psychology/equipmentandfacilities/ . Applicants should have a strong track record of peer-reviewed publications and be able to contribute teaching to our undergraduate and post-graduate programmes. Note: This is a permanent academic position (subject to usual probationary period) which is equivalent to a tenure-track assistant professor position in North America. Keele has a beautiful campus in the West Midlands of England only 40 minutes from Manchester and Birmingham and 1.5 hours by train from London. We are a friendly community of academics and students (UG, MSc, and PhD) with a diverse range of interests across Psychology including both quantitative and qualitative methods. We are situated in the Dorothy Hodgkin Building which houses our laboratories For full details of the position, please see the advertisement at: https://www.jobs.ac.uk/job/BLE960/lecturer-in-psychology/ -------------------------------------------- Dr Joseph Brooks Senior Lecturer in Psychology Research Lead, Cognitive & Biological Research Group Programme Lead, MSc Cognitive Psychology School of Psychology, Keele University Office: Dorothy Hodgkin Building 1.74 Lab Website: https://sites.google.com/view/brookslab -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.herrero66 at gmail.com Fri Jul 27 15:29:47 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Fri, 27 Jul 2018 09:29:47 -0400 Subject: [FieldTrip] iEEG cluster statistics Message-ID: Hi FT, quick question on how to perform cluster statistics multiple comparisons correction with cfg.correctm = cluster' on iEEG data. I'm preparing neighbors with the two nearest contacts to the contact in question but the code gives an error (the 'fdr' method works fine). Is this method exclusive to standard montages or can be done manually. I've tried to do it manually so that neighbors format is similar to one of the examples MEG montage but still not working. Thoughts? JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Jul 27 15:35:49 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 27 Jul 2018 13:35:49 +0000 Subject: [FieldTrip] iEEG cluster statistics In-Reply-To: References: Message-ID: What’s the error? In principle, if your neighbourhood-structure is well-defined it should work. Best, JM On 27 Jul 2018, at 15:29, Jose Herrero > wrote: Hi FT, quick question on how to perform cluster statistics multiple comparisons correction with cfg.correctm = cluster' on iEEG data. I'm preparing neighbors with the two nearest contacts to the contact in question but the code gives an error (the 'fdr' method works fine). Is this method exclusive to standard montages or can be done manually. I've tried to do it manually so that neighbors format is similar to one of the examples MEG montage but still not working. Thoughts? JHerr _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabriel.delara at med.uni-goettingen.de Fri Jul 27 17:04:33 2018 From: gabriel.delara at med.uni-goettingen.de (Amador, Gabriel) Date: Fri, 27 Jul 2018 15:04:33 +0000 Subject: [FieldTrip] scalp EEG resting-state analysis Message-ID: Dear Field trippers, My first e-mail to this list. Thanks for paying attention to this, whoever took time to read it. I am currently doing my PhD in Göttingen, at the moment running a scalp-EEG (26-channels) analysis with Fieldtrip for a dataset of healthy participants. I have a repeated-measures design, where each participant undergoes 4 sessions, with n = 20. For each session, I performed two 5' eyes-open resting-state recordings per participant: one before and one after intervention (pre-, post-). The goal is to simply detect power changes in the pre X post comparison. Recordings were segmented into 2s trials with 50% overlap followed by other pre-processing steps. I am having some doubts on the feasibility/correctness of the steps after the pre-processing. My main critical question is the procedures sequence to correctly run the Monte Carlo stats in the end (if and when to keep trials, to average trials, to average across participants, and so on). Some options available: 1. First running TFA (mtmfft, dpss,) keeping the trials. Then, appending participants with ft_appendfreq. Afterwards, stats: parameters (Montecarlo, depsamplesT, cluster correction, 5.000 iterations). First problem arises in the design matrix: Since trials are kept in the FA, they are uneven for every session (appending leads to different trials between pre X post), and also the appended data does not keep the participant as UO, so design matrix has to be design as trials in the first row. To make it work, trials have to be shortened from one condition, so they are paired (which seems obvious for depsamplesT, since it does would not accept different values in the uvar). Statistics run after doing all this, but I am not sure, since having a uvar with ~10.000 points, that were the individual trials of every session (there are 20 participants) sounds strange (there were no 10.000 participants). This option was run for one condition, significant difference happened, clusters were formed, etc. Is this reasonable? 2. First running TFA (mtmfft, dpss,) keeping the trials. After, apply ft_freqdescriptives to every subject, in oder to be able to use ft_freq_grandaverage. Apply ft_freqgrandaverage across participants, but keeping individuals (for the design matrix).After ft_ freqgrandaverage, stats as described above, with design matrix with 1:20 in the first row (uvar) and the two conditions (pre X post) at the second. This works, but leads to no clusters found (ran it on more than one condition). Doubt here is: using ft_freqdescriptives and then ft_freq_grandaverage compromises the monte carlo procedure, having just one value for each channel (the grand-averaged trials power)? Any suggestions? Thanks! Gabriel Amador de Lara wissenschaftlicher Mitarbeiter / PhD candidate Klinik für klinische Neurophysiologie / Department of Clinical Neurophysiology Universitätsmedizin / Medical Center Georg-August-Universität Göttingen Robert-Koch-Str. 40, 37075 +49 0551 3919265 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunnypitt1965 at gmail.com Fri Jul 27 20:41:12 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Fri, 27 Jul 2018 14:41:12 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON ( https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > Hello Sophie, > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > Thanks for your understanding and support. > > Best Regards, > Sunny > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > >> Hello Sophie, >> >> Thanks a lot for your clarification. This is very useful. >> >> Sunny >> >> >> On Wednesday, July 25, 2018, Arana, S.L. (Sophie) >> wrote: >> >>> Dear Sunny, >>> >>> the multi-channel NIRS data tutorial is currently under construction and >>> will hopefully be fully available in a couple of weeks. Until then, there >>> might still be some inconsistencies such as the one you have encountered. >>> >>> The variable you refer to is indeed missing. It refers to a filtered >>> version of the data, and you can created it by running the following code >>> before the epoching. >>> >>> cfg = []; >>> >>> cfg.hpfilter = 'yes'; >>> >>> cfg.hpfreq = 0.01; >>> >>> data_flt = ft_preprocessing(cfg,data_down); >>> >>> >>> This should help you to continue with the tutorial, but please do keep >>> in mind that we are currently working on it and you might encounter some >>> other inconsistencies still later on. >>> >>> >>> Best, >>> >>> Sophie >>> >>> ------------------------------ >>> *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny >>> p [sunnypitt1965 at gmail.com] >>> *Sent:* Tuesday, July 24, 2018 9:24 PM >>> *To:* fieldtrip at science.ru.nl >>> *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging >>> of multi-channel NIRS data >>> >>> Hello All Good Day, >>> >>> Hope you are doing fine, >>> >>> Thanks a lot for providing with fieldtrip which is really useful to >>> analyze fNIRS data. I have an issue in the "Preprocessing and averaging of >>> multi-channel NIRS data" tutorial. Can you please help me with this issue? >>> >>> Issue: In the "Preprocessing and averaging of multi-channel NIRS data" >>> tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel >>> >>> The "Epoch" section consists of a variable "data_flt.fsample" where >>> "data_flt" variable is not defined. Can you please inform what is this >>> variable related to? as this is needed to complete my analysis. >>> >>> >>> >>> >>> Thanks for your understanding and support >>> >>> Best Regards, >>> Sunny >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From lizhipeng3924 at gmail.com Sun Jul 29 04:55:37 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Sun, 29 Jul 2018 10:55:37 +0800 Subject: [FieldTrip] A question about MEG source reconstruction Message-ID: Dear all, When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. I would appreciate it if you could help me. Yours, zhipeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 5933 bytes Desc: not available URL: From alexandre.gramfort at inria.fr Sun Jul 29 10:03:59 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 29 Jul 2018 10:03:59 +0200 Subject: [FieldTrip] A question about MEG source reconstruction In-Reply-To: References: Message-ID: hi, indeed there is a typo: $ cd $MNE_ROOT $ ls bin/mne_setup* bin/mne_setup bin/mne_setup_matlab_csh bin/mne_setup_mri bin/mne_setup_source_space bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh depending on your shell it can be source $MNE_ROOT/bin/mne_setup_sh HTH Alex On Sun, Jul 29, 2018 at 4:58 AM zhipeng li wrote: > > External Email - Use Caution > > Dear all, > When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. > I would appreciate it if you could help me. > Yours, > zhipeng > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From lizhipeng3924 at gmail.com Mon Jul 30 03:49:11 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Mon, 30 Jul 2018 09:49:11 +0800 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 In-Reply-To: References: Message-ID: - First of all, thank you very much for your reply @ Alexandre Gramfort . - But none of the files you listed were found in bin - - This is all the files contained in bin, - I need your further help. - Yours, zhipeng 2018-07-29 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. A question about MEG source reconstruction (zhipeng li) > 2. Re: A question about MEG source reconstruction > (Alexandre Gramfort) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 29 Jul 2018 10:55:37 +0800 > From: zhipeng li > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] A question about MEG source reconstruction > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > I would appreciate it if you could help me. > Yours, > zhipeng > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180729/9711b38d/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 5933 bytes > Desc: not available > URL: attachments/20180729/9711b38d/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Sun, 29 Jul 2018 10:03:59 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] A question about MEG source reconstruction > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > hi, > > indeed there is a typo: > > $ cd $MNE_ROOT > $ ls bin/mne_setup* > bin/mne_setup bin/mne_setup_matlab_csh > bin/mne_setup_mri bin/mne_setup_source_space > bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > > depending on your shell it can be > > source $MNE_ROOT/bin/mne_setup_sh > > HTH > Alex > > On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > Dear all, > > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > > I would appreciate it if you could help me. > > Yours, > > zhipeng > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 19 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 159116 bytes Desc: not available URL: From jorn at artinis.com Mon Jul 30 08:47:25 2018 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Mon, 30 Jul 2018 08:47:25 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) Cc: FieldTrip discussion list Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From alexandre.gramfort at inria.fr Mon Jul 30 08:49:46 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Mon, 30 Jul 2018 08:49:46 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 In-Reply-To: References: Message-ID: it's the $MNE_ROOT/bin folder after setting the MNE_ROOT env variable to the folder that contains the MNE command line tools. HTH Alex On Mon, Jul 30, 2018 at 3:52 AM zhipeng li wrote: > > External Email - Use Caution > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > But none of the files you listed were found in bin > > > This is all the files contained in bin, > > I need your further help. > > Yours, > zhipeng > > > 2018-07-29 18:00 GMT+08:00 : >> >> Send fieldtrip mailing list submissions to >> fieldtrip at science.ru.nl >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> or, via email, send a message with subject or body 'help' to >> fieldtrip-request at science.ru.nl >> >> You can reach the person managing the list at >> fieldtrip-owner at science.ru.nl >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of fieldtrip digest..." >> >> >> Today's Topics: >> >> 1. A question about MEG source reconstruction (zhipeng li) >> 2. Re: A question about MEG source reconstruction >> (Alexandre Gramfort) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 29 Jul 2018 10:55:37 +0800 >> From: zhipeng li >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] A question about MEG source reconstruction >> Message-ID: >> >> Content-Type: text/plain; charset="utf-8" >> >> Dear all, >> When I was about to create a sourcemodel, I ran into a problem.The >> documentary which I refers to is Tutorial documentation>Source >> reconstruction of event-related fields using minimum-norm >> estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG >> data.When I installed MNE as their description, I found that the.sh file >> doesn't exist.The command I am using is posted below as a >> picture.Therefore, the following steps cannot be carried out. >> I would appreciate it if you could help me. >> Yours, >> zhipeng >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: image.png >> Type: image/png >> Size: 5933 bytes >> Desc: not available >> URL: >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 29 Jul 2018 10:03:59 +0200 >> From: Alexandre Gramfort >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] A question about MEG source reconstruction >> Message-ID: >> >> Content-Type: text/plain; charset="UTF-8" >> >> hi, >> >> indeed there is a typo: >> >> $ cd $MNE_ROOT >> $ ls bin/mne_setup* >> bin/mne_setup bin/mne_setup_matlab_csh >> bin/mne_setup_mri bin/mne_setup_source_space >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh >> >> depending on your shell it can be >> >> source $MNE_ROOT/bin/mne_setup_sh >> >> HTH >> Alex >> >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li wrote: >> > >> > External Email - Use Caution >> > >> > Dear all, >> > When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. >> > I would appreciate it if you could help me. >> > Yours, >> > zhipeng >> > >> > >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > https://doi.org/10.1371/journal.pcbi.1002202 >> > >> > >> > The information in this e-mail is intended only for the person to whom it is >> > addressed. If you believe this e-mail was sent to you in error and the e-mail >> > contains patient information, please contact the Partners Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you in error >> > but does not contain patient information, please contact the sender and properly >> > dispose of the e-mail. >> >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> https://doi.org/10.1371/journal.pcbi.1002202 >> >> >> ------------------------------ >> >> End of fieldtrip Digest, Vol 92, Issue 19 >> ***************************************** > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From S.Hanslmayr at bham.ac.uk Mon Jul 30 11:23:31 2018 From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr) Date: Mon, 30 Jul 2018 09:23:31 +0000 Subject: [FieldTrip] Postdoc position to work with human single neurons and LFPs, 9 days left to apply! Message-ID: <257F6C65A372A04CA41056EACC0DE7CED8783389@EX12.adf.bham.ac.uk> Dear Fieldtrippers, We are pleased to announce an open postdoc position in our group to work with human single neurons and LFP recordings in an exciting memory project funded by the ERC. The position is initially for 2 years with an option for 1 year extension. The negotiable start date is 1st Oct. Preliminary data has been collected and is waiting to be analysed. If you have strong electrophysiological analytical skills and are interested then please do not hesitate to apply here: http://www.memorybham.com/open-positions/ If you have any questions then please do not hesitate to contact me. Best wishes, Dr. Simon Hanslmayr Reader in Cognitive Neuroscience Royal Society Wolfson Research Merit Award Holder School of Psychology Hills Building 2.37 University of Birmingham Edgbaston Birmingham B15 2TT UK Tel +44 121 4146203 http://www.memorybham.com/people/#/simon-hanslmayr/ [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 8560 bytes Desc: image001.gif URL: From sunnypitt1965 at gmail.com Mon Jul 30 15:29:19 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Mon, 30 Jul 2018 09:29:19 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <007201d427d1$2d7d9500$8878bf00$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Message-ID: Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig wrote: > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* fieldtrip *On Behalf Of *Sunny p > *Sent:* Friday, July 27, 2018 20:41 > *To:* Arana, S.L. (Sophie) > *Cc:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > ------------------------------ > > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > > > Virus-free. www.avg.com > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jorn at artinis.com Mon Jul 30 15:41:40 2018 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Mon, 30 Jul 2018 15:41:40 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Message-ID: <012001d4280b$0c17baa0$24472fe0$@artinis.com> Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list ; jorn at artinis.com Cc: Arana, S.L. (Sophie) Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From sunnypitt1965 at gmail.com Mon Jul 30 16:44:40 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Mon, 30 Jul 2018 10:44:40 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <012001d4280b$0c17baa0$24472fe0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> Message-ID: Hello Jorn, Thanks a lot for your response. Yes, I just collected the data samples, My primary aim is to visualize this data on a head model using field trip. so that it will be easy to understand. Please find attached data set collected using Octamon in this email. I also created layout for this. I attached data, layout and image in this email. Thanks a lot for your support. Its very useful for my research. Best Regards, Sunny On Mon, Jul 30, 2018 at 9:41 AM, Jörn M. Horschig wrote: > Hi Sunny, > > > > The ADC channels in the tutorial are used as a trigger-channel. I am not > sure how you insert the triggers in your experiment, but the Octamon has no > direct trigger input (you could add triggers either wirelessly using a > PortaSync or directly from within Oxysoft). The ADC of the Octamon is the > battery level and not a trigger input. Depending on what you did, you have > to follow different processing steps. If you let me know more about the > events and triggers, I can let you know what to do (you could also send me > some example data and I will send you an example script back that reads in > the data in FieldTrip). > > > > With best regards, > > Jörn > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* Sunny p > *Sent:* Monday, July 30, 2018 15:29 > *To:* FieldTrip discussion list ; > jorn at artinis.com > *Cc:* Arana, S.L. (Sophie) > > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Jorn, > > > > Thanks a lot for your response. I am working with Octamon data (4*2 > Channel). I am trying to visualize the data using topo plot on head based > image following http://www.fieldtriptoolbox.org/tutorial/ > nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon > which has 48 channel). I am wondering what parameter changes should I make > to get the data for OCTAMON visualization as my data has only ADC001 and > there is no ADC002 in data for epoch section. As I am not an NIRS expert, > its difficult to figure out which parameters gives me the visualization as > its throwing errors when following the tutorial. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* fieldtrip *On Behalf Of *Sunny p > *Sent:* Friday, July 27, 2018 20:41 > *To:* Arana, S.L. (Sophie) > *Cc:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > ------------------------------ > > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > > > Virus-free. www.avg.com > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OCTAMON.oxy3 Type: application/octet-stream Size: 417156 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OCTA_layout_MAIN.mat Type: application/octet-stream Size: 1493 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Brain_PreFrontal_Cortex.PNG Type: image/png Size: 88327 bytes Desc: not available URL: From jorn at artinis.com Tue Jul 31 09:16:24 2018 From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=) Date: Tue, 31 Jul 2018 09:16:24 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <012001d4280b$0c17baa0$24472fe0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> Message-ID: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jorn at artinis.com Tue Jul 31 09:34:55 2018 From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=) Date: Tue, 31 Jul 2018 09:34:55 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Message-ID: <004d01d428a0$fae2e840$f0a8b8c0$@artinis.com> Small typo, it should of course say >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.poststim = 35; >> cfg = ft_definetrial(cfg); -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Tuesday, July 31, 2018 9:16 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Tue Jul 31 09:38:53 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 31 Jul 2018 07:38:53 +0000 Subject: [FieldTrip] field trip loreta error References: Message-ID: Dear list, See forwarded message below for a question by Tyler. Tyler, could you send your e-mails to fieldtrip at science.ru.nl? Thanks. Jan-Mathijs Begin forwarded message: From: Tyler Durden > Subject: field trip loreta error Date: 31 July 2018 at 09:20:05 GMT+2 To: > Hi all, I am brand new to fieldtrip and still fairly new to Matlab (R2014a) . I downloaded the fieldtrip toolbox (20180722) and set up paths as instructed. Now I tried to convert some loreta files I have into fieldtrip files but I keep getting this error: "Error using ft_preamble (line 82) Could not run ft_preamble_callinfo - does not seem to exist Error in loreta2fieldtrip (line 48) ft_preamble callinfo I searched the net but I could not find any satisfying answers. I then found the ft_preamble callinfo script on github and just copied and saved it in my directory as a .m file. Now that error is gone but when I want to execute loreta2fieldtrip I get another error: Error using ft_notification (line 340) unsupported LORETA format Error in ft_error (line 39) ft_notification(varargin{:}); Error in loreta2fieldtrip (line 82) ft_error('unsupported LORETA format'); I tried some stuff but as far as I can judge I converted the slor-files appropriately and I have no idea what to do with this error...Since I really want to use your tool box, it would be super if you could help me out! Best -------------- next part -------------- An HTML attachment was scrubbed... URL: From hgould at memphis.edu Tue Jul 31 15:37:06 2018 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 31 Jul 2018 13:37:06 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com>, <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:image001.png at 01D428AE.213F63D0] Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: image001.png URL: From lizhipeng3924 at gmail.com Tue Jul 31 15:52:11 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Tue, 31 Jul 2018 21:52:11 +0800 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21 In-Reply-To: References: Message-ID: - Thank you very much for your reply.@ Alexandre Gramfort But with your answer, my question remains unsolved . On my computer, I can't find any files on mne setup, including any of your list. Following the instructions on the site, I made this step - But the setup file can't be found,I hope you can give me further guidance. - Yours, - zhipeng 2018-07-30 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) > 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort) > 3. Postdoc position to work with human single neurons and LFPs, > 9 days left to apply! (Simon Hanslmayr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2018 08:47:25 +0200 > From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" > To: "'FieldTrip discussion list'" , "'Arana, > S.L. \(Sophie\)'" > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> > Content-Type: text/plain; charset="utf-8" > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > -- > Jörn M. Horschig, PhD, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> > > > > From: fieldtrip On Behalf Of Sunny p > Sent: Friday, July 27, 2018 20:41 > To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging > of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p sunnypitt1965 at gmail.com> > wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > > > _____ > > > From: fieldtrip [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [ > sunnypitt1965 at gmail.com ] > Sent: Tuesday, July 24, 2018 9:24 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " > http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > > Virus-free. utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > www.avg.com > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/577081f5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 4228 bytes > Desc: not available > URL: attachments/20180730/577081f5/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jul 2018 08:49:46 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > it's the $MNE_ROOT/bin folder > after setting the MNE_ROOT env variable to the folder that contains > the MNE command line tools. > > HTH > Alex > On Mon, Jul 30, 2018 at 3:52 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > > > But none of the files you listed were found in bin > > > > > > This is all the files contained in bin, > > > > I need your further help. > > > > Yours, > > zhipeng > > > > > > 2018-07-29 18:00 GMT+08:00 : > >> > >> Send fieldtrip mailing list submissions to > >> fieldtrip at science.ru.nl > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> or, via email, send a message with subject or body 'help' to > >> fieldtrip-request at science.ru.nl > >> > >> You can reach the person managing the list at > >> fieldtrip-owner at science.ru.nl > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of fieldtrip digest..." > >> > >> > >> Today's Topics: > >> > >> 1. A question about MEG source reconstruction (zhipeng li) > >> 2. Re: A question about MEG source reconstruction > >> (Alexandre Gramfort) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 29 Jul 2018 10:55:37 +0800 > >> From: zhipeng li > >> To: fieldtrip at science.ru.nl > >> Subject: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all, > >> When I was about to create a sourcemodel, I ran into a problem.The > >> documentary which I refers to is Tutorial documentation>Source > >> reconstruction of event-related fields using minimum-norm > >> estimation>Creating a sourcemodel for source-reconstruction of MEG or > EEG > >> data.When I installed MNE as their description, I found that the.sh file > >> doesn't exist.The command I am using is posted below as a > >> picture.Therefore, the following steps cannot be carried out. > >> I would appreciate it if you could help me. > >> Yours, > >> zhipeng > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: attachments/20180729/9711b38d/attachment-0001.html> > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: image.png > >> Type: image/png > >> Size: 5933 bytes > >> Desc: not available > >> URL: attachments/20180729/9711b38d/attachment-0001.png> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 29 Jul 2018 10:03:59 +0200 > >> From: Alexandre Gramfort > >> To: FieldTrip discussion list > >> Subject: Re: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> hi, > >> > >> indeed there is a typo: > >> > >> $ cd $MNE_ROOT > >> $ ls bin/mne_setup* > >> bin/mne_setup bin/mne_setup_matlab_csh > >> bin/mne_setup_mri bin/mne_setup_source_space > >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > >> > >> depending on your shell it can be > >> > >> source $MNE_ROOT/bin/mne_setup_sh > >> > >> HTH > >> Alex > >> > >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Dear all, > >> > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > >> > I would appreciate it if you could help me. > >> > Yours, > >> > zhipeng > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > https://doi.org/10.1371/journal.pcbi.1002202 > >> > > >> > > >> > The information in this e-mail is intended only for the person to > whom it is > >> > addressed. If you believe this e-mail was sent to you in error and > the e-mail > >> > contains patient information, please contact the Partners Compliance > HelpLine at > >> > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > >> > but does not contain patient information, please contact the sender > and properly > >> > dispose of the e-mail. > >> > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> https://doi.org/10.1371/journal.pcbi.1002202 > >> > >> > >> ------------------------------ > >> > >> End of fieldtrip Digest, Vol 92, Issue 19 > >> ***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jul 2018 09:23:31 +0000 > From: Simon Hanslmayr > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Postdoc position to work with human single > neurons and LFPs, 9 days left to apply! > Message-ID: > <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > We are pleased to announce an open postdoc position in our group to work > with human single neurons and LFP recordings in an exciting memory project > funded by the ERC. The position is initially for 2 years with an option for > 1 year extension. The negotiable start date is 1st Oct. Preliminary data > has been collected and is waiting to be analysed. If you have strong > electrophysiological analytical skills and are interested then please do > not hesitate to apply here: http://www.memorybham.com/open-positions/ > > If you have any questions then please do not hesitate to contact me. > > Best wishes, > Dr. Simon Hanslmayr > Reader in Cognitive Neuroscience > Royal Society Wolfson Research Merit Award Holder > School of Psychology > Hills Building 2.37 > University of Birmingham > Edgbaston > Birmingham > B15 2TT > UK > > Tel +44 121 4146203 > http://www.memorybham.com/people/#/simon-hanslmayr/ > [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/c066a17a/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.gif > Type: image/gif > Size: 8560 bytes > Desc: image001.gif > URL: attachments/20180730/c066a17a/attachment-0001.gif> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 21 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11167 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 171819 bytes Desc: not available URL: From Amie.Fairs at mpi.nl Tue Jul 31 16:11:15 2018 From: Amie.Fairs at mpi.nl (Fairs, Amie) Date: Tue, 31 Jul 2018 14:11:15 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 24 In-Reply-To: References: Message-ID: Hi Zhipeng, I am quite sure of your issue because any images you send in your email are scrubbed and I can't see them, but I might be able to help. I recently also had some issues following this tutorial. For me, MNE for python was accidentally downloaded at first. For instance, when I first did a 'which mne' search in my system it said [this is my specific path]: /usr/local/apps/python-2.7.11/bin/mne And this mne is not the same MNE suite that is discussed in the tutorial. This mne is 'in' python, so it contains: ls /usr/local/apps/python-2.7.11/bin/ 2to3 folia2html foliatree python rst2html.pyc rst2xetex.pyc alpino2folia folia2rst foliavalidator python2 rst2latex.py rst2xml.py build folia2txt idle python2.7 rst2latex.pyc rst2xml.pyc csv2rdf foliacat mne python2.7-config rst2man.py rstpep2html.py cygdb foliacorrect nosetests python2-config rst2man.pyc rstpep2html.pyc cython foliacount nosetests-2.7 python-config rst2odt_prepstyles.py smtpd.py cythonize foliafreqlist pip rdf2dot rst2odt_prepstyles.pyc tclsh8.5 dcoi2folia foliamerge pip2 rdfgraphisomorphism rst2odt.py virtualenv easy_install foliaquery pip2.7 rdfpipe rst2odt.pyc wish8.5 easy_install-2.7 foliaquery1 pt2to3 rdfs2dot rst2pseudoxml.py f2py foliasetdefinition ptdump rst2folia rst2pseudoxml.pyc folia2annotatedtxt foliaspec ptrepack rst2html5.py rst2s5.py folia2columns foliaspec2json pttree rst2html5.pyc rst2s5.pyc folia2dcoi foliatextcontent pydoc rst2html.py rst2xetex.py [sorry for the formatting] Maybe your system looks something like this? MNE suite actually looks something like this [with the path on my system]: ls /usr/local/apps/MNE/MNE-2.7.0-3106-Linux-x86_64/bin mne_add_patch_info mne_copy_processing_history mne_list_bem mne_redo_file_nocwd mne_add_to_meas_info mne_cov2proj mne_list_coil_def mne_remove_platform mne_add_triggers mne_create_comp_data mne_list_proj mne_rename_channels mne_analyze mne_ctf2fiff mne_list_source_space mne_sensitivity_map mne_annot2labels mne_ctf_dig2fiff mne_list_versions mne_sensor_locations mne_anonymize mne_dacq_annotator mne_make_cor_set mne_setup mne_average_estimates mne_dicom_essentials mne_make_derivations mne_setup_forward_model mne_average_forward_solutions mne_dipole_fit mne_make_eeg_layout mne_setup_mri mne_brain_vision2fiff mne_do_forward_solution mne_make_morph_maps mne_setup_sh mne_browse_raw mne_do_inverse_operator mne_make_movie mne_setup_source_space mne_change_baselines mne_edf2fiff mne_make_scalp_surfaces mne_show_environment mne_change_nave mne_epochs2mat mne_make_source_space mne_show_fiff mne_check_eeg_locations mne_epochs2mat.bin mne_make_sphere_bem mne_simu mne_check_surface mne_evoked_data_summary mne_make_uniform_stc mne_simu.bin mne_collect_transforms mne_eximia2fiff mne_map_data mne_smooth mne_compensate_data mne_fit_sphere_to_surf mne_mark_bad_channels mne_surf2bem mne_compute_mne mne_fix_mag_coil_types mne_morph_labels mne_toggle_skips mne_compute_raw_inverse mne_fix_stim14 mne_opengl_test mne_transform_points mne_convert_ctf_markers mne_flash_bem mne_organize_dicom mne_tufts2fiff mne_convert_dig_data mne_forward_solution mne_prepare_bem_model mne_version_test mne_convert_lspcov mne_insert_4D_comp mne_process_raw mne_view_manual mne_convert_mne_data mne_install_packages mne_process_stc mne_volume_data2mri mne_convert_mne_data.bin mne_inverse_operator mne_raw2mat mne_volume_source_space mne_convert_ncov mne_kit2fiff mne_raw2mat.bin mne_watershed_bem mne_convert_surface mne_launcher mne_redo_file Then you can see mne_setup_sh, and mne_setup_source_space - the two things you need. I hope maybe this is helpful? Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -----Original Message----- From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of fieldtrip-request at science.ru.nl Sent: dinsdag 31 juli 2018 15:52 To: fieldtrip at science.ru.nl Subject: fieldtrip Digest, Vol 92, Issue 24 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit https://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. Re: Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data (Herbert J Gould (hgould)) 2. Re: fieldtrip Digest, Vol 92, Issue 21 (zhipeng li) ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 Jul 2018 13:37:06 +0000 From: "Herbert J Gould (hgould)" To: FieldTrip discussion list Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861 at email.android.com> Content-Type: text/plain; charset="windows-1252" Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:image001.png at 01D428AE.213F63D0] Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: image001.png URL: ------------------------------ Message: 2 Date: Tue, 31 Jul 2018 21:52:11 +0800 From: zhipeng li To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21 Message-ID: Content-Type: text/plain; charset="utf-8" - Thank you very much for your reply.@ Alexandre Gramfort But with your answer, my question remains unsolved . On my computer, I can't find any files on mne setup, including any of your list. Following the instructions on the site, I made this step - But the setup file can't be found,I hope you can give me further guidance. - Yours, - zhipeng 2018-07-30 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) > 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort) > 3. Postdoc position to work with human single neurons and LFPs, > 9 days left to apply! (Simon Hanslmayr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2018 08:47:25 +0200 > From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" > To: "'FieldTrip discussion list'" , "'Arana, > S.L. \(Sophie\)'" > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> > Content-Type: text/plain; charset="utf-8" > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > -- > Jörn M. Horschig, PhD, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> > > > > From: fieldtrip On Behalf Of Sunny p > Sent: Friday, July 27, 2018 20:41 > To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging > of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p sunnypitt1965 at gmail.com> > wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > > > _____ > > > From: fieldtrip [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [ > sunnypitt1965 at gmail.com ] > Sent: Tuesday, July 24, 2018 9:24 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " > http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > > Virus-free. utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > www.avg.com > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/577081f5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 4228 bytes > Desc: not available > URL: attachments/20180730/577081f5/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jul 2018 08:49:46 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > it's the $MNE_ROOT/bin folder > after setting the MNE_ROOT env variable to the folder that contains > the MNE command line tools. > > HTH > Alex > On Mon, Jul 30, 2018 at 3:52 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > > > But none of the files you listed were found in bin > > > > > > This is all the files contained in bin, > > > > I need your further help. > > > > Yours, > > zhipeng > > > > > > 2018-07-29 18:00 GMT+08:00 : > >> > >> Send fieldtrip mailing list submissions to > >> fieldtrip at science.ru.nl > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> or, via email, send a message with subject or body 'help' to > >> fieldtrip-request at science.ru.nl > >> > >> You can reach the person managing the list at > >> fieldtrip-owner at science.ru.nl > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of fieldtrip digest..." > >> > >> > >> Today's Topics: > >> > >> 1. A question about MEG source reconstruction (zhipeng li) > >> 2. Re: A question about MEG source reconstruction > >> (Alexandre Gramfort) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 29 Jul 2018 10:55:37 +0800 > >> From: zhipeng li > >> To: fieldtrip at science.ru.nl > >> Subject: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all, > >> When I was about to create a sourcemodel, I ran into a problem.The > >> documentary which I refers to is Tutorial documentation>Source > >> reconstruction of event-related fields using minimum-norm > >> estimation>Creating a sourcemodel for source-reconstruction of MEG or > EEG > >> data.When I installed MNE as their description, I found that the.sh file > >> doesn't exist.The command I am using is posted below as a > >> picture.Therefore, the following steps cannot be carried out. > >> I would appreciate it if you could help me. > >> Yours, > >> zhipeng > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: attachments/20180729/9711b38d/attachment-0001.html> > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: image.png > >> Type: image/png > >> Size: 5933 bytes > >> Desc: not available > >> URL: attachments/20180729/9711b38d/attachment-0001.png> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 29 Jul 2018 10:03:59 +0200 > >> From: Alexandre Gramfort > >> To: FieldTrip discussion list > >> Subject: Re: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> hi, > >> > >> indeed there is a typo: > >> > >> $ cd $MNE_ROOT > >> $ ls bin/mne_setup* > >> bin/mne_setup bin/mne_setup_matlab_csh > >> bin/mne_setup_mri bin/mne_setup_source_space > >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > >> > >> depending on your shell it can be > >> > >> source $MNE_ROOT/bin/mne_setup_sh > >> > >> HTH > >> Alex > >> > >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Dear all, > >> > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > >> > I would appreciate it if you could help me. > >> > Yours, > >> > zhipeng > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > https://doi.org/10.1371/journal.pcbi.1002202 > >> > > >> > > >> > The information in this e-mail is intended only for the person to > whom it is > >> > addressed. If you believe this e-mail was sent to you in error and > the e-mail > >> > contains patient information, please contact the Partners Compliance > HelpLine at > >> > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > >> > but does not contain patient information, please contact the sender > and properly > >> > dispose of the e-mail. > >> > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> https://doi.org/10.1371/journal.pcbi.1002202 > >> > >> > >> ------------------------------ > >> > >> End of fieldtrip Digest, Vol 92, Issue 19 > >> ***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jul 2018 09:23:31 +0000 > From: Simon Hanslmayr > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Postdoc position to work with human single > neurons and LFPs, 9 days left to apply! > Message-ID: > <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > We are pleased to announce an open postdoc position in our group to work > with human single neurons and LFP recordings in an exciting memory project > funded by the ERC. The position is initially for 2 years with an option for > 1 year extension. The negotiable start date is 1st Oct. Preliminary data > has been collected and is waiting to be analysed. If you have strong > electrophysiological analytical skills and are interested then please do > not hesitate to apply here: http://www.memorybham.com/open-positions/ > > If you have any questions then please do not hesitate to contact me. > > Best wishes, > Dr. Simon Hanslmayr > Reader in Cognitive Neuroscience > Royal Society Wolfson Research Merit Award Holder > School of Psychology > Hills Building 2.37 > University of Birmingham > Edgbaston > Birmingham > B15 2TT > UK > > Tel +44 121 4146203 > http://www.memorybham.com/people/#/simon-hanslmayr/ > [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/c066a17a/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.gif > Type: image/gif > Size: 8560 bytes > Desc: image001.gif > URL: attachments/20180730/c066a17a/attachment-0001.gif> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 21 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11167 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 171819 bytes Desc: not available URL: ------------------------------ Subject: Digest Footer _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 ------------------------------ End of fieldtrip Digest, Vol 92, Issue 24 ***************************************** From Pranish.Kantak at UTSouthwestern.edu Tue Jul 31 18:05:38 2018 From: Pranish.Kantak at UTSouthwestern.edu (Pranish Kantak) Date: Tue, 31 Jul 2018 16:05:38 +0000 Subject: [FieldTrip] Blackrock Data Message-ID: <5E4FC234-9787-415B-8126-5A5064FCB061@utsouthwestern.edu> Hi All, I was just wondering if the functionality of using Blackrock data has been implemented into the toolbox yet? Thanks! Pranish Kantak ________________________________ UT Southwestern Medical Center The future of medicine, today. From jan.schoffelen at donders.ru.nl Tue Jul 31 20:49:38 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 31 Jul 2018 18:49:38 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> Message-ID: Dear Herbert, I have unsubscribed you. To all, note that you can manage your subscription yourself on the listservers interface, which can be reached through http://www.fieldtriptoolbox.org/discussion_list (following the first link therein). Best wishes, Jan-Mathijs Schoffelen On 31 Jul 2018, at 15:37, Herbert J Gould (hgould) > wrote: Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bahman at neuromotor.org Sun Jul 1 19:43:00 2018 From: bahman at neuromotor.org (Bahman Nasseroleslami) Date: Sun, 1 Jul 2018 18:43:00 +0100 Subject: [FieldTrip] Research Assistant Position in Neural Engineering - Trinity College Dublin, the University of Dublin, Dublin, Ireland Message-ID: Dear all, There is a research assistant position available in Academic Unit of Neurology, Trinity College Dublin, the University of Dublin, Dublin, Ireland. The position is ideally suited to an individual with a BSc/MSc degree who is considering pursuing a PhD degree in longer term. --------------------------------------- Post Specification (033160) Post Title: Research Assistant in Neural Engineering Post Status: 12 month Fixed-term Contract, Full-time Research Group / Department / School: Academic Unit of Neurology, School of Medicine, Trinity College Dublin, the University of Dublin Location: Trinity Biomedical Sciences Institute, Trinity College Dublin, the University of Dublin College Green, Dublin D02 R590, Ireland Reports to: Professor Orla Hardiman/Dr Bahman Nasseroleslami Salary: Appointment will be made on the Research Assistant (Level 1) Salary Scale at a point in line with Government Pay Policy, €21,674 to €28,423 per annum (commensurate with qualifications and experience). Appointment will be made no higher than point 10. Hours of Work: 40 hours per week Closing Date: 12 Noon (Irish Standard Time), 24 July 2018 Please note that Garda vetting will be sought in respect of individuals who come under consideration for a post. Post Summary Applications are invited for a motivated and self-driven individual for the position of research assistant with the Irish ALS Research Group, hosted in the Trinity Biomedical Sciences Institute (TBSI)'s Academic Unit of Neurology. The ideal candidate will have an undergraduate or master's degree in engineering, bioengineering, mathematics, physics, computational biology, or a cognate area. Familiarity with and/or the ability to quickly acquire skills in electrophysiological recordings and analysis (e.g. EEG/EMG), would be highly desirable as would a knowledge of computer programming (MATLAB). --------------------------------------- The detailed job description file (PDF) and the application instructions can be found online at http://jobs.tcd.ie. or directly from https://drive.google.com/file/ d/14Q7DxqobPQCjgKpZ4UJS68xTIlRvnPcd/view?usp=sharing It would be really appreciated if you could share this with those that may be interested. Sincerely Bahman -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Sun Jul 1 20:10:06 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Sun, 1 Jul 2018 14:10:06 -0400 Subject: [FieldTrip] .avg field in GA structure for interaction test Message-ID: Hi Fieldtrip, I am following the tutorial 'How to test an interaction effect using cluster-based permutation tests?' for my own dataset. It says to compute the GA for each condition (my design is 2x2 so a total of 4 GA structures) with keepindividual set to 'yes'. However, when making the difference structures, it says the assignment to the difference structure should be made using the .avg field from 2 of the previous GA structures. But with the keepindividual set to 'yes', I am getting no .avg field in these GA structures to be used. Any advice as to how solve this issue? Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Sun Jul 1 20:16:00 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sun, 1 Jul 2018 18:16:00 +0000 Subject: [FieldTrip] Concatenate different size of trials into single one trial In-Reply-To: References: Message-ID: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> Hi Yadwinder, Why would you want this? For this purpose, ft_appenddata is not your friend, if you want to ‘create a single data matrix’. It concatenate a bunch of matrices, you can use cat(2,data.trial{:}), but this will only be a meaningful operation in a very limited number of cases. Most of the time, the last time point of trial n-1 will not be temporally aligned with the first time point of trial n, and even if that were the case, trial specific filtering, baseline correction, or any trial-specific processing in general will lead to discontinuities in the signals. Best wishes, Jan-Mathijs On 30 Jun 2018, at 15:06, Yadwinder Kaur > wrote: Dear All I have pre-processed my EEG data cutting into different trials (35 trials total) using fieldtrip , now I wish to concatenate them into one single data matrix. The length of each trial varies form each other. ofcourse, ft_appenddata didn't work in this case. I would highly appreciate any help to solve this issue. Thanks in advance. Regards Yadwinder _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From yadwinder.kaur at stud.uni-greifswald.de Sun Jul 1 23:00:55 2018 From: yadwinder.kaur at stud.uni-greifswald.de (Yadwinder Kaur) Date: Sun, 01 Jul 2018 23:00:55 +0200 Subject: [FieldTrip] Concatenate different size of trials into single one trial In-Reply-To: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> References: <9261A5A2-8911-4B5B-8EF5-06970B8EEE47@donders.ru.nl> Message-ID: <3b876e61d0640121b93f7a60decaedd9@groupware.uni-greifswald.de> Hi Jan   Thanks for your reply.My idea was to extract trials (based on stimulus followed by response) , perform preprocessing and at the end concatenate them together, because my aim is to further divide the concatenated segment into four parts to perform latent variable analysis. Am I doing wrong in this way?  Thanks Regards Yadwinder On Sunday, 01-07-2018 at 20:16 Schoffelen, J.M. (Jan Mathijs) wrote: Hi Yadwinder, Why would you want this?  For this purpose, ft_appenddata is not your friend, if you want to ‘create a single data matrix’. It concatenate a bunch of matrices, you can use cat(2,data.trial{:}), but this will only be a meaningful operation in a very limited number of cases. Most of the time, the last time point of trial n-1 will not be temporally aligned with the first time point of trial n, and even if that were the case, trial specific filtering, baseline correction, or any trial-specific processing in general will lead to discontinuities in the signals. Best wishes, Jan-Mathijs On 30 Jun 2018, at 15:06, Yadwinder Kaur wrote: Dear All I have pre-processed my EEG data cutting into different trials (35 trials total) using fieldtrip , now I wish to concatenate them into one single data matrix. The length of each trial varies form each other. ofcourse, ft_appenddata didn't work in this case. I would highly appreciate any help to solve this issue. Thanks in advance. Regards Yadwinder _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From alessandro.orticoni at gmail.com Mon Jul 2 00:21:53 2018 From: alessandro.orticoni at gmail.com (Alessandro Orticoni) Date: Mon, 2 Jul 2018 00:21:53 +0200 Subject: [FieldTrip] [Fieldtrip] Line noise Removal In-Reply-To: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> References: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> Message-ID: Dear Jan-Mathijs, Thanks a lot for your reply and your tips. Actually I've already segmented the data in 30 seconds epochs, and the reason why I did it is that these are sleep data: so I should keep this length because of the night scoring. I tried to enlarge the notch too, but it still doesn't work; the spectra before and after the filtering are exactly the same. Best, Alessandro Il giorno gio 28 giu 2018 alle ore 19:35 Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> ha scritto: > Dear Alessandro, > > Given the code you provided it looks as if you have one single very long > trial that you subject to dft-filtering. If the power line fluctuations > actually do vary a bit in amplitude, which is likely (particularly given > long sections of data), the pure 50 (or 60) Hz sinusoid will get some > ‘bandwidth’, so the removal won’t be perfect. I’d recommend to call > ft_redefinetrial first, and then do a second call to ft_preprocessing with > the dftfilter switched on. Yet, I’d expect that with 30 s segments it still > won’t work that well. In this case you could widen the notch a bit by > specifying cfg.dftfreq = 50+(-n:n)./30;, with n put to a small number, e.g. > <=3. However, unless you have good reasons to have the data chopped in > half-minute segments, I’d also consider to reduce this length, because you > probably do not need to have a 1/30 Hz frequency resolution in your > spectral decomposition. > > Best wishes, > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Associate PI, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > > > On 28 Jun 2018, at 16:22, Alessandro Orticoni < > alessandro.orticoni at gmail.com> wrote: > > Dear experts, > > I'm basically a beginner in coding with Fieldtrip, and I'm having a > problem with line noise filtering. > I would like to remove it from the heart rate signal, and I tried just > typing 'yes' at the option cfg.dftfilter. > But is doesn't seem to work, since the power spectrum contains the 50Hz > and her harmonics even after the filtering. > > You can find the code in the following lines: > > %% ===FREQUENCY Pre Filtering VERIFICATION=== > fs=data.fsample; > > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'ECG 2'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.pad = 'nextpow2'; > cfg.foilim = [0.3 fs/2]; % teorema di Nyquist > freq_epoched_Cz = ft_freqanalysis(cfg, data_epoched_Cz); > > %% ===Plot Spectra=== > figure; > plot(freq_epoched_Cz.freq,mag2db(freq_epoched_Cz.powspctrm)); > > %% ===Filtering=== > cfg = []; > cfg.channel = {'ECG 2'}; > cfg.dftfilter = 'yes'; > ECG_Filtered = ft_preprocessing(cfg,data_Cz); > > cfg = []; > cfg.length = 30; % in seconds; > cfg.overlap = 0; > data_epoched_ECG_Filtered = ft_redefinetrial(cfg, ECG_Filtered); > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.pad = 'nextpow2'; > cfg.foilim = [0.3 fs/2]; % teorema di Nyquist > freq_epoched_Cz_Filtered = ft_freqanalysis(cfg, data_epoched_ECG_Filtered); > > %% ===Plot Spectra=== > > plot(freq_epoched_Cz_Filtered.freq,mag2db(freq_epoched_Cz_Filtered.powspctrm)); > > Thanks a lot. > > Kind regards, > Alessandro Orticoni > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Mon Jul 2 14:37:08 2018 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Mon, 2 Jul 2018 14:37:08 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel Message-ID: Dear Fieldtrippers, I have followed the Salzburg tutorial (http://www.fieldtriptoolbox. org/tutorial/salzburg) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. Best regards, Uri Ramirez University of Würzburg -------------- next part -------------- An HTML attachment was scrubbed... URL: From uwe.graichen at tu-ilmenau.de Mon Jul 2 14:46:06 2018 From: uwe.graichen at tu-ilmenau.de (Uwe Graichen) Date: Mon, 2 Jul 2018 14:46:06 +0200 Subject: [FieldTrip] =?utf-8?q?8th_International_Summer_School_=E2=80=9EMu?= =?utf-8?q?ltimodal_integration_of_brain_measurements_in_research_and_clin?= =?utf-8?q?ical_practice=E2=80=9C?= In-Reply-To: References: Message-ID: <0e7c5650-27bf-6225-9d8b-a651ec60c978@tu-ilmenau.de> Dear colleagues, we are pleased to announce the 8th International Summer School in Biomedical Engineering „Multimodal integration of brain measurements in research and clinical practice“, 1st – 12th October 2018 in Chengdu, China. This event stands in the tradition of a series of successful summer schools on hot themes in biomedical engineering, dedicated to intense learning in the fruitful atmosphere of tight interaction between students and world-leading specialists. This year’s summer school is devoted to EEG/MEG source reconstruction technologies in the frame work of multimodal integration of brain measurements in research and clinical practice. In particular, the 8th International Summer School on Biomedical Engineering will focus on methodological approaches and challenges, measurement devices and characteristics, types of underlying theoretic modeling, specifics of data analysis, ability to derive conclusions about neuroscientific meaning. It will cover both theoretical foundations and practical applications. We aim at a thorough understanding of the underlying mechanisms. Thus, we will develop a critical view on current applications and possible future developments. The second important aim of the summer school consists in providing contact with both leading experts in the field and other students with similar interests, thereby facilitating the exchange of ideas on latest developments in the field. Target Group: - PhD students - Advanced Master students - Researchers entering the field of brain measurement and stimulation techniques Further Information about the 8th International Summer School in Biomedical Engineering: www.bme-school.org We would be happy to receive your application. Please pass this announcement to your colleagues who might be interested. Sincerely, Pedro Antonio Valdés-Sosa Dezhong Yao Jens Haueisen Thomas Knösche From tzvetan.popov at uni-konstanz.de Mon Jul 2 16:54:54 2018 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 2 Jul 2018 16:54:54 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: References: Message-ID: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Dear Uri, the solution to the problem (mesh inflation) is outlined in this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting?s[]=natmeg&s[]=headmodel#procedure Scroll down to the section "Construct the EEG volume conduction model" Good luck, tzvetan > Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos : > > Dear Fieldtrippers, > > I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.org/tutorial/salzburg ) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. > > What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? > > The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. > > Best regards, > > Uri Ramirez > University of Würzburg > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 2 17:47:48 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 2 Jul 2018 15:47:48 +0000 Subject: [FieldTrip] [Fieldtrip] Line noise Removal In-Reply-To: References: <57F427CD-DB64-4A98-A8D6-55810F80E4AA@donders.ru.nl> Message-ID: please have a look at the following piece of documentation: http://www.fieldtriptoolbox.org/faq/why_is_there_a_residual_50hz_line-noise_component_after_applying_a_dft_filter?s[]=dftfilter Jan-Mathijs On 2 Jul 2018, at 00:21, Alessandro Orticoni > wrote: Dear Jan-Mathijs, Thanks a lot for your reply and your tips. Actually I've already segmented the data in 30 seconds epochs, and the reason why I did it is that these are sleep data: so I should keep this length because of the night scoring. I tried to enlarge the notch too, but it still doesn't work; the spectra before and after the filtering are exactly the same. Best, Alessandro Il giorno gio 28 giu 2018 alle ore 19:35 Schoffelen, J.M. (Jan Mathijs) > ha scritto: Dear Alessandro, Given the code you provided it looks as if you have one single very long trial that you subject to dft-filtering. If the power line fluctuations actually do vary a bit in amplitude, which is likely (particularly given long sections of data), the pure 50 (or 60) Hz sinusoid will get some ‘bandwidth’, so the removal won’t be perfect. I’d recommend to call ft_redefinetrial first, and then do a second call to ft_preprocessing with the dftfilter switched on. Yet, I’d expect that with 30 s segments it still won’t work that well. In this case you could widen the notch a bit by specifying cfg.dftfreq = 50+(-n:n)./30;, with n put to a small number, e.g. <=3. However, unless you have good reasons to have the data chopped in half-minute segments, I’d also consider to reduce this length, because you probably do not need to have a 1/30 Hz frequency resolution in your spectral decomposition. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Associate PI, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 28 Jun 2018, at 16:22, Alessandro Orticoni > wrote: Dear experts, I'm basically a beginner in coding with Fieldtrip, and I'm having a problem with line noise filtering. I would like to remove it from the heart rate signal, and I tried just typing 'yes' at the option cfg.dftfilter. But is doesn't seem to work, since the power spectrum contains the 50Hz and her harmonics even after the filtering. You can find the code in the following lines: %% ===FREQUENCY Pre Filtering VERIFICATION=== fs=data.fsample; cfg = []; cfg.output = 'pow'; cfg.channel = 'ECG 2'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.pad = 'nextpow2'; cfg.foilim = [0.3 fs/2]; % teorema di Nyquist freq_epoched_Cz = ft_freqanalysis(cfg, data_epoched_Cz); %% ===Plot Spectra=== figure; plot(freq_epoched_Cz.freq,mag2db(freq_epoched_Cz.powspctrm)); %% ===Filtering=== cfg = []; cfg.channel = {'ECG 2'}; cfg.dftfilter = 'yes'; ECG_Filtered = ft_preprocessing(cfg,data_Cz); cfg = []; cfg.length = 30; % in seconds; cfg.overlap = 0; data_epoched_ECG_Filtered = ft_redefinetrial(cfg, ECG_Filtered); cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.pad = 'nextpow2'; cfg.foilim = [0.3 fs/2]; % teorema di Nyquist freq_epoched_Cz_Filtered = ft_freqanalysis(cfg, data_epoched_ECG_Filtered); %% ===Plot Spectra=== plot(freq_epoched_Cz_Filtered.freq,mag2db(freq_epoched_Cz_Filtered.powspctrm)); Thanks a lot. Kind regards, Alessandro Orticoni _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maxime.ferez at gmail.com Tue Jul 3 09:57:19 2018 From: maxime.ferez at gmail.com (maxime ferez) Date: Tue, 3 Jul 2018 09:57:19 +0200 Subject: [FieldTrip] Problems with "filter_with_correction" Message-ID: Dear all, I have a question about Fieldtrip artifact-rejection. I find myself having a problem that I do not know how to solve. I am currently working on a pc a little old (~ 5 years) and my analyzes worked properly, or at least I had no bug. When I changed my pc the problem has arrived. I have an error message "Calculated filter coefficients have poles on or outside the unit circle and will not be stable. Try a higher cutoff frequency or a different type/order of filter" that appears in the "filter_with_correction" function .The problem seems to occur during the "roots" function of Matlab. I verified and the vector that is introduced is exactly the same in both cases, but after the function “roots” runs the result differs slightly and induces the error message above. Has anyone ever had this problem or know where the problem might come from? On both pcs I have exactly the same versions of Matlab (R2017a) and fieldtrip (fieldtrip-20171004 and fieldtrip-20180626). Scripts and data are also identical in all cases. I have tried several configurations but failed to find the solution: - Ubuntu 16.04 machine about 5 years -> OK - Ubuntu 16.04 machine about 2 years -> Not OK The two machines above are identical in all softwares (deployed with script in PXE) - Fedora 27 machine about 2 years -> Not OK - Ubuntu 16.04 about 2 years -> Not OK - Fedora 17 about 8 years old -> OK - Centos7 machine less than a year -> Not OK To conclude, the script only works on old hardware but this does not seem logical as an explanation. Best regards, Maxime Ferez -- Maxime Ferez, ingénieur d'étude Centre de Recherche en Neuroscience de Lyon (CRNL) Inserm équipe Dycog Bron, France -------------- next part -------------- An HTML attachment was scrubbed... URL: From urieduardo at gmail.com Tue Jul 3 11:08:14 2018 From: urieduardo at gmail.com (=?UTF-8?Q?Uri_Eduardo_Ram=C3=ADrez_Pasos?=) Date: Tue, 3 Jul 2018 11:08:14 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> References: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Message-ID: Dear Tzvetan, That worked perfectly, thank you! Are there guidelines for use of mesh inflation? E.g., does dilation by two voxels greatly bias source reconstruction? If one inflates a subject's mesh, must one then inflate all other subjects' meshes to the same degree? Thank you again, Uri 2018-07-02 16:54 GMT+02:00 Tzvetan Popov : > Dear Uri, > > the solution to the problem (mesh inflation) is outlined in this tutorial: > http://www.fieldtriptoolbox.org/tutorial/natmeg/ > dipolefitting?s[]=natmeg&s[]=headmodel#procedure > > Scroll down to the section "Construct the EEG volume conduction model" > > Good luck, > tzvetan > > > Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos < > urieduardo at gmail.com>: > > Dear Fieldtrippers, > > I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.o > rg/tutorial/salzburg) to conduct EEG source reconstruction, but it > doesn't work with some subjects' segmented mri files (whether I use dipoli > or bemcp), due to intersections between surfaces. > > What are the typical trouble-shooting steps for this situation? I tried > using a lower number of vertices for the mesh ([800 800 600]), to no avail. > Are there any guidelines for the number of vertices? > > The number of subjects in my study is limited, so I would be loathe to > exclude any subject from the analysis. > > Best regards, > > Uri Ramirez > University of Würzburg > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From m.manahova at gmail.com Tue Jul 3 11:26:10 2018 From: m.manahova at gmail.com (Mariya Manahova) Date: Tue, 3 Jul 2018 11:26:10 +0200 Subject: [FieldTrip] .avg field in GA structure for interaction test In-Reply-To: References: Message-ID: Hi Paul, With keepindividual = 'yes', your parameter of interest is 'individual'. So try using cfg.parameter = 'individual' (instead of cfg.parameter = 'avg' which is probably the default) and that should work. All the best, Marisha On Sun, Jul 1, 2018 at 8:11 PM Paul Dhami wrote: > Hi Fieldtrip, > > I am following the tutorial 'How to test an interaction effect using > cluster-based permutation tests?' for my own dataset. It says to compute > the GA for each condition (my design is 2x2 so a total of 4 GA structures) > with keepindividual set to 'yes'. However, when making the difference > structures, it says the assignment to the difference structure should be > made using the .avg field from 2 of the previous GA structures. But with > the keepindividual set to 'yes', I am getting no .avg field in these GA > structures to be used. Any advice as to how solve this issue? > > Best, > Paul > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Tue Jul 3 11:36:54 2018 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Tue, 3 Jul 2018 11:36:54 +0200 Subject: [FieldTrip] Problems with ft_prepare_headmodel In-Reply-To: References: <4E774233-7C2D-416F-8F6E-F994BA209C70@uni-konstanz.de> Message-ID: Dear Uri, > That worked perfectly, thank you! Are there guidelines for use of mesh inflation? no there aren’t any. > E.g., does dilation by two voxels greatly bias source reconstruction? no > If one inflates a subject's mesh, must one then inflate all other subjects' meshes to the same degree? I would do as minimum as possible and only there when needed. Best tzvetan > > Thank you again, > Uri > > 2018-07-02 16:54 GMT+02:00 Tzvetan Popov >: > Dear Uri, > > the solution to the problem (mesh inflation) is outlined in this tutorial: http://www.fieldtriptoolbox.org/tutorial/natmeg/dipolefitting?s[]=natmeg&s[]=headmodel#procedure > > Scroll down to the section "Construct the EEG volume conduction model" > > Good luck, > tzvetan > > >> Am 02.07.2018 um 14:37 schrieb Uri Eduardo Ramírez Pasos >: >> >> Dear Fieldtrippers, >> >> I have followed the Salzburg tutorial (http://www.fieldtriptoolbox.org/tutorial/salzburg ) to conduct EEG source reconstruction, but it doesn't work with some subjects' segmented mri files (whether I use dipoli or bemcp), due to intersections between surfaces. >> >> What are the typical trouble-shooting steps for this situation? I tried using a lower number of vertices for the mesh ([800 800 600]), to no avail. Are there any guidelines for the number of vertices? >> >> The number of subjects in my study is limited, so I would be loathe to exclude any subject from the analysis. >> >> Best regards, >> >> Uri Ramirez >> University of Würzburg >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdhami06 at gmail.com Wed Jul 4 02:54:37 2018 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 3 Jul 2018 20:54:37 -0400 Subject: [FieldTrip] Submitting a correlation matrix for cluster-based permutation Message-ID: Hi FieldTripers, I was hoping to do a correlation between two sets of EEG datasets in a channel x time fashion. For each (channel,time), I ran a rho correlation between the two EEG datas, and stored the resulting coefficients in a matrix with the dimensions of channel and time. I was hoping to apply a cluster-based permutation testing to correct for multiple comparisons, but as the file I was hoping to submit is a raw matrix, I was hoping for some guidance as to 1) whether this is even an appropriate way of achieving a cluster-corrected correlation matrix and 2) how to implement this with the correlation matrix. Any help would be greatly appreciated. Thank you. Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Jul 4 08:58:47 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 4 Jul 2018 06:58:47 +0000 Subject: [FieldTrip] Submitting a correlation matrix for cluster-based permutation In-Reply-To: References: Message-ID: <54A52603-0F1E-48F0-9141-C8C27A1656FC@donders.ru.nl> Do you have a null hypothesis? What is it you would want to permute? If you just have scalar value per channel/time point, there’s not much you can do. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 4 Jul 2018, at 02:54, Paul Dhami > wrote: Hi FieldTripers, I was hoping to do a correlation between two sets of EEG datasets in a channel x time fashion. For each (channel,time), I ran a rho correlation between the two EEG datas, and stored the resulting coefficients in a matrix with the dimensions of channel and time. I was hoping to apply a cluster-based permutation testing to correct for multiple comparisons, but as the file I was hoping to submit is a raw matrix, I was hoping for some guidance as to 1) whether this is even an appropriate way of achieving a cluster-corrected correlation matrix and 2) how to implement this with the correlation matrix. Any help would be greatly appreciated. Thank you. Paul _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From ablenkmann at gmail.com Fri Jul 6 21:38:15 2018 From: ablenkmann at gmail.com (Alejandro Blenkmann) Date: Fri, 6 Jul 2018 12:38:15 -0700 Subject: [FieldTrip] Neuroscience Lab Engineer Permanent position - University of Oslo, Norway Message-ID: Hi FieldTripers, There is a Lab Engineer Permanent position available in Oslo. https://www.jobbnorge.no/ledige-stillinger/stilling/154793 < https://www.jobbnorge.no/ledige-stillinger/stilling/154793> Best, Alejandro -- Alejandro Blenkmann, PhD Postdoctoral Fellow Front Neurolab Department of Psychology University of Oslo -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Jul 6 21:43:04 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 6 Jul 2018 21:43:04 +0200 Subject: [FieldTrip] Problems with "filter_with_correction" In-Reply-To: References: Message-ID: Hi Maxime, I wouldn't know why this would occur if everything else is the same, except that perhaps your current MATLAB in combination with your OS uses slightly different implementations of filter functions from e.g. another toolbox/other MATLAB versions. In any case, as the function suggests, these problems typically occur for me when the low-pass frequency that is requested is too low for what the data and filter allows. The artefact detection functions probably uses a low/bandpass filter so try increasing the low cutoff, changing the filter order, or the filter type. You might also try using longer trial-lengths. cheers, Stephen On 3 July 2018 at 09:57, maxime ferez wrote: > Dear all, > > I have a question about Fieldtrip artifact-rejection. I find myself having > a problem that I do not know how to solve. I am currently working on a pc a > little old (~ 5 years) and my analyzes worked properly, or at least I had > no bug. When I changed my pc the problem has arrived. I have an error > message "Calculated filter coefficients have poles on or outside the unit > circle and will not be stable. Try a higher cutoff frequency or a different > type/order of filter" that appears in the "filter_with_correction" function > .The problem seems to occur during the "roots" function of Matlab. I > verified and the vector that is introduced is exactly the same in both > cases, but after the function “roots” runs the result differs slightly > and induces the error message above. Has anyone ever had this problem or > know where the problem might come from? On both pcs I have exactly the same > versions of Matlab (R2017a) and fieldtrip (fieldtrip-20171004 and > fieldtrip-20180626). Scripts and data are also identical in all cases. I > have tried several configurations but failed to find the solution: > > - Ubuntu 16.04 machine about 5 years -> OK > > - Ubuntu 16.04 machine about 2 years -> Not OK > > The two machines above are identical in all softwares (deployed with > script in PXE) > > - Fedora 27 machine about 2 years -> Not OK > > - Ubuntu 16.04 about 2 years -> Not OK > > - Fedora 17 about 8 years old -> OK > > - Centos7 machine less than a year -> Not OK > > To conclude, the script only works on old hardware but this does not seem > logical as an explanation. > > Best regards, > > > > Maxime Ferez > > > -- > Maxime Ferez, ingénieur d'étude > Centre de Recherche en Neuroscience de Lyon (CRNL) > Inserm > équipe Dycog > Bron, France > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lindseyrtate at ou.edu Mon Jul 9 06:59:13 2018 From: lindseyrtate at ou.edu (Tate, Lindsey R.) Date: Mon, 9 Jul 2018 04:59:13 +0000 Subject: [FieldTrip] Adding MRI Overlay to ft_sourceplot Images Message-ID: Hello fieldtrip community, I have a project with a lot of source analysis of EEG data. I'm using ft_sourceanalysis and ft_sourceplot. I would like to add standard (e.g., Colin 27) MRI slices to these images as an overlay (underlay?) for reference. Is there a way to do this? How do I align the MRI with my source space? Example code for ft_sourceanalysis and ft_sourceplot are provided below my signature in case you need the reference. Thank you, Lindsey Tate PhD Candidate University of Oklahoma lindseyrtate at ou.edu /// %baseline period source analysis cfg = []; cfg.elec = elec ; cfg.method = 'dics'; cfg.frequency = 25 ; cfg.grid = grid; cfg.headmodel = headmodel; cfg.dics.projectnoise = 'yes'; cfg.dics.lambda = 0; cfg.latency = -0.7490 ; [presource25] = ft_sourceanalysis(cfg, prefreq25) %from ft_freqanalysis %same is done for a post-stimulus period, called pmsource25; code omitted for brevity %difference between pre- and post-stimulus periods source25diff = pmsource25 ; source25diff.avg.pow = (pmsource25.avg.pow - presource25.avg.pow) ./ presource25.avg.pow; %interpolate the difference between pre- and post-stimulus periods cfg = []; cfg.downsample = 2; cfg.parameter = 'avg.pow'; source25DiffInt = ft_sourceinterpolate(cfg, source25diff, grid); %plot cfg = []; cfg.method = 'slice'; cfg.funparameter = 'avg.pow'; cfg.maskparameter = cfg.funparameter; cfg.funcolorlim = [-1 2]; cfg.opacitylim = [-5 1]; cfg.opacitymap = 'rampup'; ft_sourceplot(cfg, source25DiffInt); -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon Jul 9 08:01:33 2018 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 9 Jul 2018 08:01:33 +0200 Subject: [FieldTrip] Adding MRI Overlay to ft_sourceplot Images In-Reply-To: References: Message-ID: Hi Lindsey, What is "grid" bases on? Is this the individual mri or a standard mri? In any case, you can use ft_sourceinterpolate to interpolate to a standard MRI. Then, you can set the anatomy parameter in ft_spurceplot. Check the details of both functions for the relevant cfg settings. Hope this helps, Cheers, Julian Tate, Lindsey R. schrieb am Mo. 9. Juli 2018 um 07:35: > Hello fieldtrip community, > > > I have a project with a lot of source analysis of EEG data. I'm using > ft_sourceanalysis and ft_sourceplot. I would like to add standard (e.g., > Colin 27) MRI slices to these images as an overlay (underlay?) for > reference. Is there a way to do this? How do I align the MRI with my source > space? > > > Example code for ft_sourceanalysis and ft_sourceplot are provided below my > signature in case you need the reference. > > > Thank you, > > > Lindsey Tate > PhD Candidate > University of Oklahoma > lindseyrtate at ou.edu > > > /// > > %baseline period source analysis > > cfg = []; > cfg.elec = elec ; > cfg.method = 'dics'; > cfg.frequency = 25 ; > cfg.grid = grid; > cfg.headmodel = headmodel; > cfg.dics.projectnoise = 'yes'; > cfg.dics.lambda = 0; > cfg.latency = -0.7490 ; > [presource25] = ft_sourceanalysis(cfg, prefreq25) %from ft_freqanalysis > > %same is done for a post-stimulus period, called pmsource25; code omitted > for brevity > > %difference between pre- and post-stimulus periods > source25diff = pmsource25 ; > source25diff.avg.pow = (pmsource25.avg.pow - presource25.avg.pow) ./ > presource25.avg.pow; > > %interpolate the difference between pre- and post-stimulus periods > cfg = []; > cfg.downsample = 2; > cfg.parameter = 'avg.pow'; > source25DiffInt = ft_sourceinterpolate(cfg, source25diff, grid); > > %plot > cfg = []; > cfg.method = 'slice'; > cfg.funparameter = 'avg.pow'; > cfg.maskparameter = cfg.funparameter; > cfg.funcolorlim = [-1 2]; > cfg.opacitylim = [-5 1]; > cfg.opacitymap = 'rampup'; > ft_sourceplot(cfg, source25DiffInt); > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.maye at uke.de Mon Jul 9 10:15:33 2018 From: a.maye at uke.de (Alexander Maye) Date: Mon, 9 Jul 2018 10:15:33 +0200 Subject: [FieldTrip] Call for Participation: summer school on 'mind reading technology' Message-ID: <7471317.dIuGlEM9So@mars> Dear colleagues, Below I forward an announcement for the above-mentioned summer school which readers of this list may find interesting. Best regards, Alexnder Maye. ---------- Weitergeleitete Nachricht ---------- Betreff: [CML] Call for Participation: summer school on 'mind reading technology' Datum: Donnerstag, 5. Juli 2018, 09:44:08 CEST Von: Dan Zhang An: cml at informatik.uni-hamburg.de Kopie: 洪波 Dear colleagues, Dr. Bo Hong and I are organizing a summer school during August 13-17 in Beijing. The topic of this summer school is ‘mind reading technology’ and we have invited the leading scientists in this field to give lectures. Please help us spread out the message and please contact us if you are interested. Many thanks in advance! Best, Dan -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- A non-text attachment was scrubbed... Name: Program of 2018 ISSNE.pdf Type: application/pdf Size: 115677 bytes Desc: Program of 2018 ISSNE.pdf URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ISSNE2018 Flyer.pdf Type: application/pdf Size: 474936 bytes Desc: ISSNE2018 Flyer.pdf URL: From krugliakova.es at gmail.com Tue Jul 10 21:36:19 2018 From: krugliakova.es at gmail.com (Elena Krugliakova) Date: Tue, 10 Jul 2018 21:36:19 +0200 Subject: [FieldTrip] phase-amplitude coupling measure Message-ID: Dear FieldTrip community, I have a question related to the ft_crossfrequencyanalysis: which phase - amplitude coupling measure for EEG is the least affected by the signal-to-noise ratio? If I have two conditions and in one of them the power of high frequency is much stronger (better signal-to-noise ratio), what would be the best measure to compare the coupling between the phase of slow frequency and the amplitude of high frequency? Thank you! Kind Regards, Elena Krugliakova -------------- next part -------------- An HTML attachment was scrubbed... URL: From maximilien.chaumon at gmail.com Fri Jul 13 18:20:21 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Fri, 13 Jul 2018 18:20:21 +0200 Subject: [FieldTrip] git repo quite big. How to save space? Message-ID: Dear all, I have several copies of FieldTrip for several projects shared with others. Each has its own copy of FieldTrip, which is at the moment a 1.7GB folder, of which 1GB is taken by the .git directory. Would there be an easy way to prune the repository where needed? Best, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From christophe.grova at mcgill.ca Sun Jul 15 14:42:58 2018 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Sun, 15 Jul 2018 12:42:58 +0000 Subject: [FieldTrip] Postdoctoral Fellowship in Multimodal Neuroimaging of Sleep and Cognition at Concordia PERFORM centre In-Reply-To: References: , Message-ID: Dear colleagues, We are presently recruiting a Postdoctoral fellow in Multimodal Neuroimaging of Sleep and Cognition. This position consists in a prestigious Horizon Postdoctoral Fellowship at Concordia University, in Montréal (Québec, Canada). The fellow will have the opportunity to setup and conduct advanced neuroimaging studies in clinical and healthy samples, as well as to analyze and write up findings of previously collected human neuroimaging data. He/she will also have the opportunity to develop and evaluate new multimodal data analysis approaches, as for instance the study of sleep patterns combining high-density Electro-EncephaloGraphy (EEG) with functional Magnetic Resonance Imaging and for the very first time EEG with Near-Infra Red Spectroscopy (NIRS) during whole night recordings. These techniques will allow addressing links between bioelectrical neuronal activity and hemodynamic processes during sleep. He/she will be based at Concordia University (Montreal, Quebec), jointly supervised by Dr. Christophe Grova PhD and Dr. Thanh Dang-Vu MD-PhD, and will work in a highly multidisciplinary environment (neurosciences, kinesiology, physics, engineering, psychology) and in collaboration with multiple academic and hospital institutions in Montreal (PERFORM Center, Centre de Recherche de l’Institut Universitaire de Gériatrie de Montréal [CRIUGM], Montreal Neurological Institute [MNI]). The research themes that will be addressed by the Fellow will include: * The neural mechanisms of sleep, sleep deprivation and sleep disorders (chronic insomnia, central disorders of hypersomnolence), and their relationship with cognition. * Developing and evaluating methods dedicated to the analysis of multimodal neuroimaging data for sleep studies: (i) simultaneous EEG/fMRI, and (2) simultaneous EEG/NIRS, including the analysis of functional connectivity and brain network analysis The PERFORM Centre is a 8,000 m2 research facility including eight inter-related research platforms, such as a state of the art sleep laboratory (3 bedrooms with polysomnography and high-density EEG) and a fully equipped imaging suite (3T MRI, high-density EEG, NIRS, TMS, SPECT-CT, PET-CT, Ultrasound and Dexa) entirely dedicated to research (http://www.concordia.ca/research/perform.html ). Applicants must have a PhD (or close to completion) in a related field (e.g., neurosciences, computer science, (bio)medical engineering, physics). Experience in the analysis of hemodynamic signals from fMRI or NIRS is important. Applicants should have strong knowledge of Matlab and/or experience in analysis of neuroimaging, excellent organizational skills, an aptitude for teamwork, good writing skills and a productive publication record. Experience in one or more aspects of the research themes will constitute an asset. Salary will consist of 47,500 $/year (plus benefits) for 2 years. The position has a flexible start date. Interested applicants should submit their application as described in the following link, before September 1st 2018: http://www.concordia.ca/sgs/postdoctoral-fellows/funding/horizon/descriptions/5007.html Review of applications will begin as they are received and will continue until the position has been filled. All requests for additional information should also be directed to them. Only those candidates selected to interview will be contacted. Dr. Christophe Grova, Ph.D, Dr. Thanh Dang-Vu, M.D., Ph.D. Associate Professor Associate Professor, Neurologist, Department of Physics, Concordia U. Adjunct Professor in Biomedical Engineering, Concordia University Research Chair in Sleep, Neuroimaging and Cognitive Health, Neurology & Neurosurgery, McGill U. christophe.grova at concordia.ca Department of Health, Kinesiology and Applied Physiology, Concordia U. Assoc. Director for Clinical Research, CRIUGM tt.dangvu at concordia.ca For more information about our current research programs, please visit the lab websites: https://www.concordia.ca/artsci/physics/research/grova-research-group.html https://scnlab.com *************************** Christophe Grova, PhD Associate Professor, Physics Dpt, Concordia University PERFORM centre, Concordia University, Chair of PERFORM Applied Bio-Imaging Committee (ABC) Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute - epilepsy group Centre de Recherches en Mathématiques Physics Dpt Concordia University - Loyola Campus - Office SP 365.12 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Phone: (514) 848-2424 ext.4221 Biomedical Engineering Department McGill University - Room 304 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 Phone : (514) 398 2516 Fax : (514) 398 7461 email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca web: Explore Concordia: http://explore.concordia.ca/christophe-grova Physics, Concordia University: http://www.concordia.ca/artsci/physics/faculty.html?fpid=christophe-grova McGill University: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** [X] -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauppe.s at gmail.com Mon Jul 16 00:09:30 2018 From: sauppe.s at gmail.com (Sebastian Sauppe) Date: Mon, 16 Jul 2018 00:09:30 +0200 Subject: [FieldTrip] Error using ft_clusterplot: unsupported dimord unknown_freq_time Message-ID: Dear FieldTrip list users, I am trying to analyze a between-subjects experiment with cluster-based permutation tests. In setting up the tests, I followed the tutorial on the FieldTrip site (http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_freq#between-trial_experiments ). However, when I try to plot the results, I get the error „Error using ft_clusterplot (line 161) unsupported dimord unknown_freq_time“. I am very new to FieldTrip and its probably a rookie mistake that I am making but I’d be very grateful if someone who knows could point out what I might be doing wrong here. Here is the code: %% run cluster-based permutation test % set up cfg for ft_freqstatistics cfg = []; cfg.channel = 'all'; cfg.latency = 'all'; cfg.frequency = 'all'; cfg.method = 'montecarlo'; cfg.statistic = 'ft_statfun_indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 20; % to make it quick % prepare_neighbours determines what electrodes may form clusters cfg_neighb.method = 'distance'; cfg.neighbours = ft_prepare_neighbours(cfg_neighb, freq_IPFV); cfg.spmversion = 'spm12'; design = zeros(1,size(freq_IPFV.powspctrm,1) + size(freq_PFV.powspctrm,1)); design(1,1:size(freq_IPFV.powspctrm,1)) = 1; design(1,(size(freq_IPFV.powspctrm,1)+1):(size(freq_IPFV.powspctrm,1)+... size(freq_PFV.powspctrm,1))) = 2; cfg.design = design; cfg.ivar = 1; [stat] = ft_freqstatistics(cfg, freq_IPFV, freq_PFV); %% plot the results cfg = []; cfg.keeptrials = 'no'; freqdesc_IPFV = ft_freqdescriptives(cfg, freq_IPFV); freqdesc_PFV = ft_freqdescriptives(cfg, freq_PFV); stat.raweffect = freqdesc_IPFV.powspctrm - freqdesc_PFV.powspctrm; cfg = []; cfg.alpha = 0.025; cfg.parameter = 'raweffect'; cfg.zlim = [-1e-27 1e-27]; cfg.layout = 'GSN-HydroCel-129.sfp'; layout = ft_prepare_layout(cfg); cfg.layout = layout; ft_clusterplot(cfg, stat); Kind regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Phillip.Alday at mpi.nl Mon Jul 16 08:59:22 2018 From: Phillip.Alday at mpi.nl (Alday, Phillip) Date: Mon, 16 Jul 2018 06:59:22 +0000 Subject: [FieldTrip] git repo quite big. How to save space? In-Reply-To: References: Message-ID: <6002072a-9c62-bd54-34b0-fffc464db833@mpi.nl> There are a few things you can do: 1. Garbage collection and re-packing to get git to re-organize itself into a more compact layout : git gc --aggressive If that takes too long, do it without --aggressive : it will be much faster although potentially not as effective. 2. Use shallow clones (i.e. ones missing older history). 3. Clone from one local copy to another -- if the clones are on the same file system, then git will use hard links and git objects common to both repositories will be "shared" and only take up space equal to one instance. Note that garbage collection, re-packing, etc. can break this and lead to each clone having its own copies. 4. Don't keep a copy of FieldTrip in each project and start using paths, version management, etc. more effectively. You definitely should know which version of the software you used for a given analysis for reproducibility/replicability, but there are more efficient ways to do that than keeping a local copy. This is not meant to be harsh, but just trying to address a potential "XY problem" (https://meta.stackexchange.com/questions/66377/what-is-the-xy-problem). Best, Phillip Date: Fri, 13 Jul 2018 18:20:21 +0200 > From: Maximilien Chaumon > To: FieldTrip discussion list > Subject: [FieldTrip] git repo quite big. How to save space? > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I have several copies of FieldTrip for several projects shared with others. > Each has its own copy of FieldTrip, which is at the moment a 1.7GB folder, > of which 1GB is taken by the .git directory. Would there be an easy way to > prune the repository where needed? > > Best, > Max > From Amie.Fairs at mpi.nl Tue Jul 17 09:57:48 2018 From: Amie.Fairs at mpi.nl (Fairs, Amie) Date: Tue, 17 Jul 2018 07:57:48 +0000 Subject: [FieldTrip] Missing templates for planar gradients Message-ID: Dear FieldTrip list, Apologies for what seems like a silly question. I am calculating the planar gradient for my MEG data because it was recorded from axial gradiometers (on a CTF system with a 275 layout). I'm following the FieldTrip tutorial to calculate the planar gradient, and I would like to use the method 'template' to do so, and then specify a pre-existing template. From reading about which templates are shipped with FieldTrip (http://www.fieldtriptoolbox.org/template/neighbours) I think a bunch of templates should be found in FieldTrip, including the CTF 275 neighbourhood template. However, in my FieldTrip version there are no templates (the template folder is just empty). When I run ft_prepare_neighbours, specifying cfg.template = 'template' and cfg.template = 'CTF275_neighb.mat', I get an error message saying 'Template file could not be found'. Does anyone know where I can get hold of this template? I can't find a way to download other than downloading a new version of FieldTrip and seeing if it is there. The FieldTrip version I am using is fieldtrip-20170918 (so much after the 2011 template intro), on a Windows 7 computer, and matlab R2016a. I also calculated the planar gradient using the method 'triangulation' to check it isn't a data bug somehow, but that works perfectly fine (though I'd prefer the template option). Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Arana at donders.ru.nl Tue Jul 17 10:26:07 2018 From: S.Arana at donders.ru.nl (Arana, S.L. (Sophie)) Date: Tue, 17 Jul 2018 08:26:07 +0000 Subject: [FieldTrip] Missing templates for planar gradients In-Reply-To: References: Message-ID: Hi Amie, have you tried downloading the template file directly from the GitHub repo? https://github.com/fieldtrip/fieldtrip/tree/master/template/neighbours Best, Sophie ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Fairs, Amie [Amie.Fairs at mpi.nl] Sent: Tuesday, July 17, 2018 9:57 AM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Missing templates for planar gradients Dear FieldTrip list, Apologies for what seems like a silly question. I am calculating the planar gradient for my MEG data because it was recorded from axial gradiometers (on a CTF system with a 275 layout). I'm following the FieldTrip tutorial to calculate the planar gradient, and I would like to use the method 'template' to do so, and then specify a pre-existing template. From reading about which templates are shipped with FieldTrip (http://www.fieldtriptoolbox.org/template/neighbours) I think a bunch of templates should be found in FieldTrip, including the CTF 275 neighbourhood template. However, in my FieldTrip version there are no templates (the template folder is just empty). When I run ft_prepare_neighbours, specifying cfg.template = 'template' and cfg.template = 'CTF275_neighb.mat', I get an error message saying 'Template file could not be found'. Does anyone know where I can get hold of this template? I can't find a way to download other than downloading a new version of FieldTrip and seeing if it is there. The FieldTrip version I am using is fieldtrip-20170918 (so much after the 2011 template intro), on a Windows 7 computer, and matlab R2016a. I also calculated the planar gradient using the method 'triangulation' to check it isn't a data bug somehow, but that works perfectly fine (though I'd prefer the template option). Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauppe.s at gmail.com Thu Jul 19 09:01:59 2018 From: sauppe.s at gmail.com (Sebastian Sauppe) Date: Thu, 19 Jul 2018 09:01:59 +0200 Subject: [FieldTrip] Averaging over frequencies in ft_freqstatistics Message-ID: Dear FieldTrip list, I am testing different frequency bands with cluster-based permutation tests using ft_freqstatistics. For this, I use cfg.avgoverfreq = ‚yes‘ when setting up the test. However, I am unsure about how FieldTrip actually handles the frequency averaging. Does it take the mean power of the specified frequencies or does it take the power of the mean frequency? This is the relevant code I use: ... cfg.frequency = [3 8]; cfg.avgoverfreq = 'yes‘; ... [stat] = ft_freqstatistics(cfg, data_A, data_B); In my data, I have the following frequencies: [3.9062 4.8828 6.1035 7.0801 8.0566 9.0332 10.0098]. In the statistics output, after averaging over frequencies stat.freq returns only 6.0059. This is the mean of the frequencies between 3 and 8. But I can’t see whether somehow the power of that frequency was assessed in the test or whether the power of all frequencies in that band was first averaged and then tested. Regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 -------------- next part -------------- An HTML attachment was scrubbed... URL: From 007abhisheksamal at gmail.com Fri Jul 20 14:52:14 2018 From: 007abhisheksamal at gmail.com (Abhishek Samal) Date: Fri, 20 Jul 2018 18:22:14 +0530 Subject: [FieldTrip] Error in using EMG channel as trial definition Message-ID: Sir, This is Abhishek. I am trying to analyse Motor Evoked field MEG data. I have been trying to use the EMG channel as the trial definition for the triggers of epoch creation. But when I use the script that is given in tutorial definition I am getting the following error. The Input cfg = []; cfg.dataset = 'preetham_lt_motor_raw_tsss_mc.fif'; cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 0.5; cfg.trialfun = 'trialfun_emgdetect'; cfg = ft_definetrial(cfg); data = ft_preprocessing(cfg); The Error 306 MEG channel locations transformed Reading preetham_lt_motor_raw_tsss_mc.fif ... Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... Range : 124000 ... 669999 = 62.000 ... 335.000 secs Ready. Reading 124000 ... 669999 = 62.000 ... 335.000 secs... [done] found 0 events created 210265 trials the call to "ft_definetrial" took 528 seconds 306 MEG channel locations transformed Reading preetham_lt_motor_raw_tsss_mc.fif ... Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... Range : 124000 ... 669999 = 62.000 ... 335.000 secs Ready. processing channel { 'EOG001' 'ECG002' 'EEG001' 'EEG002' 'EEG003' 'EEG004' 'EEG005' 'EEG006' 'EEG007' 'EEG008' 'EEG009' 'EEG010' 'EEG011' 'EEG012' 'EEG013' 'EEG014' 'EEG015' 'EEG016' 'EEG017' 'EEG018' 'EEG019' 'EEG020' 'EEG021' 'EEG022' 'EEG023' 'EEG024' 'EEG025' 'EXCI' 'IASX+' 'IASX-' 'IASY+' 'IASY-' 'IASZ+' 'IASZ-' 'IAS_DX' 'IAS_DY' 'IAS_X' 'IAS_Y' 'IAS_Z' 'MEG0111' 'MEG0112' 'MEG0113' 'MEG0121' 'MEG0122' 'MEG0123' 'MEG0131' 'MEG0132' 'MEG0133' 'MEG0141' 'MEG0142' 'MEG0143' 'MEG0211' 'MEG0212' 'MEG0213' 'MEG0221' 'MEG0222' 'MEG0223' 'MEG0231' 'MEG0232' 'MEG0233' 'MEG0241' 'MEG0242' 'MEG0243' 'MEG0311' 'MEG0312' 'MEG0313' 'MEG0321' 'MEG0322' 'MEG0323' 'MEG0331' 'MEG0332' 'MEG0333' 'MEG0341' 'MEG0342' 'MEG0343' 'MEG0411' 'MEG0412' 'MEG0413' 'MEG0421' 'MEG0422' 'MEG0423' 'MEG0431' 'MEG0432' 'MEG0433' 'MEG0441' 'MEG0442' 'MEG0443' 'MEG0511' 'MEG0512' 'MEG0513' 'MEG0521' 'MEG0522' 'MEG0523' 'MEG0531' 'MEG0532' 'MEG0533' 'MEG0541' 'MEG0542' 'MEG0543' 'MEG0611' 'MEG0612' 'MEG0613' 'MEG0621' 'MEG0622' 'MEG0623' 'MEG0631' 'MEG0632' 'MEG0633' 'MEG0641' 'MEG0642' 'MEG0643' 'MEG0711' 'MEG0712' 'MEG0713' 'MEG0721' 'MEG0722' 'MEG0723' 'MEG0731' 'MEG0732' 'MEG0733' 'MEG0741' 'MEG0742' 'MEG0743' 'MEG0811' 'MEG0812' 'MEG0813' 'MEG0821' 'MEG0822' 'MEG0823' 'MEG0911' 'MEG0912' 'MEG0913' 'MEG0921' 'MEG0922' 'MEG0923' 'MEG0931' 'MEG0932' 'MEG0933' 'MEG0941' 'MEG0942' 'MEG0943' 'MEG1011' 'MEG1012' 'MEG1013' 'MEG1021' 'MEG1022' 'MEG1023' 'MEG1031' 'MEG1032' 'MEG1033' 'MEG1041' 'MEG1042' 'MEG1043' 'MEG1111' 'MEG1112' 'MEG1113' 'MEG1121' 'MEG1122' 'MEG1123' 'MEG1131' 'MEG1132' 'MEG1133' 'MEG1141' 'MEG1142' 'MEG1143' 'MEG1211' 'MEG1212' 'MEG1213' 'MEG1221' 'MEG1222' 'MEG1223' 'MEG1231' 'MEG1232' 'MEG1233' 'MEG1241' 'MEG1242' 'MEG1243' 'MEG1311' 'MEG1312' 'MEG1313' 'MEG1321' 'MEG1322' 'MEG1323' 'MEG1331' 'MEG1332' 'MEG1333' 'MEG1341' 'MEG1342' 'MEG1343' 'MEG1411' 'MEG1412' 'MEG1413' 'MEG1421' 'MEG1422' 'MEG1423' 'MEG1431' 'MEG1432' 'MEG1433' 'MEG1441' 'MEG1442' 'MEG1443' 'MEG1511' 'MEG1512' 'MEG1513' 'MEG1521' 'MEG1522' 'MEG1523' 'MEG1531' 'MEG1532' 'MEG1533' 'MEG1541' 'MEG1542' 'MEG1543' 'MEG1611' 'MEG1612' 'MEG1613' 'MEG1621' 'MEG1622' 'MEG1623' 'MEG1631' 'MEG1632' 'MEG1633' 'MEG1641' 'MEG1642' 'MEG1643' 'MEG1711' 'MEG1712' 'MEG1713' 'MEG1721' 'MEG1722' 'MEG1723' 'MEG1731' 'MEG1732' 'MEG1733' 'MEG1741' 'MEG1742' 'MEG1743' 'MEG1811' 'MEG1812' 'MEG1813' 'MEG1821' 'MEG1822' 'MEG1823' 'MEG1831' 'MEG1832' 'MEG1833' 'MEG1841' 'MEG1842' 'MEG1843' 'MEG1911' 'MEG1912' 'MEG1913' 'MEG1921' 'MEG1922' 'MEG1923' 'MEG1931' 'MEG1932' 'MEG1933' 'MEG1941' 'MEG1942' 'MEG1943' 'MEG2011' 'MEG2012' 'MEG2013' 'MEG2021' 'MEG2022' 'MEG2023' 'MEG2031' 'MEG2032' 'MEG2033' 'MEG2041' 'MEG2042' 'MEG2043' 'MEG2111' 'MEG2112' 'MEG2113' 'MEG2121' 'MEG2122' 'MEG2123' 'MEG2131' 'MEG2132' 'MEG2133' 'MEG2141' 'MEG2142' 'MEG2143' 'MEG2211' 'MEG2212' 'MEG2213' 'MEG2221' 'MEG2222' 'MEG2223' 'MEG2231' 'MEG2232' 'MEG2233' 'MEG2241' 'MEG2242' 'MEG2243' 'MEG2311' 'MEG2312' 'MEG2313' 'MEG2321' 'MEG2322' 'MEG2323' 'MEG2331' 'MEG2332' 'MEG2333' 'MEG2341' 'MEG2342' 'MEG2343' 'MEG2411' 'MEG2412' 'MEG2413' 'MEG2421' 'MEG2422' 'MEG2423' 'MEG2431' 'MEG2432' 'MEG2433' 'MEG2441' 'MEG2442' 'MEG2443' 'MEG2511' 'MEG2512' 'MEG2513' 'MEG2521' 'MEG2522' 'MEG2523' 'MEG2531' 'MEG2532' 'MEG2533' 'MEG2541' 'MEG2542' 'MEG2543' 'MEG2611' 'MEG2612' 'MEG2613' 'MEG2621' 'MEG2622' 'MEG2623' 'MEG2631' 'MEG2632' 'MEG2633' 'MEG2641' 'MEG2642' 'MEG2643' 'STI101' 'SYS201' 'CHPI001' 'CHPI002' 'CHPI003' 'CHPI004' 'CHPI005' 'CHPI006' 'CHPI007' 'CHPI008' 'CHPI009' } reading and preprocessing reading and preprocessing trial 1 from 210265 Reading 264027 ... 4792reading and preprocessing trial 2 from 210265 Reading 327742 ... 4802reading and preprocessing trial 3 from 210265 . . . . . Reading 635443 ... 66reading and preprocessing trial 116 from 210265 Error using ft_read_data (line 225) cannot read data after the end of the file Error in ft_preprocessing (line 582) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); I am new to fieldtrip. Please help me with the above error. Regards, Abhishek. -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri Jul 20 15:00:04 2018 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 20 Jul 2018 15:00:04 +0200 Subject: [FieldTrip] Error in using EMG channel as trial definition In-Reply-To: References: Message-ID: <6B3105DE-53A4-4490-97A0-C7CC497B2B14@gmail.com> Dear Abhishek, this error occurs if less time than specified in cfg.trialdef.poststim is left after the last event code. In other words, you are trying to cut out more trials with a fixed latency than you have data. Please note that it appears as if your trial definition based on the EMG channel fails (see the „found 0 events“ notice and the rather large number of trials). I suggest going back to your trial function and checking whether everything works as intended there. Good luck, Julian ________________ Prof. Dr. Julian Keil Biological Psychology Olshausenstrasse 62 - R. 306 24118 Kiel, Germany +49 - 0431 - 880 - 4872 http://www.biopsych.uni-kiel.de/en Department of Psychiatry and Psychotherapy Charité at St. Hedwig-Hospital Große Hamburger Strasse 5-11 10115 Berlin, Germany +030 - 2311 - 1879 www.multisensorymind.com > Am 20.07.2018 um 14:52 schrieb Abhishek Samal <007abhisheksamal at gmail.com>: > > Sir, > This is Abhishek. I am trying to analyse Motor Evoked field MEG data. I have been trying to use the EMG channel as the trial definition for the triggers of epoch creation. But when I use the script that is given in tutorial definition I am getting the following error. > > The Input > > cfg = []; > cfg.dataset = 'preetham_lt_motor_raw_tsss_mc.fif'; > cfg.trialdef.prestim = 1; > cfg.trialdef.poststim = 0.5; > cfg.trialfun = 'trialfun_emgdetect'; > cfg = ft_definetrial(cfg); > data = ft_preprocessing(cfg); > > The Error > > 306 MEG channel locations transformed > Reading preetham_lt_motor_raw_tsss_mc.fif ... > Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... > Range : 124000 ... 669999 = 62.000 ... 335.000 secs > Ready. > Reading 124000 ... 669999 = 62.000 ... 335.000 secs... [done] > found 0 events > created 210265 trials > the call to "ft_definetrial" took 528 seconds > 306 MEG channel locations transformed > Reading preetham_lt_motor_raw_tsss_mc.fif ... > Opening raw data file preetham_lt_motor_raw_tsss_mc.fif... > Range : 124000 ... 669999 = 62.000 ... 335.000 secs > Ready. > processing channel { 'EOG001' 'ECG002' 'EEG001' 'EEG002' 'EEG003' 'EEG004' 'EEG005' 'EEG006' 'EEG007' 'EEG008' 'EEG009' 'EEG010' 'EEG011' 'EEG012' 'EEG013' 'EEG014' 'EEG015' 'EEG016' 'EEG017' 'EEG018' 'EEG019' 'EEG020' 'EEG021' 'EEG022' 'EEG023' 'EEG024' 'EEG025' 'EXCI' 'IASX+' 'IASX-' 'IASY+' 'IASY-' 'IASZ+' 'IASZ-' 'IAS_DX' 'IAS_DY' 'IAS_X' 'IAS_Y' 'IAS_Z' 'MEG0111' 'MEG0112' 'MEG0113' 'MEG0121' 'MEG0122' 'MEG0123' 'MEG0131' 'MEG0132' 'MEG0133' 'MEG0141' 'MEG0142' 'MEG0143' 'MEG0211' 'MEG0212' 'MEG0213' 'MEG0221' 'MEG0222' 'MEG0223' 'MEG0231' 'MEG0232' 'MEG0233' 'MEG0241' 'MEG0242' 'MEG0243' 'MEG0311' 'MEG0312' 'MEG0313' 'MEG0321' 'MEG0322' 'MEG0323' 'MEG0331' 'MEG0332' 'MEG0333' 'MEG0341' 'MEG0342' 'MEG0343' 'MEG0411' 'MEG0412' 'MEG0413' 'MEG0421' 'MEG0422' 'MEG0423' 'MEG0431' 'MEG0432' 'MEG0433' 'MEG0441' 'MEG0442' 'MEG0443' 'MEG0511' 'MEG0512' 'MEG0513' 'MEG0521' 'MEG0522' 'MEG0523' 'MEG0531' 'MEG0532' 'MEG0533' 'MEG0541' 'MEG0542' 'MEG0543' 'MEG0611' 'MEG0612' 'MEG0613' 'MEG0621' 'MEG0622' 'MEG0623' 'MEG0631' 'MEG0632' 'MEG0633' 'MEG0641' 'MEG0642' 'MEG0643' 'MEG0711' 'MEG0712' 'MEG0713' 'MEG0721' 'MEG0722' 'MEG0723' 'MEG0731' 'MEG0732' 'MEG0733' 'MEG0741' 'MEG0742' 'MEG0743' 'MEG0811' 'MEG0812' 'MEG0813' 'MEG0821' 'MEG0822' 'MEG0823' 'MEG0911' 'MEG0912' 'MEG0913' 'MEG0921' 'MEG0922' 'MEG0923' 'MEG0931' 'MEG0932' 'MEG0933' 'MEG0941' 'MEG0942' 'MEG0943' 'MEG1011' 'MEG1012' 'MEG1013' 'MEG1021' 'MEG1022' 'MEG1023' 'MEG1031' 'MEG1032' 'MEG1033' 'MEG1041' 'MEG1042' 'MEG1043' 'MEG1111' 'MEG1112' 'MEG1113' 'MEG1121' 'MEG1122' 'MEG1123' 'MEG1131' 'MEG1132' 'MEG1133' 'MEG1141' 'MEG1142' 'MEG1143' 'MEG1211' 'MEG1212' 'MEG1213' 'MEG1221' 'MEG1222' 'MEG1223' 'MEG1231' 'MEG1232' 'MEG1233' 'MEG1241' 'MEG1242' 'MEG1243' 'MEG1311' 'MEG1312' 'MEG1313' 'MEG1321' 'MEG1322' 'MEG1323' 'MEG1331' 'MEG1332' 'MEG1333' 'MEG1341' 'MEG1342' 'MEG1343' 'MEG1411' 'MEG1412' 'MEG1413' 'MEG1421' 'MEG1422' 'MEG1423' 'MEG1431' 'MEG1432' 'MEG1433' 'MEG1441' 'MEG1442' 'MEG1443' 'MEG1511' 'MEG1512' 'MEG1513' 'MEG1521' 'MEG1522' 'MEG1523' 'MEG1531' 'MEG1532' 'MEG1533' 'MEG1541' 'MEG1542' 'MEG1543' 'MEG1611' 'MEG1612' 'MEG1613' 'MEG1621' 'MEG1622' 'MEG1623' 'MEG1631' 'MEG1632' 'MEG1633' 'MEG1641' 'MEG1642' 'MEG1643' 'MEG1711' 'MEG1712' 'MEG1713' 'MEG1721' 'MEG1722' 'MEG1723' 'MEG1731' 'MEG1732' 'MEG1733' 'MEG1741' 'MEG1742' 'MEG1743' 'MEG1811' 'MEG1812' 'MEG1813' 'MEG1821' 'MEG1822' 'MEG1823' 'MEG1831' 'MEG1832' 'MEG1833' 'MEG1841' 'MEG1842' 'MEG1843' 'MEG1911' 'MEG1912' 'MEG1913' 'MEG1921' 'MEG1922' 'MEG1923' 'MEG1931' 'MEG1932' 'MEG1933' 'MEG1941' 'MEG1942' 'MEG1943' 'MEG2011' 'MEG2012' 'MEG2013' 'MEG2021' 'MEG2022' 'MEG2023' 'MEG2031' 'MEG2032' 'MEG2033' 'MEG2041' 'MEG2042' 'MEG2043' 'MEG2111' 'MEG2112' 'MEG2113' 'MEG2121' 'MEG2122' 'MEG2123' 'MEG2131' 'MEG2132' 'MEG2133' 'MEG2141' 'MEG2142' 'MEG2143' 'MEG2211' 'MEG2212' 'MEG2213' 'MEG2221' 'MEG2222' 'MEG2223' 'MEG2231' 'MEG2232' 'MEG2233' 'MEG2241' 'MEG2242' 'MEG2243' 'MEG2311' 'MEG2312' 'MEG2313' 'MEG2321' 'MEG2322' 'MEG2323' 'MEG2331' 'MEG2332' 'MEG2333' 'MEG2341' 'MEG2342' 'MEG2343' 'MEG2411' 'MEG2412' 'MEG2413' 'MEG2421' 'MEG2422' 'MEG2423' 'MEG2431' 'MEG2432' 'MEG2433' 'MEG2441' 'MEG2442' 'MEG2443' 'MEG2511' 'MEG2512' 'MEG2513' 'MEG2521' 'MEG2522' 'MEG2523' 'MEG2531' 'MEG2532' 'MEG2533' 'MEG2541' 'MEG2542' 'MEG2543' 'MEG2611' 'MEG2612' 'MEG2613' 'MEG2621' 'MEG2622' 'MEG2623' 'MEG2631' 'MEG2632' 'MEG2633' 'MEG2641' 'MEG2642' 'MEG2643' 'STI101' 'SYS201' 'CHPI001' 'CHPI002' 'CHPI003' 'CHPI004' 'CHPI005' 'CHPI006' 'CHPI007' 'CHPI008' 'CHPI009' } > reading and preprocessing > reading and preprocessing trial 1 from 210265 > Reading 264027 ... 4792reading and preprocessing trial 2 from 210265 > Reading 327742 ... 4802reading and preprocessing trial 3 from 210265 > . > . > . > . > . > Reading 635443 ... 66reading and preprocessing trial 116 from 210265 > Error using ft_read_data (line 225) > cannot read data after the end of the file > > Error in ft_preprocessing (line 582) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, > 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat); > > > > I am new to fieldtrip. Please help me with the above error. > Regards, > Abhishek. > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: Message signed with OpenPGP URL: From apple.h99 at gmail.com Fri Jul 20 15:54:00 2018 From: apple.h99 at gmail.com (sara h) Date: Fri, 20 Jul 2018 18:24:00 +0430 Subject: [FieldTrip] Access to fieldtrip mailing list Message-ID: Dear all Hi I'm new with filedtrip and I'm going to search in fieldtrip mailing list but the list is not accessible and the webpage is not reachable. does any one have this issue?? how can I sove it? thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 23 10:55:24 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 23 Jul 2018 08:55:24 +0000 Subject: [FieldTrip] Access to fieldtrip mailing list In-Reply-To: References: Message-ID: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> Hi Sara, It works for me at the moment, so I don’t know what was/is causing your problem. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 20 Jul 2018, at 15:54, sara h > wrote: Dear all Hi I'm new with filedtrip and I'm going to search in fieldtrip mailing list but the list is not accessible and the webpage is not reachable. does any one have this issue?? how can I sove it? thanks _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon Jul 23 10:58:46 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 23 Jul 2018 08:58:46 +0000 Subject: [FieldTrip] Averaging over frequencies in ft_freqstatistics In-Reply-To: References: Message-ID: Hi Sebastian, ft_freqstatistics averages the power across the frequency bins, that have their bin-centre within the range specified by cfg.frequency. The output frequency in stat.freq represents the average of the bin-centres that went into the computation. No re-estimation of the power at this frequency is done. Best wishes, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 19 Jul 2018, at 09:01, Sebastian Sauppe > wrote: Dear FieldTrip list, I am testing different frequency bands with cluster-based permutation tests using ft_freqstatistics. For this, I use cfg.avgoverfreq = ‚yes‘ when setting up the test. However, I am unsure about how FieldTrip actually handles the frequency averaging. Does it take the mean power of the specified frequencies or does it take the power of the mean frequency? This is the relevant code I use: ... cfg.frequency = [3 8]; cfg.avgoverfreq = 'yes‘; ... [stat] = ft_freqstatistics(cfg, data_A, data_B); In my data, I have the following frequencies: [3.9062 4.8828 6.1035 7.0801 8.0566 9.0332 10.0098]. In the statistics output, after averaging over frequencies stat.freq returns only 6.0059. This is the mean of the frequencies between 3 and 8. But I can’t see whether somehow the power of that frequency was assessed in the test or whether the power of all frequencies in that band was first averaged and then tested. Regards, Sebastian ----------- Dr. Sebastian Sauppe Department of Comparative Linguistics, University of Zurich Homepage: https://sites.google.com/site/sauppes/ Twitter: @SebastianSauppe Google Scholar Citations: https://scholar.google.de/citations?user=wEtciKQAAAAJ ResearchGate: http://www.researchgate.net/profile/Sebastian_Sauppe ORCID ID: http://orcid.org/0000-0001-8670-8197 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rdm146 at newark.rutgers.edu Tue Jul 24 01:45:43 2018 From: rdm146 at newark.rutgers.edu (Ravi Mill) Date: Mon, 23 Jul 2018 23:45:43 +0000 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel Message-ID: Dear Fieldtrippers I've been scouring the FT documentation and mailing list but can't seem to find the answer to a fairly simple question (which seems to have remained unanswered previously https://mailman.science.ru.nl/pipermail/fieldtrip/2016-August/010816.html): how does one know the size/'radius' of the individual source gridpoints modeled by Fieldtrip? I've been warping MNI template source models (with RO selected from a functional atlas of ~300 regions) to individual subject MRI headmodels to extract source timeseries via LCMV beamformer. In ft_prepare_sourcemodel there are seemingly options to control the *spacing* between gridpoints in a whole-brain source grid (cfg.grid.resolution), but nothing to control how large the individual sources are (either for whole-brain grids, or a priori cfg.grid.pos values that I've been using). Does this mean that the size of individual gridpoints cannot be changed within ft_prepare_sourcemodel? Are they also in absolute terms fairly small (e.g. ~1mm)? If so, is the only way to extract 'larger' sources to fit a whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), identify gridpoints after ft_sourceanalysis that fall within a specified Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and then e.g. average over all those gridpoints? I'm concerned that larger source gridpoints might have larger SNR... Thanks in advance! Ravi -- Ravi Mill, PhD Post-doctoral researcher Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers University -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.spaak at donders.ru.nl Tue Jul 24 09:16:06 2018 From: e.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 24 Jul 2018 09:16:06 +0200 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel In-Reply-To: References: Message-ID: Hi Ravi, Beamforming will estimate source activity at *point* sources; in other words, the grid points have no spatial extent (i.e., they are zero-dimensional). > If so, is the only way to extract 'larger' sources to fit a > whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), > identify gridpoints after ft_sourceanalysis that fall within a specified > Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and > then e.g. average over all those gridpoints? Yes, that is definitely a valid approach. You will probably not need to use such a finely spaced grid if you end up averaging over grid points anyway. Typically, the spatial filters for neighbouring grid points will be highly correlated. Best, Eelke > > > Thanks in advance! > > Ravi > > > -- > Ravi Mill, PhD > Post-doctoral researcher > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers University > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > From apple.h99 at gmail.com Tue Jul 24 12:07:30 2018 From: apple.h99 at gmail.com (sara h) Date: Tue, 24 Jul 2018 14:37:30 +0430 Subject: [FieldTrip] Access to fieldtrip mailing list In-Reply-To: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> References: <2B90014C-FC7A-4129-B55D-6996EADFA4B0@donders.ru.nl> Message-ID: Hi Jan yes it is ok for me now too. thank you regards Sara On Mon, Jul 23, 2018 at 1:43 PM Schoffelen, J.M. (Jan Mathijs) < jan.schoffelen at donders.ru.nl> wrote: > Hi Sara, > It works for me at the moment, so I don’t know what was/is causing your > problem. > Best wishes, > Jan-Mathijs > > J.M.Schoffelen, MD PhD > Senior Researcher, VIDI-fellow - PI, language in interaction > Telephone: +31-24-3614793 > Physical location: room 00.028 > Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands > > > On 20 Jul 2018, at 15:54, sara h wrote: > > Dear all > Hi > > I'm new with filedtrip and I'm going to search in fieldtrip mailing list > but the list is not accessible and the webpage is not reachable. does any > one have this issue?? how can I sove it? > > thanks > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunnypitt1965 at gmail.com Tue Jul 24 21:24:19 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Tue, 24 Jul 2018 15:24:19 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Message-ID: Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From rdm146 at newark.rutgers.edu Tue Jul 24 23:59:02 2018 From: rdm146 at newark.rutgers.edu (Ravi Mill) Date: Tue, 24 Jul 2018 21:59:02 +0000 Subject: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel In-Reply-To: References: , Message-ID: Many thanks for clarifying that Eelke! ________________________________ From: fieldtrip on behalf of Eelke Spaak Sent: Tuesday, July 24, 2018 3:16:06 AM To: FieldTrip discussion list Subject: Re: [FieldTrip] Query about source/gridpoint size after ft_prepare_sourcemodel Hi Ravi, Beamforming will estimate source activity at *point* sources; in other words, the grid points have no spatial extent (i.e., they are zero-dimensional). > If so, is the only way to extract 'larger' sources to fit a > whole-brain grid (e.g. using the 4mm-spaced source template provided by FT), > identify gridpoints after ft_sourceanalysis that fall within a specified > Euclidean distance (e.g. 5mm) of the functional atlas MNI coordinates, and > then e.g. average over all those gridpoints? Yes, that is definitely a valid approach. You will probably not need to use such a finely spaced grid if you end up averaging over grid points anyway. Typically, the spatial filters for neighbouring grid points will be highly correlated. Best, Eelke > > > Thanks in advance! > > Ravi > > > -- > Ravi Mill, PhD > Post-doctoral researcher > Center for Molecular and Behavioral Neuroscience (CMBN) > Rutgers University > > > _______________________________________________ > fieldtrip mailing list > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=tqWRL8OWLPKt73S8XFXfPIoyeYVV60WTJuZVW3Vil%2Fs%3D&reserved=0 > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=nx%2B1yhLpHm1tXwX1KjTK6qwhvnWyk%2FWZMTAm5xp9Qbg%3D&reserved=0 > _______________________________________________ fieldtrip mailing list https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=tqWRL8OWLPKt73S8XFXfPIoyeYVV60WTJuZVW3Vil%2Fs%3D&reserved=0 https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=02%7C01%7Crdm146%40newark.rutgers.edu%7C1dcfb4b1321140b73da208d5f1359683%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C1%7C636680134821023490&sdata=nx%2B1yhLpHm1tXwX1KjTK6qwhvnWyk%2FWZMTAm5xp9Qbg%3D&reserved=0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.Arana at donders.ru.nl Wed Jul 25 13:49:56 2018 From: S.Arana at donders.ru.nl (Arana, S.L. (Sophie)) Date: Wed, 25 Jul 2018 11:49:56 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:ii_jk039gcg0_164cdbfadfb3de10] Thanks for your understanding and support Best Regards, Sunny -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: image.png URL: From sunnypitt1965 at gmail.com Wed Jul 25 14:22:33 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Wed, 25 Jul 2018 08:22:33 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) wrote: > Dear Sunny, > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > Best, > > Sophie > > ------------------------------ > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > Hope you are doing fine, > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > Thanks for your understanding and support > > Best Regards, > Sunny > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From Silvia.Formica at UGent.be Thu Jul 26 09:57:32 2018 From: Silvia.Formica at UGent.be (Silvia Formica) Date: Thu, 26 Jul 2018 07:57:32 +0000 Subject: [FieldTrip] ft_freqanalysis wavelet problem Message-ID: <1532591852846.46333@UGent.be> Dear all, I am new to fieldtrip so I apologize in advance if my question is trivial. I am trying to run a time frequency analysis with Morlet wavelets. Here is the code I am using: cfg = []; cfg.channel = 1:64; cfg.method = 'wavelet'; cfg.pad = 10; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 4:1:30; cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz TFRwave = ft_freqanalysis(cfg, data_clean); Where data_clean is the struct containing my trials. All my trials are the same length. When I run this code, I get the following warning: Warning: output time-bins are different from input time-bins trial 1, frequency 26 (29.00 Hz) Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) [...] I have no idea what this means. Any suggestion? Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot: cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.zlim = [-3e-27 3e-27]; cfg.showlabels = 'yes'; cfg.layout = 'biosemi64.lay'; figure ft_multiplotTFR(cfg, TFRwave) When I check the content of my TFRwave I can see it is not made of NaNs. Is the problem due to the setting cfg.zlim? It is not clear to me how to set it. Thanks in advance for any help! Silvia -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Jul 26 11:32:36 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 26 Jul 2018 11:32:36 +0200 Subject: [FieldTrip] ft_freqanalysis wavelet problem In-Reply-To: <1532591852846.46333@UGent.be> References: <1532591852846.46333@UGent.be> Message-ID: Dear Silvia, The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information, speeding it up as well) Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options. Best wishes, Stephen On 26 July 2018 at 09:57, Silvia Formica wrote: > Dear all, > > > I am new to fieldtrip so I apologize in advance if my question is trivial. > > I am trying to run a time frequency analysis with Morlet wavelets. > > Here is the code I am using: > > > cfg = []; > cfg.channel = 1:64; > cfg.method = 'wavelet'; > cfg.pad = 10; > cfg.width = 7; > cfg.output = 'pow'; > cfg.foi = 4:1:30; > cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz > TFRwave = ft_freqanalysis(cfg, data_clean); > > > Where data_clean is the struct containing my trials. All my trials are > the same length. > > When I run this code, I get the following warning: > > Warning: output time-bins are different from input time-bins > trial 1, frequency 26 (29.00 Hz) > Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) > Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) > Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) > Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) > [...] > > I have no idea what this means. Any suggestion? > > Despite the warning, the TRFwave is computed, but when I try to plot it I > get a completely blue output. Here is the code I am using for the plot: > > cfg = []; > cfg.baseline = [-0.5 -0.1]; > cfg.baselinetype = 'absolute'; > cfg.zlim = [-3e-27 3e-27]; > cfg.showlabels = 'yes'; > cfg.layout = 'biosemi64.lay'; > figure > ft_multiplotTFR(cfg, TFRwave) > > > When I check the content of my TFRwave I can see it is not made of NaNs. > Is the problem due to the setting cfg.zlim? It is not clear to me how to > set it. > > Thanks in advance for any help! > > Silvia > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Silvia.Formica at UGent.be Thu Jul 26 12:45:26 2018 From: Silvia.Formica at UGent.be (Silvia Formica) Date: Thu, 26 Jul 2018 10:45:26 +0000 Subject: [FieldTrip] ft_freqanalysis wavelet problem In-Reply-To: References: <1532591852846.46333@UGent.be>, Message-ID: <1532601927049.21531@UGent.be> Dear Stephen, thanks a lot for your reply. I actually figured out the baseline was the issue, as I was computing the Morlet on a shorter time-window and I was trying to baseline-correct with an interval that was outside of my TFR. With this adjustment I do see the plot as I expected it. Concerning the warning on the cfg.toi, I chose on purpose the step according to my sampling rate, but I will consider increasing it. My concern is that I might somehow be losing information due to this mismatch between input and output time-bins. Thanks! Best, Silvia ________________________________ From: fieldtrip on behalf of Stephen Whitmarsh Sent: 26 July 2018 11:32 To: FieldTrip discussion list Subject: Re: [FieldTrip] ft_freqanalysis wavelet problem Dear Silvia, The warning seems reasonable to me, as the output times probably don't map perfectly on the input times. (BTW, your cfg.toi is rather dense, given that you use a width of 7, you can probably increase the time intervals a lot without losing much information, speeding it up as well) Why you get a 'blue output' is hard to say, but you can set the zlim e.g. as 'absmax'. Take a look at the ft_freqanalysis function help in the beginning of the code (or type 'help ft_freqanalysis' in the MATLAB command window), to see your options there. You might want to play with a baseline correction in ft_freqanalysis to help visualise data with is otherwise affected with 1/f power. Also, check out FieldTrip visualisation tutorial, which should help you explore the options. Best wishes, Stephen On 26 July 2018 at 09:57, Silvia Formica > wrote: Dear all, I am new to fieldtrip so I apologize in advance if my question is trivial. I am trying to run a time frequency analysis with Morlet wavelets. Here is the code I am using: cfg = []; cfg.channel = 1:64; cfg.method = 'wavelet'; cfg.pad = 10; cfg.width = 7; cfg.output = 'pow'; cfg.foi = 4:1:30; cfg.toi = 0:0.0039:2; % my sampling rate is 512 Hz TFRwave = ft_freqanalysis(cfg, data_clean); Where data_clean is the struct containing my trials. All my trials are the same length. When I run this code, I get the following warning: Warning: output time-bins are different from input time-bins trial 1, frequency 26 (29.00 Hz) Warning: output time-bins aretrial 2, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 3, frequency 24 (27.00 Hz) Warning: output time-bins aretrial 4, frequency 25 (28.00 Hz) Warning: output time-bins aretrial 5, frequency 23 (26.00 Hz) [...] I have no idea what this means. Any suggestion? Despite the warning, the TRFwave is computed, but when I try to plot it I get a completely blue output. Here is the code I am using for the plot: cfg = []; cfg.baseline = [-0.5 -0.1]; cfg.baselinetype = 'absolute'; cfg.zlim = [-3e-27 3e-27]; cfg.showlabels = 'yes'; cfg.layout = 'biosemi64.lay'; figure ft_multiplotTFR(cfg, TFRwave) When I check the content of my TFRwave I can see it is not made of NaNs. Is the problem due to the setting cfg.zlim? It is not clear to me how to set it. Thanks in advance for any help! Silvia _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From brooks.jl at gmail.com Thu Jul 26 19:22:44 2018 From: brooks.jl at gmail.com (Joseph Brooks) Date: Thu, 26 Jul 2018 18:22:44 +0100 Subject: [FieldTrip] Lecturer (Assistant Prof Equivalent) in Psychology @ Keele University, UK Message-ID: Job Link: https://www.jobs.ac.uk/job/BLE960/lecturer-in-psychology/ Deadline: 9 Aug 2018 Psychology at Keele University (UK) is looking for an excellent researcher to join one or more of our growing research groups in Cognitive & Biological Psych, Social & Developmental, or Health & Wellbeing. We welcome applicants from across psychology but particularly those using quantitative methods. For Cognitive/Cog Neuro applicants, we have a new 64 channel Biosemi EEG laboratory, Eyelink eyetracking lab, Virtual Reality lab, Biopac psychophysiology labs, an MRI access agreement with Liverpool, and good links with Stoke University Hospital and Keele Medical School for neuropsych patient recruitment. More on facilities at https://www.keele.ac.uk/psychology/equipmentandfacilities/ . Applicants should have a strong track record of peer-reviewed publications and be able to contribute teaching to our undergraduate and post-graduate programmes. Note: This is a permanent academic position (subject to usual probationary period) which is equivalent to a tenure-track assistant professor position in North America. Keele has a beautiful campus in the West Midlands of England only 40 minutes from Manchester and Birmingham and 1.5 hours by train from London. We are a friendly community of academics and students (UG, MSc, and PhD) with a diverse range of interests across Psychology including both quantitative and qualitative methods. We are situated in the Dorothy Hodgkin Building which houses our laboratories For full details of the position, please see the advertisement at: https://www.jobs.ac.uk/job/BLE960/lecturer-in-psychology/ -------------------------------------------- Dr Joseph Brooks Senior Lecturer in Psychology Research Lead, Cognitive & Biological Research Group Programme Lead, MSc Cognitive Psychology School of Psychology, Keele University Office: Dorothy Hodgkin Building 1.74 Lab Website: https://sites.google.com/view/brookslab -------------- next part -------------- An HTML attachment was scrubbed... URL: From jose.herrero66 at gmail.com Fri Jul 27 15:29:47 2018 From: jose.herrero66 at gmail.com (Jose Herrero) Date: Fri, 27 Jul 2018 09:29:47 -0400 Subject: [FieldTrip] iEEG cluster statistics Message-ID: Hi FT, quick question on how to perform cluster statistics multiple comparisons correction with cfg.correctm = cluster' on iEEG data. I'm preparing neighbors with the two nearest contacts to the contact in question but the code gives an error (the 'fdr' method works fine). Is this method exclusive to standard montages or can be done manually. I've tried to do it manually so that neighbors format is similar to one of the examples MEG montage but still not working. Thoughts? JHerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri Jul 27 15:35:49 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 27 Jul 2018 13:35:49 +0000 Subject: [FieldTrip] iEEG cluster statistics In-Reply-To: References: Message-ID: What’s the error? In principle, if your neighbourhood-structure is well-defined it should work. Best, JM On 27 Jul 2018, at 15:29, Jose Herrero > wrote: Hi FT, quick question on how to perform cluster statistics multiple comparisons correction with cfg.correctm = cluster' on iEEG data. I'm preparing neighbors with the two nearest contacts to the contact in question but the code gives an error (the 'fdr' method works fine). Is this method exclusive to standard montages or can be done manually. I've tried to do it manually so that neighbors format is similar to one of the examples MEG montage but still not working. Thoughts? JHerr _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gabriel.delara at med.uni-goettingen.de Fri Jul 27 17:04:33 2018 From: gabriel.delara at med.uni-goettingen.de (Amador, Gabriel) Date: Fri, 27 Jul 2018 15:04:33 +0000 Subject: [FieldTrip] scalp EEG resting-state analysis Message-ID: Dear Field trippers, My first e-mail to this list. Thanks for paying attention to this, whoever took time to read it. I am currently doing my PhD in Göttingen, at the moment running a scalp-EEG (26-channels) analysis with Fieldtrip for a dataset of healthy participants. I have a repeated-measures design, where each participant undergoes 4 sessions, with n = 20. For each session, I performed two 5' eyes-open resting-state recordings per participant: one before and one after intervention (pre-, post-). The goal is to simply detect power changes in the pre X post comparison. Recordings were segmented into 2s trials with 50% overlap followed by other pre-processing steps. I am having some doubts on the feasibility/correctness of the steps after the pre-processing. My main critical question is the procedures sequence to correctly run the Monte Carlo stats in the end (if and when to keep trials, to average trials, to average across participants, and so on). Some options available: 1. First running TFA (mtmfft, dpss,) keeping the trials. Then, appending participants with ft_appendfreq. Afterwards, stats: parameters (Montecarlo, depsamplesT, cluster correction, 5.000 iterations). First problem arises in the design matrix: Since trials are kept in the FA, they are uneven for every session (appending leads to different trials between pre X post), and also the appended data does not keep the participant as UO, so design matrix has to be design as trials in the first row. To make it work, trials have to be shortened from one condition, so they are paired (which seems obvious for depsamplesT, since it does would not accept different values in the uvar). Statistics run after doing all this, but I am not sure, since having a uvar with ~10.000 points, that were the individual trials of every session (there are 20 participants) sounds strange (there were no 10.000 participants). This option was run for one condition, significant difference happened, clusters were formed, etc. Is this reasonable? 2. First running TFA (mtmfft, dpss,) keeping the trials. After, apply ft_freqdescriptives to every subject, in oder to be able to use ft_freq_grandaverage. Apply ft_freqgrandaverage across participants, but keeping individuals (for the design matrix).After ft_ freqgrandaverage, stats as described above, with design matrix with 1:20 in the first row (uvar) and the two conditions (pre X post) at the second. This works, but leads to no clusters found (ran it on more than one condition). Doubt here is: using ft_freqdescriptives and then ft_freq_grandaverage compromises the monte carlo procedure, having just one value for each channel (the grand-averaged trials power)? Any suggestions? Thanks! Gabriel Amador de Lara wissenschaftlicher Mitarbeiter / PhD candidate Klinik für klinische Neurophysiologie / Department of Clinical Neurophysiology Universitätsmedizin / Medical Center Georg-August-Universität Göttingen Robert-Koch-Str. 40, 37075 +49 0551 3919265 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunnypitt1965 at gmail.com Fri Jul 27 20:41:12 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Fri, 27 Jul 2018 14:41:12 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON ( https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > Hello Sophie, > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > Thanks for your understanding and support. > > Best Regards, > Sunny > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > >> Hello Sophie, >> >> Thanks a lot for your clarification. This is very useful. >> >> Sunny >> >> >> On Wednesday, July 25, 2018, Arana, S.L. (Sophie) >> wrote: >> >>> Dear Sunny, >>> >>> the multi-channel NIRS data tutorial is currently under construction and >>> will hopefully be fully available in a couple of weeks. Until then, there >>> might still be some inconsistencies such as the one you have encountered. >>> >>> The variable you refer to is indeed missing. It refers to a filtered >>> version of the data, and you can created it by running the following code >>> before the epoching. >>> >>> cfg = []; >>> >>> cfg.hpfilter = 'yes'; >>> >>> cfg.hpfreq = 0.01; >>> >>> data_flt = ft_preprocessing(cfg,data_down); >>> >>> >>> This should help you to continue with the tutorial, but please do keep >>> in mind that we are currently working on it and you might encounter some >>> other inconsistencies still later on. >>> >>> >>> Best, >>> >>> Sophie >>> >>> ------------------------------ >>> *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny >>> p [sunnypitt1965 at gmail.com] >>> *Sent:* Tuesday, July 24, 2018 9:24 PM >>> *To:* fieldtrip at science.ru.nl >>> *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging >>> of multi-channel NIRS data >>> >>> Hello All Good Day, >>> >>> Hope you are doing fine, >>> >>> Thanks a lot for providing with fieldtrip which is really useful to >>> analyze fNIRS data. I have an issue in the "Preprocessing and averaging of >>> multi-channel NIRS data" tutorial. Can you please help me with this issue? >>> >>> Issue: In the "Preprocessing and averaging of multi-channel NIRS data" >>> tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel >>> >>> The "Epoch" section consists of a variable "data_flt.fsample" where >>> "data_flt" variable is not defined. Can you please inform what is this >>> variable related to? as this is needed to complete my analysis. >>> >>> >>> >>> >>> Thanks for your understanding and support >>> >>> Best Regards, >>> Sunny >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 4228 bytes Desc: not available URL: From lizhipeng3924 at gmail.com Sun Jul 29 04:55:37 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Sun, 29 Jul 2018 10:55:37 +0800 Subject: [FieldTrip] A question about MEG source reconstruction Message-ID: Dear all, When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. I would appreciate it if you could help me. Yours, zhipeng -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 5933 bytes Desc: not available URL: From alexandre.gramfort at inria.fr Sun Jul 29 10:03:59 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Sun, 29 Jul 2018 10:03:59 +0200 Subject: [FieldTrip] A question about MEG source reconstruction In-Reply-To: References: Message-ID: hi, indeed there is a typo: $ cd $MNE_ROOT $ ls bin/mne_setup* bin/mne_setup bin/mne_setup_matlab_csh bin/mne_setup_mri bin/mne_setup_source_space bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh depending on your shell it can be source $MNE_ROOT/bin/mne_setup_sh HTH Alex On Sun, Jul 29, 2018 at 4:58 AM zhipeng li wrote: > > External Email - Use Caution > > Dear all, > When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. > I would appreciate it if you could help me. > Yours, > zhipeng > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From lizhipeng3924 at gmail.com Mon Jul 30 03:49:11 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Mon, 30 Jul 2018 09:49:11 +0800 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 In-Reply-To: References: Message-ID: - First of all, thank you very much for your reply @ Alexandre Gramfort . - But none of the files you listed were found in bin - - This is all the files contained in bin, - I need your further help. - Yours, zhipeng 2018-07-29 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. A question about MEG source reconstruction (zhipeng li) > 2. Re: A question about MEG source reconstruction > (Alexandre Gramfort) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 29 Jul 2018 10:55:37 +0800 > From: zhipeng li > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] A question about MEG source reconstruction > Message-ID: > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > I would appreciate it if you could help me. > Yours, > zhipeng > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180729/9711b38d/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 5933 bytes > Desc: not available > URL: attachments/20180729/9711b38d/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Sun, 29 Jul 2018 10:03:59 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] A question about MEG source reconstruction > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > hi, > > indeed there is a typo: > > $ cd $MNE_ROOT > $ ls bin/mne_setup* > bin/mne_setup bin/mne_setup_matlab_csh > bin/mne_setup_mri bin/mne_setup_source_space > bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > > depending on your shell it can be > > source $MNE_ROOT/bin/mne_setup_sh > > HTH > Alex > > On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > Dear all, > > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > > I would appreciate it if you could help me. > > Yours, > > zhipeng > > > > > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 19 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 159116 bytes Desc: not available URL: From jorn at artinis.com Mon Jul 30 08:47:25 2018 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Mon, 30 Jul 2018 08:47:25 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) Cc: FieldTrip discussion list Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From alexandre.gramfort at inria.fr Mon Jul 30 08:49:46 2018 From: alexandre.gramfort at inria.fr (Alexandre Gramfort) Date: Mon, 30 Jul 2018 08:49:46 +0200 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 In-Reply-To: References: Message-ID: it's the $MNE_ROOT/bin folder after setting the MNE_ROOT env variable to the folder that contains the MNE command line tools. HTH Alex On Mon, Jul 30, 2018 at 3:52 AM zhipeng li wrote: > > External Email - Use Caution > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > But none of the files you listed were found in bin > > > This is all the files contained in bin, > > I need your further help. > > Yours, > zhipeng > > > 2018-07-29 18:00 GMT+08:00 : >> >> Send fieldtrip mailing list submissions to >> fieldtrip at science.ru.nl >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> or, via email, send a message with subject or body 'help' to >> fieldtrip-request at science.ru.nl >> >> You can reach the person managing the list at >> fieldtrip-owner at science.ru.nl >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of fieldtrip digest..." >> >> >> Today's Topics: >> >> 1. A question about MEG source reconstruction (zhipeng li) >> 2. Re: A question about MEG source reconstruction >> (Alexandre Gramfort) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Sun, 29 Jul 2018 10:55:37 +0800 >> From: zhipeng li >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] A question about MEG source reconstruction >> Message-ID: >> >> Content-Type: text/plain; charset="utf-8" >> >> Dear all, >> When I was about to create a sourcemodel, I ran into a problem.The >> documentary which I refers to is Tutorial documentation>Source >> reconstruction of event-related fields using minimum-norm >> estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG >> data.When I installed MNE as their description, I found that the.sh file >> doesn't exist.The command I am using is posted below as a >> picture.Therefore, the following steps cannot be carried out. >> I would appreciate it if you could help me. >> Yours, >> zhipeng >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: image.png >> Type: image/png >> Size: 5933 bytes >> Desc: not available >> URL: >> >> ------------------------------ >> >> Message: 2 >> Date: Sun, 29 Jul 2018 10:03:59 +0200 >> From: Alexandre Gramfort >> To: FieldTrip discussion list >> Subject: Re: [FieldTrip] A question about MEG source reconstruction >> Message-ID: >> >> Content-Type: text/plain; charset="UTF-8" >> >> hi, >> >> indeed there is a typo: >> >> $ cd $MNE_ROOT >> $ ls bin/mne_setup* >> bin/mne_setup bin/mne_setup_matlab_csh >> bin/mne_setup_mri bin/mne_setup_source_space >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh >> >> depending on your shell it can be >> >> source $MNE_ROOT/bin/mne_setup_sh >> >> HTH >> Alex >> >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li wrote: >> > >> > External Email - Use Caution >> > >> > Dear all, >> > When I was about to create a sourcemodel, I ran into a problem.The documentary which I refers to is Tutorial documentation>Source reconstruction of event-related fields using minimum-norm estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG data.When I installed MNE as their description, I found that the.sh file doesn't exist.The command I am using is posted below as a picture.Therefore, the following steps cannot be carried out. >> > I would appreciate it if you could help me. >> > Yours, >> > zhipeng >> > >> > >> > >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > https://doi.org/10.1371/journal.pcbi.1002202 >> > >> > >> > The information in this e-mail is intended only for the person to whom it is >> > addressed. If you believe this e-mail was sent to you in error and the e-mail >> > contains patient information, please contact the Partners Compliance HelpLine at >> > http://www.partners.org/complianceline . If the e-mail was sent to you in error >> > but does not contain patient information, please contact the sender and properly >> > dispose of the e-mail. >> >> >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> _______________________________________________ >> fieldtrip mailing list >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> https://doi.org/10.1371/journal.pcbi.1002202 >> >> >> ------------------------------ >> >> End of fieldtrip Digest, Vol 92, Issue 19 >> ***************************************** > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. From S.Hanslmayr at bham.ac.uk Mon Jul 30 11:23:31 2018 From: S.Hanslmayr at bham.ac.uk (Simon Hanslmayr) Date: Mon, 30 Jul 2018 09:23:31 +0000 Subject: [FieldTrip] Postdoc position to work with human single neurons and LFPs, 9 days left to apply! Message-ID: <257F6C65A372A04CA41056EACC0DE7CED8783389@EX12.adf.bham.ac.uk> Dear Fieldtrippers, We are pleased to announce an open postdoc position in our group to work with human single neurons and LFP recordings in an exciting memory project funded by the ERC. The position is initially for 2 years with an option for 1 year extension. The negotiable start date is 1st Oct. Preliminary data has been collected and is waiting to be analysed. If you have strong electrophysiological analytical skills and are interested then please do not hesitate to apply here: http://www.memorybham.com/open-positions/ If you have any questions then please do not hesitate to contact me. Best wishes, Dr. Simon Hanslmayr Reader in Cognitive Neuroscience Royal Society Wolfson Research Merit Award Holder School of Psychology Hills Building 2.37 University of Birmingham Edgbaston Birmingham B15 2TT UK Tel +44 121 4146203 http://www.memorybham.com/people/#/simon-hanslmayr/ [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.gif Type: image/gif Size: 8560 bytes Desc: image001.gif URL: From sunnypitt1965 at gmail.com Mon Jul 30 15:29:19 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Mon, 30 Jul 2018 09:29:19 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <007201d427d1$2d7d9500$8878bf00$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Message-ID: Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig wrote: > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* fieldtrip *On Behalf Of *Sunny p > *Sent:* Friday, July 27, 2018 20:41 > *To:* Arana, S.L. (Sophie) > *Cc:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > ------------------------------ > > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > > > Virus-free. www.avg.com > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jorn at artinis.com Mon Jul 30 15:41:40 2018 From: jorn at artinis.com (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) Date: Mon, 30 Jul 2018 15:41:40 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> Message-ID: <012001d4280b$0c17baa0$24472fe0$@artinis.com> Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list ; jorn at artinis.com Cc: Arana, S.L. (Sophie) Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From sunnypitt1965 at gmail.com Mon Jul 30 16:44:40 2018 From: sunnypitt1965 at gmail.com (Sunny p) Date: Mon, 30 Jul 2018 10:44:40 -0400 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <012001d4280b$0c17baa0$24472fe0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> Message-ID: Hello Jorn, Thanks a lot for your response. Yes, I just collected the data samples, My primary aim is to visualize this data on a head model using field trip. so that it will be easy to understand. Please find attached data set collected using Octamon in this email. I also created layout for this. I attached data, layout and image in this email. Thanks a lot for your support. Its very useful for my research. Best Regards, Sunny On Mon, Jul 30, 2018 at 9:41 AM, Jörn M. Horschig wrote: > Hi Sunny, > > > > The ADC channels in the tutorial are used as a trigger-channel. I am not > sure how you insert the triggers in your experiment, but the Octamon has no > direct trigger input (you could add triggers either wirelessly using a > PortaSync or directly from within Oxysoft). The ADC of the Octamon is the > battery level and not a trigger input. Depending on what you did, you have > to follow different processing steps. If you let me know more about the > events and triggers, I can let you know what to do (you could also send me > some example data and I will send you an example script back that reads in > the data in FieldTrip). > > > > With best regards, > > Jörn > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* Sunny p > *Sent:* Monday, July 30, 2018 15:29 > *To:* FieldTrip discussion list ; > jorn at artinis.com > *Cc:* Arana, S.L. (Sophie) > > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Jorn, > > > > Thanks a lot for your response. I am working with Octamon data (4*2 > Channel). I am trying to visualize the data using topo plot on head based > image following http://www.fieldtriptoolbox.org/tutorial/ > nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon > which has 48 channel). I am wondering what parameter changes should I make > to get the data for OCTAMON visualization as my data has only ADC001 and > there is no ADC002 in data for epoch section. As I am not an NIRS expert, > its difficult to figure out which parameters gives me the visualization as > its throwing errors when following the tutorial. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > > *--Jörn M. Horschig, PhD*, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter > > > > > *From:* fieldtrip *On Behalf Of *Sunny p > *Sent:* Friday, July 27, 2018 20:41 > *To:* Arana, S.L. (Sophie) > *Cc:* FieldTrip discussion list > *Subject:* Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > ------------------------------ > > *From:* fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [ > sunnypitt1965 at gmail.com] > *Sent:* Tuesday, July 24, 2018 9:24 PM > *To:* fieldtrip at science.ru.nl > *Subject:* [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > > > Virus-free. www.avg.com > > > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OCTAMON.oxy3 Type: application/octet-stream Size: 417156 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: OCTA_layout_MAIN.mat Type: application/octet-stream Size: 1493 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Brain_PreFrontal_Cortex.PNG Type: image/png Size: 88327 bytes Desc: not available URL: From jorn at artinis.com Tue Jul 31 09:16:24 2018 From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=) Date: Tue, 31 Jul 2018 09:16:24 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <012001d4280b$0c17baa0$24472fe0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> Message-ID: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jorn at artinis.com Tue Jul 31 09:34:55 2018 From: jorn at artinis.com (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=) Date: Tue, 31 Jul 2018 09:34:55 +0200 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Message-ID: <004d01d428a0$fae2e840$f0a8b8c0$@artinis.com> Small typo, it should of course say >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.poststim = 35; >> cfg = ft_definetrial(cfg); -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Tuesday, July 31, 2018 9:16 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie _____ From: fieldtrip [fieldtrip-bounces at science.ru.nl ] on behalf of Sunny p [sunnypitt1965 at gmail.com ] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Tue Jul 31 09:38:53 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 31 Jul 2018 07:38:53 +0000 Subject: [FieldTrip] field trip loreta error References: Message-ID: Dear list, See forwarded message below for a question by Tyler. Tyler, could you send your e-mails to fieldtrip at science.ru.nl? Thanks. Jan-Mathijs Begin forwarded message: From: Tyler Durden > Subject: field trip loreta error Date: 31 July 2018 at 09:20:05 GMT+2 To: > Hi all, I am brand new to fieldtrip and still fairly new to Matlab (R2014a) . I downloaded the fieldtrip toolbox (20180722) and set up paths as instructed. Now I tried to convert some loreta files I have into fieldtrip files but I keep getting this error: "Error using ft_preamble (line 82) Could not run ft_preamble_callinfo - does not seem to exist Error in loreta2fieldtrip (line 48) ft_preamble callinfo I searched the net but I could not find any satisfying answers. I then found the ft_preamble callinfo script on github and just copied and saved it in my directory as a .m file. Now that error is gone but when I want to execute loreta2fieldtrip I get another error: Error using ft_notification (line 340) unsupported LORETA format Error in ft_error (line 39) ft_notification(varargin{:}); Error in loreta2fieldtrip (line 82) ft_error('unsupported LORETA format'); I tried some stuff but as far as I can judge I converted the slor-files appropriately and I have no idea what to do with this error...Since I really want to use your tool box, it would be super if you could help me out! Best -------------- next part -------------- An HTML attachment was scrubbed... URL: From hgould at memphis.edu Tue Jul 31 15:37:06 2018 From: hgould at memphis.edu (Herbert J Gould (hgould)) Date: Tue, 31 Jul 2018 13:37:06 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com>, <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:image001.png at 01D428AE.213F63D0] Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: image001.png URL: From lizhipeng3924 at gmail.com Tue Jul 31 15:52:11 2018 From: lizhipeng3924 at gmail.com (zhipeng li) Date: Tue, 31 Jul 2018 21:52:11 +0800 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21 In-Reply-To: References: Message-ID: - Thank you very much for your reply.@ Alexandre Gramfort But with your answer, my question remains unsolved . On my computer, I can't find any files on mne setup, including any of your list. Following the instructions on the site, I made this step - But the setup file can't be found,I hope you can give me further guidance. - Yours, - zhipeng 2018-07-30 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) > 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort) > 3. Postdoc position to work with human single neurons and LFPs, > 9 days left to apply! (Simon Hanslmayr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2018 08:47:25 +0200 > From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" > To: "'FieldTrip discussion list'" , "'Arana, > S.L. \(Sophie\)'" > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> > Content-Type: text/plain; charset="utf-8" > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > -- > Jörn M. Horschig, PhD, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> > > > > From: fieldtrip On Behalf Of Sunny p > Sent: Friday, July 27, 2018 20:41 > To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging > of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p sunnypitt1965 at gmail.com> > wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > > > _____ > > > From: fieldtrip [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [ > sunnypitt1965 at gmail.com ] > Sent: Tuesday, July 24, 2018 9:24 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " > http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > > Virus-free. utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > www.avg.com > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/577081f5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 4228 bytes > Desc: not available > URL: attachments/20180730/577081f5/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jul 2018 08:49:46 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > it's the $MNE_ROOT/bin folder > after setting the MNE_ROOT env variable to the folder that contains > the MNE command line tools. > > HTH > Alex > On Mon, Jul 30, 2018 at 3:52 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > > > But none of the files you listed were found in bin > > > > > > This is all the files contained in bin, > > > > I need your further help. > > > > Yours, > > zhipeng > > > > > > 2018-07-29 18:00 GMT+08:00 : > >> > >> Send fieldtrip mailing list submissions to > >> fieldtrip at science.ru.nl > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> or, via email, send a message with subject or body 'help' to > >> fieldtrip-request at science.ru.nl > >> > >> You can reach the person managing the list at > >> fieldtrip-owner at science.ru.nl > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of fieldtrip digest..." > >> > >> > >> Today's Topics: > >> > >> 1. A question about MEG source reconstruction (zhipeng li) > >> 2. Re: A question about MEG source reconstruction > >> (Alexandre Gramfort) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 29 Jul 2018 10:55:37 +0800 > >> From: zhipeng li > >> To: fieldtrip at science.ru.nl > >> Subject: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all, > >> When I was about to create a sourcemodel, I ran into a problem.The > >> documentary which I refers to is Tutorial documentation>Source > >> reconstruction of event-related fields using minimum-norm > >> estimation>Creating a sourcemodel for source-reconstruction of MEG or > EEG > >> data.When I installed MNE as their description, I found that the.sh file > >> doesn't exist.The command I am using is posted below as a > >> picture.Therefore, the following steps cannot be carried out. > >> I would appreciate it if you could help me. > >> Yours, > >> zhipeng > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: attachments/20180729/9711b38d/attachment-0001.html> > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: image.png > >> Type: image/png > >> Size: 5933 bytes > >> Desc: not available > >> URL: attachments/20180729/9711b38d/attachment-0001.png> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 29 Jul 2018 10:03:59 +0200 > >> From: Alexandre Gramfort > >> To: FieldTrip discussion list > >> Subject: Re: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> hi, > >> > >> indeed there is a typo: > >> > >> $ cd $MNE_ROOT > >> $ ls bin/mne_setup* > >> bin/mne_setup bin/mne_setup_matlab_csh > >> bin/mne_setup_mri bin/mne_setup_source_space > >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > >> > >> depending on your shell it can be > >> > >> source $MNE_ROOT/bin/mne_setup_sh > >> > >> HTH > >> Alex > >> > >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Dear all, > >> > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > >> > I would appreciate it if you could help me. > >> > Yours, > >> > zhipeng > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > https://doi.org/10.1371/journal.pcbi.1002202 > >> > > >> > > >> > The information in this e-mail is intended only for the person to > whom it is > >> > addressed. If you believe this e-mail was sent to you in error and > the e-mail > >> > contains patient information, please contact the Partners Compliance > HelpLine at > >> > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > >> > but does not contain patient information, please contact the sender > and properly > >> > dispose of the e-mail. > >> > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> https://doi.org/10.1371/journal.pcbi.1002202 > >> > >> > >> ------------------------------ > >> > >> End of fieldtrip Digest, Vol 92, Issue 19 > >> ***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jul 2018 09:23:31 +0000 > From: Simon Hanslmayr > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Postdoc position to work with human single > neurons and LFPs, 9 days left to apply! > Message-ID: > <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > We are pleased to announce an open postdoc position in our group to work > with human single neurons and LFP recordings in an exciting memory project > funded by the ERC. The position is initially for 2 years with an option for > 1 year extension. The negotiable start date is 1st Oct. Preliminary data > has been collected and is waiting to be analysed. If you have strong > electrophysiological analytical skills and are interested then please do > not hesitate to apply here: http://www.memorybham.com/open-positions/ > > If you have any questions then please do not hesitate to contact me. > > Best wishes, > Dr. Simon Hanslmayr > Reader in Cognitive Neuroscience > Royal Society Wolfson Research Merit Award Holder > School of Psychology > Hills Building 2.37 > University of Birmingham > Edgbaston > Birmingham > B15 2TT > UK > > Tel +44 121 4146203 > http://www.memorybham.com/people/#/simon-hanslmayr/ > [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/c066a17a/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.gif > Type: image/gif > Size: 8560 bytes > Desc: image001.gif > URL: attachments/20180730/c066a17a/attachment-0001.gif> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 21 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11167 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 171819 bytes Desc: not available URL: From Amie.Fairs at mpi.nl Tue Jul 31 16:11:15 2018 From: Amie.Fairs at mpi.nl (Fairs, Amie) Date: Tue, 31 Jul 2018 14:11:15 +0000 Subject: [FieldTrip] fieldtrip Digest, Vol 92, Issue 24 In-Reply-To: References: Message-ID: Hi Zhipeng, I am quite sure of your issue because any images you send in your email are scrubbed and I can't see them, but I might be able to help. I recently also had some issues following this tutorial. For me, MNE for python was accidentally downloaded at first. For instance, when I first did a 'which mne' search in my system it said [this is my specific path]: /usr/local/apps/python-2.7.11/bin/mne And this mne is not the same MNE suite that is discussed in the tutorial. This mne is 'in' python, so it contains: ls /usr/local/apps/python-2.7.11/bin/ 2to3 folia2html foliatree python rst2html.pyc rst2xetex.pyc alpino2folia folia2rst foliavalidator python2 rst2latex.py rst2xml.py build folia2txt idle python2.7 rst2latex.pyc rst2xml.pyc csv2rdf foliacat mne python2.7-config rst2man.py rstpep2html.py cygdb foliacorrect nosetests python2-config rst2man.pyc rstpep2html.pyc cython foliacount nosetests-2.7 python-config rst2odt_prepstyles.py smtpd.py cythonize foliafreqlist pip rdf2dot rst2odt_prepstyles.pyc tclsh8.5 dcoi2folia foliamerge pip2 rdfgraphisomorphism rst2odt.py virtualenv easy_install foliaquery pip2.7 rdfpipe rst2odt.pyc wish8.5 easy_install-2.7 foliaquery1 pt2to3 rdfs2dot rst2pseudoxml.py f2py foliasetdefinition ptdump rst2folia rst2pseudoxml.pyc folia2annotatedtxt foliaspec ptrepack rst2html5.py rst2s5.py folia2columns foliaspec2json pttree rst2html5.pyc rst2s5.pyc folia2dcoi foliatextcontent pydoc rst2html.py rst2xetex.py [sorry for the formatting] Maybe your system looks something like this? MNE suite actually looks something like this [with the path on my system]: ls /usr/local/apps/MNE/MNE-2.7.0-3106-Linux-x86_64/bin mne_add_patch_info mne_copy_processing_history mne_list_bem mne_redo_file_nocwd mne_add_to_meas_info mne_cov2proj mne_list_coil_def mne_remove_platform mne_add_triggers mne_create_comp_data mne_list_proj mne_rename_channels mne_analyze mne_ctf2fiff mne_list_source_space mne_sensitivity_map mne_annot2labels mne_ctf_dig2fiff mne_list_versions mne_sensor_locations mne_anonymize mne_dacq_annotator mne_make_cor_set mne_setup mne_average_estimates mne_dicom_essentials mne_make_derivations mne_setup_forward_model mne_average_forward_solutions mne_dipole_fit mne_make_eeg_layout mne_setup_mri mne_brain_vision2fiff mne_do_forward_solution mne_make_morph_maps mne_setup_sh mne_browse_raw mne_do_inverse_operator mne_make_movie mne_setup_source_space mne_change_baselines mne_edf2fiff mne_make_scalp_surfaces mne_show_environment mne_change_nave mne_epochs2mat mne_make_source_space mne_show_fiff mne_check_eeg_locations mne_epochs2mat.bin mne_make_sphere_bem mne_simu mne_check_surface mne_evoked_data_summary mne_make_uniform_stc mne_simu.bin mne_collect_transforms mne_eximia2fiff mne_map_data mne_smooth mne_compensate_data mne_fit_sphere_to_surf mne_mark_bad_channels mne_surf2bem mne_compute_mne mne_fix_mag_coil_types mne_morph_labels mne_toggle_skips mne_compute_raw_inverse mne_fix_stim14 mne_opengl_test mne_transform_points mne_convert_ctf_markers mne_flash_bem mne_organize_dicom mne_tufts2fiff mne_convert_dig_data mne_forward_solution mne_prepare_bem_model mne_version_test mne_convert_lspcov mne_insert_4D_comp mne_process_raw mne_view_manual mne_convert_mne_data mne_install_packages mne_process_stc mne_volume_data2mri mne_convert_mne_data.bin mne_inverse_operator mne_raw2mat mne_volume_source_space mne_convert_ncov mne_kit2fiff mne_raw2mat.bin mne_watershed_bem mne_convert_surface mne_launcher mne_redo_file Then you can see mne_setup_sh, and mne_setup_source_space - the two things you need. I hope maybe this is helpful? Best, Amie ----------------------------------------------------- Amie Fairs PhD candidate International Max Planck Research School for Language Sciences Max Planck Institute for Psycholinguistics PO Box 310 | 6500 AH Nijmegen | The Netherlands Email: amie.fairs at mpi.nl | Phone: +31(0)243521381 -----Original Message----- From: fieldtrip [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of fieldtrip-request at science.ru.nl Sent: dinsdag 31 juli 2018 15:52 To: fieldtrip at science.ru.nl Subject: fieldtrip Digest, Vol 92, Issue 24 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit https://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. Re: Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data (Herbert J Gould (hgould)) 2. Re: fieldtrip Digest, Vol 92, Issue 21 (zhipeng li) ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 Jul 2018 13:37:06 +0000 From: "Herbert J Gould (hgould)" To: FieldTrip discussion list Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Message-ID: <0pyb6vhuqo1su9hhxc79wnld.1533044221861 at email.android.com> Content-Type: text/plain; charset="windows-1252" Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. [cid:image001.png at 01D428AE.213F63D0] Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 4228 bytes Desc: image001.png URL: ------------------------------ Message: 2 Date: Tue, 31 Jul 2018 21:52:11 +0800 From: zhipeng li To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 21 Message-ID: Content-Type: text/plain; charset="utf-8" - Thank you very much for your reply.@ Alexandre Gramfort But with your answer, my question remains unsolved . On my computer, I can't find any files on mne setup, including any of your list. Following the instructions on the site, I made this step - But the setup file can't be found,I hope you can give me further guidance. - Yours, - zhipeng 2018-07-30 18:00 GMT+08:00 : > Send fieldtrip mailing list submissions to > fieldtrip at science.ru.nl > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > or, via email, send a message with subject or body 'help' to > fieldtrip-request at science.ru.nl > > You can reach the person managing the list at > fieldtrip-owner at science.ru.nl > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of fieldtrip digest..." > > > Today's Topics: > > 1. Re: Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data (=?utf-8?Q?J=C3=B6rn_M._Horschig?=) > 2. Re: fieldtrip Digest, Vol 92, Issue 19 (Alexandre Gramfort) > 3. Postdoc position to work with human single neurons and LFPs, > 9 days left to apply! (Simon Hanslmayr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Jul 2018 08:47:25 +0200 > From: "=?utf-8?Q?J=C3=B6rn_M._Horschig?=" > To: "'FieldTrip discussion list'" , "'Arana, > S.L. \(Sophie\)'" > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and > averaging of multi-channel NIRS data > Message-ID: <007201d427d1$2d7d9500$8878bf00$@artinis.com> > Content-Type: text/plain; charset="utf-8" > > Hi Sunny, > > > > Yes, the FieldTrip NIRS plugin works for all our devices. > > > > With best regards, > > Jörn > > > > -- > Jörn M. Horschig, PhD, Project Leader & Software Engineer > Artinis Medical Systems | +31 481 350 980 > > Sign up for our NIRS newsletter manage1.com/subscribe?u=6bef931b76193f0e3d1dfe654&id=550bfdab46> > > > > From: fieldtrip On Behalf Of Sunny p > Sent: Friday, July 27, 2018 20:41 > To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging > of multi-channel NIRS data > > > > Hello Sophie, > > > > Once this tutorial is fully developed, Can we use this for OCTAMON ( > https://www.artinis.com/octamon/) ? > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: > > Hello Sophie, > > > > Thanks a lot for providing this code. I am making some changes that are > useful. Can you please inform what is the variable 'data_func' in the code > relates to. This is the last undefined variable in code. > > > > Thanks for your understanding and support. > > > > Best Regards, > > Sunny > > > > On Wed, Jul 25, 2018 at 8:22 AM, Sunny p sunnypitt1965 at gmail.com> > wrote: > > Hello Sophie, > > > > Thanks a lot for your clarification. This is very useful. > > > > Sunny > > > > On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: > > Dear Sunny, > > > > the multi-channel NIRS data tutorial is currently under construction and > will hopefully be fully available in a couple of weeks. Until then, there > might still be some inconsistencies such as the one you have encountered. > > > > The variable you refer to is indeed missing. It refers to a filtered > version of the data, and you can created it by running the following code > before the epoching. > > > > cfg = []; > > cfg.hpfilter = 'yes'; > > cfg.hpfreq = 0.01; > > data_flt = ft_preprocessing(cfg,data_down); > > > > This should help you to continue with the tutorial, but please do keep in > mind that we are currently working on it and you might encounter some other > inconsistencies still later on. > > > > Best, > > Sophie > > > > > _____ > > > From: fieldtrip [fieldtrip-bounces at science.ru.nl fieldtrip-bounces at science.ru.nl> ] on behalf of Sunny p [ > sunnypitt1965 at gmail.com ] > Sent: Tuesday, July 24, 2018 9:24 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of > multi-channel NIRS data > > Hello All Good Day, > > > > Hope you are doing fine, > > > > Thanks a lot for providing with fieldtrip which is really useful to > analyze fNIRS data. I have an issue in the "Preprocessing and averaging of > multi-channel NIRS data" tutorial. Can you please help me with this issue? > > > > Issue: In the "Preprocessing and averaging of multi-channel NIRS data" > tutorial " > http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel > > > > The "Epoch" section consists of a variable "data_flt.fsample" where > "data_flt" variable is not defined. Can you please inform what is this > variable related to? as this is needed to complete my analysis. > > > > > > > > > > Thanks for your understanding and support > > > > Best Regards, > Sunny > > > > > > > > > > > utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > > Virus-free. utm_source=link&utm_campaign=sig-email&utm_content=emailclient> > www.avg.com > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/577081f5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.png > Type: image/png > Size: 4228 bytes > Desc: not available > URL: attachments/20180730/577081f5/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Mon, 30 Jul 2018 08:49:46 +0200 > From: Alexandre Gramfort > To: FieldTrip discussion list > Subject: Re: [FieldTrip] fieldtrip Digest, Vol 92, Issue 19 > Message-ID: > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > it's the $MNE_ROOT/bin folder > after setting the MNE_ROOT env variable to the folder that contains > the MNE command line tools. > > HTH > Alex > On Mon, Jul 30, 2018 at 3:52 AM zhipeng li > wrote: > > > > External Email - Use Caution > > > > First of all, thank you very much for your reply @ Alexandre Gramfort . > > > > But none of the files you listed were found in bin > > > > > > This is all the files contained in bin, > > > > I need your further help. > > > > Yours, > > zhipeng > > > > > > 2018-07-29 18:00 GMT+08:00 : > >> > >> Send fieldtrip mailing list submissions to > >> fieldtrip at science.ru.nl > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> or, via email, send a message with subject or body 'help' to > >> fieldtrip-request at science.ru.nl > >> > >> You can reach the person managing the list at > >> fieldtrip-owner at science.ru.nl > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of fieldtrip digest..." > >> > >> > >> Today's Topics: > >> > >> 1. A question about MEG source reconstruction (zhipeng li) > >> 2. Re: A question about MEG source reconstruction > >> (Alexandre Gramfort) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Sun, 29 Jul 2018 10:55:37 +0800 > >> From: zhipeng li > >> To: fieldtrip at science.ru.nl > >> Subject: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> mail.gmail.com> > >> Content-Type: text/plain; charset="utf-8" > >> > >> Dear all, > >> When I was about to create a sourcemodel, I ran into a problem.The > >> documentary which I refers to is Tutorial documentation>Source > >> reconstruction of event-related fields using minimum-norm > >> estimation>Creating a sourcemodel for source-reconstruction of MEG or > EEG > >> data.When I installed MNE as their description, I found that the.sh file > >> doesn't exist.The command I am using is posted below as a > >> picture.Therefore, the following steps cannot be carried out. > >> I would appreciate it if you could help me. > >> Yours, > >> zhipeng > >> -------------- next part -------------- > >> An HTML attachment was scrubbed... > >> URL: attachments/20180729/9711b38d/attachment-0001.html> > >> -------------- next part -------------- > >> A non-text attachment was scrubbed... > >> Name: image.png > >> Type: image/png > >> Size: 5933 bytes > >> Desc: not available > >> URL: attachments/20180729/9711b38d/attachment-0001.png> > >> > >> ------------------------------ > >> > >> Message: 2 > >> Date: Sun, 29 Jul 2018 10:03:59 +0200 > >> From: Alexandre Gramfort > >> To: FieldTrip discussion list > >> Subject: Re: [FieldTrip] A question about MEG source reconstruction > >> Message-ID: > >> gmail.com> > >> Content-Type: text/plain; charset="UTF-8" > >> > >> hi, > >> > >> indeed there is a typo: > >> > >> $ cd $MNE_ROOT > >> $ ls bin/mne_setup* > >> bin/mne_setup bin/mne_setup_matlab_csh > >> bin/mne_setup_mri bin/mne_setup_source_space > >> bin/mne_setup_forward_model bin/mne_setup_matlab_sh bin/mne_setup_sh > >> > >> depending on your shell it can be > >> > >> source $MNE_ROOT/bin/mne_setup_sh > >> > >> HTH > >> Alex > >> > >> On Sun, Jul 29, 2018 at 4:58 AM zhipeng li > wrote: > >> > > >> > External Email - Use Caution > >> > > >> > Dear all, > >> > When I was about to create a sourcemodel, I ran into a problem.The > documentary which I refers to is Tutorial documentation>Source > reconstruction of event-related fields using minimum-norm > estimation>Creating a sourcemodel for source-reconstruction of MEG or EEG > data.When I installed MNE as their description, I found that the.sh file > doesn't exist.The command I am using is posted below as a > picture.Therefore, the following steps cannot be carried out. > >> > I would appreciate it if you could help me. > >> > Yours, > >> > zhipeng > >> > > >> > > >> > > >> > > >> > _______________________________________________ > >> > fieldtrip mailing list > >> > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > https://doi.org/10.1371/journal.pcbi.1002202 > >> > > >> > > >> > The information in this e-mail is intended only for the person to > whom it is > >> > addressed. If you believe this e-mail was sent to you in error and > the e-mail > >> > contains patient information, please contact the Partners Compliance > HelpLine at > >> > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > >> > but does not contain patient information, please contact the sender > and properly > >> > dispose of the e-mail. > >> > >> > >> > >> ------------------------------ > >> > >> Subject: Digest Footer > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> _______________________________________________ > >> fieldtrip mailing list > >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> https://doi.org/10.1371/journal.pcbi.1002202 > >> > >> > >> ------------------------------ > >> > >> End of fieldtrip Digest, Vol 92, Issue 19 > >> ***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > https://doi.org/10.1371/journal.pcbi.1002202 > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > properly > > dispose of the e-mail. > > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Jul 2018 09:23:31 +0000 > From: Simon Hanslmayr > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Postdoc position to work with human single > neurons and LFPs, 9 days left to apply! > Message-ID: > <257F6C65A372A04CA41056EACC0DE7CED8783389 at EX12.adf.bham.ac.uk> > Content-Type: text/plain; charset="utf-8" > > Dear Fieldtrippers, > > We are pleased to announce an open postdoc position in our group to work > with human single neurons and LFP recordings in an exciting memory project > funded by the ERC. The position is initially for 2 years with an option for > 1 year extension. The negotiable start date is 1st Oct. Preliminary data > has been collected and is waiting to be analysed. If you have strong > electrophysiological analytical skills and are interested then please do > not hesitate to apply here: http://www.memorybham.com/open-positions/ > > If you have any questions then please do not hesitate to contact me. > > Best wishes, > Dr. Simon Hanslmayr > Reader in Cognitive Neuroscience > Royal Society Wolfson Research Merit Award Holder > School of Psychology > Hills Building 2.37 > University of Birmingham > Edgbaston > Birmingham > B15 2TT > UK > > Tel +44 121 4146203 > http://www.memorybham.com/people/#/simon-hanslmayr/ > [http://www.nature.com/content/sr/ebm/1248_2014_Branded_Sig_460x80_v1.gif] > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20180730/c066a17a/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image001.gif > Type: image/gif > Size: 8560 bytes > Desc: image001.gif > URL: attachments/20180730/c066a17a/attachment-0001.gif> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > https://doi.org/10.1371/journal.pcbi.1002202 > > > ------------------------------ > > End of fieldtrip Digest, Vol 92, Issue 21 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11167 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 171819 bytes Desc: not available URL: ------------------------------ Subject: Digest Footer _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 ------------------------------ End of fieldtrip Digest, Vol 92, Issue 24 ***************************************** From Pranish.Kantak at UTSouthwestern.edu Tue Jul 31 18:05:38 2018 From: Pranish.Kantak at UTSouthwestern.edu (Pranish Kantak) Date: Tue, 31 Jul 2018 16:05:38 +0000 Subject: [FieldTrip] Blackrock Data Message-ID: <5E4FC234-9787-415B-8126-5A5064FCB061@utsouthwestern.edu> Hi All, I was just wondering if the functionality of using Blackrock data has been implemented into the toolbox yet? Thanks! Pranish Kantak ________________________________ UT Southwestern Medical Center The future of medicine, today. From jan.schoffelen at donders.ru.nl Tue Jul 31 20:49:38 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Tue, 31 Jul 2018 18:49:38 +0000 Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data In-Reply-To: <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> References: <007201d427d1$2d7d9500$8878bf00$@artinis.com> <012001d4280b$0c17baa0$24472fe0$@artinis.com> <002801d4289e$646e96e0$2d4bc4a0$@artinis.com> <0pyb6vhuqo1su9hhxc79wnld.1533044221861@email.android.com> Message-ID: Dear Herbert, I have unsubscribed you. To all, note that you can manage your subscription yourself on the listservers interface, which can be reached through http://www.fieldtriptoolbox.org/discussion_list (following the first link therein). Best wishes, Jan-Mathijs Schoffelen On 31 Jul 2018, at 15:37, Herbert J Gould (hgould) > wrote: Please eliminate me from the mailing list. I have retired. Thank you. Sent from my Verizon Wireless 4G LTE smartphone -------- Original message -------- From: "Jörn M. Horschig" Date:07/31/2018 2:18 AM (GMT-06:00) To: 'FieldTrip discussion list' Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, Thanks for sending the data. As discussed offline, there are no events in these data. You can also verify this using fieldtrip by running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); The output will be: Warning: no trialfun was specified, using ft_trialfun_general In ft_definetrial at line 138 evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.5 no trials have been defined yet, see FT_DEFINETRIAL for further help found 1 events created 0 trials the call to "ft_definetrial" took 1 seconds The found event corresponds to the individual values of the AD channel, which in this case is the battery level (so not very useful for you right now). You can still read in the oxy3-data running this code: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\OCTAMON.oxy3'; >> data = ft_preprocessing(cfg); The output will be: processing channel { 'Rx1-Tx1 [839nm]' 'Rx1-Tx1 [757nm]' 'Rx1-Tx2 [839nm]' 'Rx1-Tx2 [757nm]' 'Rx1-Tx3 [839nm]' 'Rx1-Tx3 [757nm]' 'Rx1-Tx4 [839nm]' 'Rx1-Tx4 [757nm]' 'Rx2-Tx5 [839nm]' 'Rx2-Tx5 [757nm]' 'Rx2-Tx6 [839nm]' 'Rx2-Tx6 [757nm]' 'Rx2-Tx7 [839nm]' 'Rx2-Tx7 [757nm]' 'Rx2-Tx8 [839nm]' 'Rx2-Tx8 [757nm]' 'ADC001' } reading and preprocessing reading and preprocessing trial 1 from 1 the call to "ft_preprocessing" took 2 seconds You also sent another data file with events. The rationale here is equivalent to above. First, check the data for events: >> cfg = []; >> cfg.dataset = 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3'; >> cfg.trialdef.eventtype = '?'; >> ft_definetrial(cfg); With the output being: evaluating trialfunction 'ft_trialfun_general' reading the header from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' reading the events from 'D:\Data\Customers\Sunny Pitt\SunnyFinger.oxy3' the following events were found in the datafile event type: 'ADC001' with event values: 1.4 event type: 'event' with event values: 'A' 'B' 'C' 'D' no trials have been defined yet, see FT_DEFINETRIAL for further help found 5 events created 0 trials the call to "ft_definetrial" took 3 seconds I am not sure what your events mean, but you are then able to define trials according to these events, e.g. >> cfg.trialdef.eventtype = 'event'; >> cfg.trialdef.eventvalue = 'B'; >> cfg.trialdef.prestim = 5; >> cfg.trialdef.prestim = 35; >> cfg = ft_definetrial(cfg); This would create a trial definition for event B, starting 5 second before event B ending 35 seconds after event B. Reading in the data would then go via: >> data = ft_preprocessing(cfg); The usage is 100% equivalent to standard FieldTrip conventions, so you can follow any tutorial on the FieldTrip wiki and try it with your NIRS data (but keep the fundamental difference between EEG and fNIRS in mind). I hope this helps to get started! Btw, if someone wants to do a combined EEG-fNIRS analysis using FieldTrip, give me a shout. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Jörn M. Horschig Sent: Monday, July 30, 2018 15:42 To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hi Sunny, The ADC channels in the tutorial are used as a trigger-channel. I am not sure how you insert the triggers in your experiment, but the Octamon has no direct trigger input (you could add triggers either wirelessly using a PortaSync or directly from within Oxysoft). The ADC of the Octamon is the battery level and not a trigger input. Depending on what you did, you have to follow different processing steps. If you let me know more about the events and triggers, I can let you know what to do (you could also send me some example data and I will send you an example script back that reads in the data in FieldTrip). With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: Sunny p > Sent: Monday, July 30, 2018 15:29 To: FieldTrip discussion list >; jorn at artinis.com Cc: Arana, S.L. (Sophie) > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Jorn, Thanks a lot for your response. I am working with Octamon data (4*2 Channel). I am trying to visualize the data using topo plot on head based image following http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel#epoch (nirs multi channel tutorial based on Oxymon which has 48 channel). I am wondering what parameter changes should I make to get the data for OCTAMON visualization as my data has only ADC001 and there is no ADC002 in data for epoch section. As I am not an NIRS expert, its difficult to figure out which parameters gives me the visualization as its throwing errors when following the tutorial. Thanks for your understanding and support. Best Regards, Sunny On Mon, Jul 30, 2018 at 2:47 AM, Jörn M. Horschig > wrote: Hi Sunny, Yes, the FieldTrip NIRS plugin works for all our devices. With best regards, Jörn -- Jörn M. Horschig, PhD, Project Leader & Software Engineer Artinis Medical Systems | +31 481 350 980 Sign up for our NIRS newsletter From: fieldtrip > On Behalf Of Sunny p Sent: Friday, July 27, 2018 20:41 To: Arana, S.L. (Sophie) > Cc: FieldTrip discussion list > Subject: Re: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello Sophie, Once this tutorial is fully developed, Can we use this for OCTAMON (https://www.artinis.com/octamon/) ? Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 12:35 PM, Sunny p > wrote: Hello Sophie, Thanks a lot for providing this code. I am making some changes that are useful. Can you please inform what is the variable 'data_func' in the code relates to. This is the last undefined variable in code. Thanks for your understanding and support. Best Regards, Sunny On Wed, Jul 25, 2018 at 8:22 AM, Sunny p > wrote: Hello Sophie, Thanks a lot for your clarification. This is very useful. Sunny On Wednesday, July 25, 2018, Arana, S.L. (Sophie) > wrote: Dear Sunny, the multi-channel NIRS data tutorial is currently under construction and will hopefully be fully available in a couple of weeks. Until then, there might still be some inconsistencies such as the one you have encountered. The variable you refer to is indeed missing. It refers to a filtered version of the data, and you can created it by running the following code before the epoching. cfg = []; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.01; data_flt = ft_preprocessing(cfg,data_down); This should help you to continue with the tutorial, but please do keep in mind that we are currently working on it and you might encounter some other inconsistencies still later on. Best, Sophie ________________________________ From: fieldtrip [fieldtrip-bounces at science.ru.nl] on behalf of Sunny p [sunnypitt1965 at gmail.com] Sent: Tuesday, July 24, 2018 9:24 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] Regarding Tutorial: Preprocessing and averaging of multi-channel NIRS data Hello All Good Day, Hope you are doing fine, Thanks a lot for providing with fieldtrip which is really useful to analyze fNIRS data. I have an issue in the "Preprocessing and averaging of multi-channel NIRS data" tutorial. Can you please help me with this issue? Issue: In the "Preprocessing and averaging of multi-channel NIRS data" tutorial " http://www.fieldtriptoolbox.org/tutorial/nirs_multichannel The "Epoch" section consists of a variable "data_flt.fsample" where "data_flt" variable is not defined. Can you please inform what is this variable related to? as this is needed to complete my analysis. Thanks for your understanding and support Best Regards, Sunny [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png] Virus-free. www.avg.com _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 _______________________________________________ fieldtrip mailing list https://mailman.science.ru.nl/mailman/listinfo/fieldtrip https://doi.org/10.1371/journal.pcbi.1002202 -------------- next part -------------- An HTML attachment was scrubbed... URL: