From 22735819 at student.uwa.edu.au Sun Mar 1 06:38:41 2020 From: 22735819 at student.uwa.edu.au (Jamie Vo (22735819)) Date: Sun, 1 Mar 2020 05:38:41 +0000 Subject: [Simnibs-discuss] RTMS parameters Message-ID: Hi to whoever it may concern, I am currently a second year student studying at the University at Western Australia, and am using SIMNIBS to model RTMS simulations on the brain. I was wondering if there are any options where we can input parameters for the magnetic field strength. Furthermore, is there any way to edit coil parameters, such as wire diameters and number of windings on the coil. Kind regards, Jamie Vo -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Mon Mar 2 11:30:38 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Mon, 2 Mar 2020 11:30:38 +0100 Subject: [Simnibs-discuss] RTMS parameters In-Reply-To: References: Message-ID: Hello, /I am currently a second year student studying at the University at Western Australia, and am using SIMNIBS to model RTMS simulations on the brain. I was wondering if there are any options where we can input parameters for the magnetic field strength./ I assume you mean the dI/dt parameter? If so, this is dependent on simulator, coil model, and pulse type used. What are you using for your study? /Furthermore, is there any way to edit coil parameters, such as wire diameters and //number of windings on the coil./ / / Not very easily, as we represent the coils either using magnetic dipoles (.ccd files) or magnetic vector potentials in a volume (dA/dt), therefore do store information about underlying geometry.? But of course you could create your own coil models based on some geometry. Best Regards, Guilherme On 01/03/2020 06.38, Jamie Vo (22735819) wrote: > Hi to whoever it may concern, > > I am currently a second year student studying at the University at > Western Australia, and am using SIMNIBS to model RTMS simulations on > the brain. I was wondering if there are any options where we can input > parameters for the magnetic field strength. > > Furthermore, is there any way to edit coil parameters, such as wire > diameters and number of windings on the coil. > > Kind regards, > > Jamie Vo > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From xiaxzhao at mail.ustc.edu.cn Tue Mar 3 10:57:33 2020 From: xiaxzhao at mail.ustc.edu.cn (xiaxzhao at mail.ustc.edu.cn) Date: Tue, 3 Mar 2020 17:57:33 +0800 (GMT+08:00) Subject: [Simnibs-discuss] Problem of User Registration Message-ID: <19a72ab.661f2.1709fd4438a.Coremail.xiaxzhao@mail.ustc.edu.cn> Hello! ???? I am currently a postgraduate in mainland China, and I want to download simNIBs for the purpose of academic.But it seems that I have problems in user registration. I send a picture as attachment, and hopefully can get feedback of my problem. It would be gratefully appreciated. Thanks! best -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: prob.png Type: image/png Size: 82417 bytes Desc: not available URL: From Jade.Jackson at mrc-cbu.cam.ac.uk Tue Mar 3 16:05:55 2020 From: Jade.Jackson at mrc-cbu.cam.ac.uk (Jade Jackson) Date: Tue, 3 Mar 2020 15:05:55 +0000 Subject: [Simnibs-discuss] Position window and efield Message-ID: <4911e81ba4514a528f13648cf5ca45cb@mrc-cbu.cam.ac.uk> Dear developers, Thank you for developing this toolbox. I have specific MNI coordinates that I want to stimulate and I want to understand whether the stimulation will spread to a control ROI, and if so, to what degree. I have a couple of very basic questions, in the position window, and next to the dropdown box for the EEG cap positions, are these x y z coordinates that I can input in MNI space? Also, if I generate a model with stimulation to specific coordinates and then calculate the norm Efield at the control ROI, what does the output equate to? How can I know if this is equivalent to say their motor threshold? Thanks, Jade -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Tue Mar 3 17:25:33 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Tue, 3 Mar 2020 17:25:33 +0100 Subject: [Simnibs-discuss] Position window and efield In-Reply-To: <4911e81ba4514a528f13648cf5ca45cb@mrc-cbu.cam.ac.uk> References: <4911e81ba4514a528f13648cf5ca45cb@mrc-cbu.cam.ac.uk> Message-ID: <5dfb5d1d-11a6-6011-fe33-67b7c88f2ce7@drcmr.dk> Dear Jade, Thanks a lot for your interest in SimNIBS. /in the position window, and next to the dropdown box for the EEG cap positions, are these x y z coordinates that I can input in MNI space?/ These positions are in world space of the input scan. However, you can easily transform between subject space and MNI space. Please see here for more information: https://simnibs.github.io/simnibs/build/html/documentation/coordinates.html You could also skip the GUI completely and setup simulations with python or matlab scripts where you input MNI coordinates directly. Examples: https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TMS_MNI.m https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TMS_MNI.py /Also, if I generate a model with stimulation to specific coordinates and then calculate the norm Efield at the control ROI, what does the output equate to? How can I know if this is equivalent to say their motor threshold? / / / The output is an electric field in V/m. We know that electric fields and motor threshold in TMS are correlated (see https://doi.org/10.1093/cercor/bhw292, https://doi.org/10.1016/j.neuroimage.2019.116486, https://doi.org/ 10.1016/j.brs.2017.09.011 ). But the relationship between the two is complex. So we can't say at the moment that if the electric field in a given region (for example hand knob) is above a certain value you will for sure an MEP, but rather that a larger electric field increases the probability of getting an MEP. Best Regards, Guilherme On 03/03/2020 16.05, Jade Jackson wrote: > > Dear developers, > > > Thank you for developing this toolbox. I have specific MNI coordinates > that I want to stimulate and I want to understand whether the > stimulation will spread to a control ROI, and if so, to what degree. > > I have a couple of very basic questions, in the position window, and > next to the dropdown box for the EEG cap positions, are these x y z > coordinates that I can input in MNI space? Also, if I generate a model > with stimulation to specific coordinates and then calculate the norm > Efield at the control ROI, what does the output equate to? How can I > know if this is equivalent to say their motor threshold? > > Thanks, > > Jade > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Wed Mar 4 09:28:23 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Wed, 4 Mar 2020 09:28:23 +0100 Subject: [Simnibs-discuss] Question about the Scripting Simulations/Optimizations In-Reply-To: <43906438-d42a-f0a7-2096-dd3917327154@riken.jp> References: <87831c52-19bf-8e7f-7884-187a5d622344@riken.jp> <8beaec8e-01ed-391a-074a-e10dea05336a@drcmr.dk> <18e50613-36f4-fa84-6c88-08a84449eeb5@riken.jp> <8eb6aedf-ac3b-22c4-051e-76ed33b23fab@drcmr.dk> <572c6f11-1703-1ae6-d3d0-304287257b6c@riken.jp> <87cc8ab8-a416-2430-7185-131abf810142@drcmr.dk> <43906438-d42a-f0a7-2096-dd3917327154@riken.jp> Message-ID: Dear Dr. Zama, Thank you for your interest and for reporting the issue! On 04/03/2020 02.37, Takuro ZAMA wrote: > Dear Dr. Saturnino, > > Thank you for your speedy handling and advice. > I am so excited to use the new version. > I will try it soon, and keep the channelnr variable unset. > > I sincerely appreciate your kind support. > From next time, I will post to the public mailing list. > > Best regards, > Takuro > > On 2020/03/03 22:15, Guilherme B Saturnino wrote: >> Dear Dr. Zama, >> >> >> There was a problem in setting up the leadfields with 2-layer >> electrodes. Thanks a lot for pointing this out. We just released >> version 3.1.2 with a fix. >> >> Even thought the problem was not with "channelnr", I would still like >> to strongly advise you to keep this variable unset. >> >> >> Best Regards, >> >> Guilherme >> >> >> >> >> 28/02/2020 17.23, Takuro ZAMA wrote: >> >>> Dear Dr. Saturnino, >>> >>> Thank you for your information. I got it about the function of the >>> "channelnr" option. >>> I commented out that lines to unset "channelnr". >>> However, I still get same error as follows: >>> -------------- >>> [ simnibs ]CRITICAL: Uncaught exception >>> Traceback (most recent call last): >>> ? File >>> "c:\Users\zama\AppData\Local\SimNIBS\miniconda3\envs\simnibs_env\lib\site-packages\simnibs\simulation\cond.py", >>> line 154, in test_numerical >>> ??? c = float(v) >>> TypeError: float() argument must be a string or a number, not >>> 'NoneType' >>> >>> During handling of the above exception, another exception occurred: >>> >>> TypeError: The value 100 in cond_list is not numerical >>> ------------------ >>> >>> Do you have any other idea? >>> >>> Best regards, >>> Takuro >>> >>> >>> >>> On 2020/02/28 17:44, Guilherme B Saturnino wrote: >>>> Dear Dr. Zama, >>>> >>>> >>>> Thanks for sending the script. >>>> >>>> I see you are setting all "channelnr" to 2 in line 74 and "1" in >>>> line 90. Please remove this lines and just leave "channelnr" unset. >>>> This option basically says which electrodes should be >>>> "short-circuited" together, and it is very tricky to use it in tDCS >>>> optimization. We might just remove this option in a near future. >>>> >>>> >>>> Best Regards, >>>> >>>> Guilherme >>>> >>>> >>>> On 27/02/2020 06.48, Takuro ZAMA wrote: >>>>> Dear Dr. Saturnino, >>>>> >>>>> Thank you for your kind support. >>>>> >>>>>>> It depends. The one in the link I sent you is. But the one in >>>>>>> m2m_subID/eeg_positions/ is in subject spaece >>>>> I am sorry for not explaining sufficiently. >>>>> This is consistent with my perception. >>>>> >>>>>>> Could you please send me your script? >>>>> Sure. Please find the attached as .txt and .m files. >>>>> >>>>> Best regards, >>>>> Takuro >>>>> >>>>> On 2020/02/25 20:47, Guilherme B Saturnino wrote: >>>>>> Dear Dr. Zama, >>>>>> >>>>>> >>>>>> Thanks a lot for the feedback and to allow us to publish this >>>>>> exchange. >>>>>> >>>>>> /In "EEG10-10_UI_Jurak_2007.csv", the position is described in >>>>>> the MNI coordinate system, right? >>>>>> / >>>>>> >>>>>> / >>>>>> / >>>>>> >>>>>> It depends. The one in the link I sent you is. But the one in >>>>>> m2m_subID/eeg_positions/ is in subject spaece >>>>>> >>>>>> / >>>>>> //In "EEG10-10_UI_Jurak_2007.csv", the position is described in >>>>>> the MNI coordinate system, right? // >>>>>> //It seems we have no choice but to translate the cheek position >>>>>> in subject space to MNI space via "subject2mni_coords" . // >>>>>> //For your information, I processed with the following steps: // >>>>>> //1) I decided cheek position visually for each subject (N = 5). // >>>>>> //2) I translated the position to MNI space and averaged. // >>>>>> //3) I added the averaged MNI position to the CSV file as a new >>>>>> electrode. / >>>>>> >>>>>> >>>>>> I think this makes a lot of sense >>>>>> >>>>>> >>>>>> / >>>>>> //I have new question about the optimization. // >>>>>> //Now, I am trying to change the electrode setting (e.g., shape, >>>>>> size). // >>>>>> //I prepared the tdcs_lf.electrode(1)~tdcs_lf.electrode(N). // >>>>>> //N means the number of all electrodes except the "Fiducial". // >>>>>> //These had following fields: // >>>>>> //- channelnr // >>>>>> //- dimensions // >>>>>> //- shape // >>>>>> //- thickness // >>>>>> //- centre // >>>>>> //- pos_ydir // >>>>>> //- plug.shape // >>>>>> //- plug.dimensions // >>>>>> //- plug.centre // >>>>>> //// >>>>>> //The examples of the result of placeing electrode are >>>>>> follows:--------------- // >>>>>> //? // >>>>>> //[ simnibs ]INFO: Placing Electrode: // >>>>>> //definition: plane // >>>>>> //shape: ellipse // >>>>>> //centre: [ 20.1864 -80.4478 -38.9034] // >>>>>> //pos_ydir: [] // >>>>>> //dimensions: [20, 20] // >>>>>> //thickness:[5, 2] // >>>>>> //channelnr: 76 // >>>>>> //number of holes: 0 // >>>>>> //// >>>>>> //[ simnibs ]INFO: Placing Electrode: // >>>>>> //definition: plane // >>>>>> //shape: rect // >>>>>> //centre: [-45.0869? 81.2591 -41.0414] // >>>>>> //pos_ydir: [] // >>>>>> //dimensions: [50, 50] // >>>>>> //thickness:[5, 2] // >>>>>> //channelnr: 77 // >>>>>> //number of holes: 0 // >>>>>> //? // >>>>>> //-------------------------- // >>>>>> //// >>>>>> //After the "[ simnibs ]INFO: Using isotropic conductivities", >>>>>> program output following error:------------------------ // >>>>>> //[ simnibs ]CRITICAL: Uncaught exception // >>>>>> //Traceback (most recent call last): // >>>>>> //? File "SIMNIBSDIR\simulation\cond.py", line 154, in >>>>>> test_numerical // >>>>>> //??? c = float(v) // >>>>>> //TypeError: float() argument must be a string or a number, not >>>>>> 'NoneType' // >>>>>> //During handling of the above exception, another exception >>>>>> occurred: // >>>>>> //TypeError: The value 100 in cond_list is not numerical // >>>>>> //-------------------- // >>>>>> //// >>>>>> //Do you have any idea about this error? // >>>>>> //My electrode setting is wrong? / >>>>>> >>>>>> >>>>>> Could you please send me your script? >>>>>> >>>>>> >>>>>> Best Regards, >>>>>> >>>>>> Guilherme >>>>>> >>>>>> On 25/02/2020 04.22, Takuro ZAMA wrote: >>>>>>> Dear Dr. Saturnino, >>>>>>> >>>>>>> I am sorry for the late response. I was trying what you told me. >>>>>>> Thanks to your support, the simulation and optimization worked >>>>>>> well! >>>>>>> Sure, please publish this discussion in the public mailing list. >>>>>>> >>>>>>> In "EEG10-10_UI_Jurak_2007.csv", the position is described in >>>>>>> the MNI coordinate system, right? >>>>>>> It seems we have no choice but to translate the cheek position >>>>>>> in subject space to MNI space via "subject2mni_coords" . >>>>>>> For your information, I processed with the following steps: >>>>>>> 1) I decided cheek position visually for each subject (N = 5). >>>>>>> 2) I translated the position to MNI space and averaged. >>>>>>> 3) I added the averaged MNI position to the CSV file as a new >>>>>>> electrode. >>>>>>> >>>>>>> I have new question about the optimization. >>>>>>> Now, I am trying to change the electrode setting (e.g., shape, >>>>>>> size). >>>>>>> I prepared the tdcs_lf.electrode(1)~tdcs_lf.electrode(N). >>>>>>> N means the number of all electrodes except the "Fiducial". >>>>>>> These had following fields: >>>>>>> - channelnr >>>>>>> - dimensions >>>>>>> - shape >>>>>>> - thickness >>>>>>> - centre >>>>>>> - pos_ydir >>>>>>> - plug.shape >>>>>>> - plug.dimensions >>>>>>> - plug.centre >>>>>>> >>>>>>> The examples of the result of placeing electrode are >>>>>>> follows:--------------- >>>>>>> ? >>>>>>> [ simnibs ]INFO: Placing Electrode: >>>>>>> definition: plane >>>>>>> shape: ellipse >>>>>>> centre: [ 20.1864 -80.4478 -38.9034] >>>>>>> pos_ydir: [] >>>>>>> dimensions: [20, 20] >>>>>>> thickness:[5, 2] >>>>>>> channelnr: 76 >>>>>>> number of holes: 0 >>>>>>> >>>>>>> [ simnibs ]INFO: Placing Electrode: >>>>>>> definition: plane >>>>>>> shape: rect >>>>>>> centre: [-45.0869? 81.2591 -41.0414] >>>>>>> pos_ydir: [] >>>>>>> dimensions: [50, 50] >>>>>>> thickness:[5, 2] >>>>>>> channelnr: 77 >>>>>>> number of holes: 0 >>>>>>> ? >>>>>>> -------------------------- >>>>>>> >>>>>>> After the "[ simnibs ]INFO: Using isotropic conductivities", >>>>>>> program output following error:------------------------ >>>>>>> [ simnibs ]CRITICAL: Uncaught exception >>>>>>> Traceback (most recent call last): >>>>>>> ? File "SIMNIBSDIR\simulation\cond.py", line 154, in test_numerical >>>>>>> ??? c = float(v) >>>>>>> TypeError: float() argument must be a string or a number, not >>>>>>> 'NoneType' >>>>>>> During handling of the above exception, another exception occurred: >>>>>>> TypeError: The value 100 in cond_list is not numerical >>>>>>> -------------------- >>>>>>> >>>>>>> Do you have any idea about this error? >>>>>>> My electrode setting is wrong? >>>>>>> >>>>>>> Best regards, >>>>>>> Takuro Zama >>>>>>> >>>>>>> On 2020/02/20 22:22, Guilherme B Saturnino wrote: >>>>>>>> Dear Dr. Zama, >>>>>>>> >>>>>>>> >>>>>>>> Thank you for your interest in SimNIBS! >>>>>>>> >>>>>>>> >>>>>>>> 1. Yes, you can. I think the best way to do this is to define >>>>>>>> another electrode cap ".csv" file with the additional positions >>>>>>>> you want. You can either: >>>>>>>> >>>>>>>> A) Add the new position to the file >>>>>>>> m2m_subID/eeg_positions/EEG10-10_UI_Jurak_2007.csv >>>>>>>> >>>>>>>> B) Download this file >>>>>>>> , >>>>>>>> modify it to add the new electrode,? and run the >>>>>>>> mni2subject_coords >>>>>>>> >>>>>>>> command line tool to bring the eeg positions to subject space. >>>>>>>> Afterwards, when running the leadfield, add /leadfield.eeg_cap >>>>>>>> = 'path/to/cap.csv'/ >>>>>>>> >>>>>>>> 2. Yes, this would be the constraint on the number of >>>>>>>> electrodes. Just set for example /opt.max_active_electrodes = >>>>>>>> 2//./ >>>>>>>> >>>>>>>> 3. Yes, you need to define cheek positions in MNI space and >>>>>>>> follow the instructions (1B) above. >>>>>>>> >>>>>>>> >>>>>>>> Best Regards, >>>>>>>> >>>>>>>> Guilherme Saturnino >>>>>>>> >>>>>>>> >>>>>>>> I feel other people could also benefit from this discussion. >>>>>>>> Can I publish it in our public mailing list? >>>>>>>> >>>>>>>> On 20/02/2020 11.34, Takuro ZAMA wrote: >>>>>>>>> Dear Sir or Madam, >>>>>>>>> >>>>>>>>> I am Takuro Zama, and a research scientist at the RIKEN in Japan. >>>>>>>>> I have started to use the simNIBS for tES. Thank you for the >>>>>>>>> wonderful tool! >>>>>>>>> >>>>>>>>> I am trying to reconstruct mesh images using T1- and T2-images >>>>>>>>> with "headreco" and to simulate tES for each subject. >>>>>>>>> The return electrode position is considering the cheek >>>>>>>>> position, and I would like to optimize where the electrodes >>>>>>>>> should be placed to stimulate the specified brain region. >>>>>>>>> I have following questions about the Scripting: >>>>>>>>> >>>>>>>>> 1. Can I use a extracephalic position in optimization? >>>>>>>>> Sometimes, a return electrode of tES is set on a extracephalic >>>>>>>>> position such as cheek. >>>>>>>>> Since I am considering EEG measurement during tDCS, I also >>>>>>>>> would like to put the return electrode on the cheek to keep >>>>>>>>> the number of EEG electrodes. >>>>>>>>> Can I optimize the electrodes position taking into account the >>>>>>>>> cheek position? >>>>>>>>> >>>>>>>>> 2. Can optimization output only one pair of electrodes? >>>>>>>>> If I perform optimization based on the electrode arrangement >>>>>>>>> of EEG10-10_UI_Jurak_2007, I can get the combination of >>>>>>>>> multiple electrodes. >>>>>>>>> I would like to get pair, which is optimized by 2 electrodes, >>>>>>>>> because I use 2 electrodes for stimulation. >>>>>>>>> Is the optimization just a suggestion and is the simulation, >>>>>>>>> which is based on the optimization result, recommended >>>>>>>>> eventually? >>>>>>>>> >>>>>>>>> 3. Can I get a coordinates of cheek position automatically? >>>>>>>>> When run a simulation with cheek position, I would like to >>>>>>>>> determine the coordinates of the cheek position based on >>>>>>>>> specific criteria like the EEG10-10 electrode. >>>>>>>>> However, cheek coordinates are not included in "m2m_subID / >>>>>>>>> eeg_positions / EEG10-10_UI_Jurak_2007.csv" which is >>>>>>>>> automatically calculated by "haedreco". >>>>>>>>> Is there any way to get automatically the cheek coordinates on >>>>>>>>> the subject-space? >>>>>>>>> If I can do that, the simulation in CUI will be more comfortable. >>>>>>>>> >>>>>>>>> Yours faithfully, >>>>>>>>> Takuro Zama >>>>> >>> > From guilhermebs at drcmr.dk Fri Mar 6 11:27:22 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Fri, 6 Mar 2020 11:27:22 +0100 Subject: [Simnibs-discuss] Problem of User Registration In-Reply-To: <19a72ab.661f2.1709fd4438a.Coremail.xiaxzhao@mail.ustc.edu.cn> References: <19a72ab.661f2.1709fd4438a.Coremail.xiaxzhao@mail.ustc.edu.cn> Message-ID: <72aeb31a-a47d-7530-fded-00e92b91cd51@drcmr.dk> Hello, We applied some changes to the website. Please try again and inform us if the CAPTCHA shows up. Best Regards, Guilherme On 03/03/2020 10.57, xiaxzhao at mail.ustc.edu.cn wrote: > Hello! > ???? > ? ?I am currently a postgraduate in mainland China, and I want to > download simNIBs for the purpose of academic.But it seems that I have > problems in user registration. > ? ?I send a picture as attachment, and hopefully can get feedback of > my problem. It would be gratefully appreciated. Thanks! > best > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From xiaxzhao at mail.ustc.edu.cn Tue Mar 10 14:08:19 2020 From: xiaxzhao at mail.ustc.edu.cn (xiaxzhao at mail.ustc.edu.cn) Date: Tue, 10 Mar 2020 21:08:19 +0800 (GMT+08:00) Subject: [Simnibs-discuss] How to run TACs stimulation in SimNIBS In-Reply-To: <19a72ab.661f2.1709fd4438a.Coremail.xiaxzhao@mail.ustc.edu.cn> References: <19a72ab.661f2.1709fd4438a.Coremail.xiaxzhao@mail.ustc.edu.cn> Message-ID: <704d927d.ee79.170c48f70e3.Coremail.xiaxzhao@mail.ustc.edu.cn> Hello? Although I have searched the issues of TACS stimulation in simNIBS, and I know why it could work in simNIBS. I still cannot find any instruction on how to perform TACS in simNIBS, can I get any instruction of how to perform TACS in GUI or in scripts? Any further replay is appreciated, thanks a lot and have a nice day. Best, Xinzhao -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Tue Mar 10 17:48:16 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Tue, 10 Mar 2020 17:48:16 +0100 Subject: [Simnibs-discuss] How to run TACs stimulation in SimNIBS In-Reply-To: <704d927d.ee79.170c48f70e3.Coremail.xiaxzhao@mail.ustc.edu.cn> References: <19a72ab.661f2.1709fd4438a.Coremail.xiaxzhao@mail.ustc.edu.cn> <704d927d.ee79.170c48f70e3.Coremail.xiaxzhao@mail.ustc.edu.cn> Message-ID: <9caace8d-bdae-6602-d228-e576aeade33e@drcmr.dk> Hi, To simulate tACS in SimNIBS, we take advantage of the fact that the temporal component of the field and the spatial component of the field are independent. This means that you can just simulate a tDCS field and that will also tell you how a TACS field will be distributed in the brain. Please see: https://simnibs.github.io/simnibs/build/html/faq.html#can-simnibs-simulate-tacs Best Regards, Guilherme On 10/03/2020 14.08, xiaxzhao at mail.ustc.edu.cn wrote: > Hello? > ? ?Although I have searched the issues of TACS stimulation in simNIBS, > and I know why it could work in simNIBS. I still cannot find any > instruction on how to perform TACS in simNIBS, can I get any > instruction of how to perform TACS in GUI or in scripts? > ? ?Any further replay is appreciated, thanks a lot and have a nice day. > Best, Xinzhao > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From Mariacarla.Memeo at iit.it Fri Mar 13 13:00:03 2020 From: Mariacarla.Memeo at iit.it (Mariacarla Memeo) Date: Fri, 13 Mar 2020 12:00:03 +0000 Subject: [Simnibs-discuss] info about cTBS Message-ID: <4ae2d54c2e0343ea82c6f3195e002f5c@iit.it> To whom it may concerns, I'm Mariacarla Memeo and I work at the Italian Institute of technology, in the Cognition Motion and Neuroscience (CMON) Unit. We usually use the TMS with a single pulse protocol but recently we used a continuous theta burst stimulation as in Huang et al., 2005 (DOI: 10.1016/j.neuron.2004.12.033): cTBS with three pulses at 50 Hz repeatedly applied at intervals of 200 ms (5 Hz) for 40 s. I tried your software for a single pulse protocol and I find it really useful but I was wondering if there is a way to implement other TMS protocols, like the one I reported. Thank you for your time. Best, ******************************************************** Mariacarla Memeo, PhD C'MON Unit - Fondazione Istituto Italiano di Tecnologia Center for Human Technologies Via Enrico Melen 83, 16152 , building B, 7? floor Phone: +39 010 8172239 IIT webpage: https://www.iit.it/people/mariacarla-memeo RG webpage: https://www.researchgate.net/profile/Mariacarla_Memeo ******************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Fri Mar 13 16:38:46 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Fri, 13 Mar 2020 16:38:46 +0100 Subject: [Simnibs-discuss] info about cTBS In-Reply-To: <4ae2d54c2e0343ea82c6f3195e002f5c@iit.it> References: <4ae2d54c2e0343ea82c6f3195e002f5c@iit.it> Message-ID: <7d2df9b5-a4d8-df05-9850-ee6d5378d798@drcmr.dk> Hello, In TMS, the time component and the spatial component of the fields are decoupled. That means that we can write E(x, t) = E(x)T(t) E(x) is a component which is dependent on coil geometry, coil position, and subject head geometry. That is what SimNIBS calculates. T(t) Depends only in pulse shape and stimulation intensity. It does not affect the spatial distribution of the field, but rather acts as a scaling parameter. For TMS, T(t) = dI(t)/dt, that is, the rate of change of current through the coil. This means that SimNIBS does not assume any particular time dynamics. Rather, it takes a snapshot at the field at a single time point, typically at the peak dI/dt value. For more time points, all you need to do is to scale the field accordingly. However, the peak dI/dt value is dependent on coil model, stimulator model, pulse shape and pulse intensity. In some stimulator models, this value is shown in the screen after a pulse. For more information, please see: https://simnibs.github.io/simnibs/build/html/faq.html#what-is-the-di-dt-in-tms-simulations Best, Guilherme On 13/03/2020 13.00, Mariacarla Memeo wrote: > > To whom it may concerns, > > I?m Mariacarla Memeo and I work at the Italian Institute of > technology, in the Cognition Motion and Neuroscience (CMON > ) > Unit. We usually use the TMS with a single pulse protocol but recently > we used a continuous theta burst stimulation as in Huang et al., 2005 > (DOI: 10.1016/j.neuron.2004.12.033): cTBS with three pulses at 50 Hz > repeatedly applied at intervals of 200 ms (5 Hz) for 40 s. > > I tried your software for a single pulse protocol and I find it really > useful but I was wondering if there is a way to implement other TMS > protocols, like the one I reported. > > Thank you for your time. > > Best, > > ******************************************************** > > *Mariacarla Memeo*, PhD > > C?MON Unit - Fondazione Istituto Italiano di Tecnologia > > Center for Human Technologies > > Via Enrico Melen 83, 16152 , building B, 7? floor > > Phone: +39 010 8172239 > > IIT webpage: https://www.iit.it/people/mariacarla-memeo > > RG webpage: https://www.researchgate.net/profile/Mariacarla_Memeo > > ******************************************************** > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jane.Tan at murdoch.edu.au Thu Mar 19 06:06:09 2020 From: Jane.Tan at murdoch.edu.au (Jane Tan) Date: Thu, 19 Mar 2020 05:06:09 +0000 Subject: [Simnibs-discuss] normE values in MNI space Message-ID: Hi SimNIBS Team, I found some negative values in my nifti volume for normE in MNI space, and I thought something must have gone awry during the segmentation process for my head mesh (created using headreco (with cat) on a MNI152 T1-weighted image). However, the head mesh looks okay when I checked it with gmsh. The headreco_log doesn't seem to indicate any issues either - at least not to my untrained eye. I do not have access to freeview, and couldn't do a proper check via headreco. I'm also wondering if it might be due to normE not being very accurate as a result of registration to the MNI template? Your suggestions would be greatly appreciated. I am happy to provide my head mesh and segmentation results if that would be of any help. best regards, Jane Best regards, Jane -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jane.Tan at murdoch.edu.au Thu Mar 19 06:06:09 2020 From: Jane.Tan at murdoch.edu.au (Jane Tan) Date: Thu, 19 Mar 2020 05:06:09 +0000 Subject: [Simnibs-discuss] normE values in MNI space Message-ID: Hi SimNIBS Team, I found some negative values in my nifti volume for normE in MNI space, and I thought something must have gone awry during the segmentation process for my head mesh (created using headreco (with cat) on a MNI152 T1-weighted image). However, the head mesh looks okay when I checked it with gmsh. The headreco_log doesn't seem to indicate any issues either - at least not to my untrained eye. I do not have access to freeview, and couldn't do a proper check via headreco. I'm also wondering if it might be due to normE not being very accurate as a result of registration to the MNI template? Your suggestions would be greatly appreciated. I am happy to provide my head mesh and segmentation results if that would be of any help. best regards, Jane Best regards, Jane -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Thu Mar 19 09:08:43 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Thu, 19 Mar 2020 09:08:43 +0100 Subject: [Simnibs-discuss] normE values in MNI space In-Reply-To: References: Message-ID: <5cceb207-5e23-c0c6-36dd-35ede63f07ba@drcmr.dk> Dear Jane, How many negative values are there? This is likely an artifact due to spline interpolation of the electric field from the original space to MNI space. Best Regards, Guilherme On 19/03/2020 06.06, Jane Tan wrote: > Hi SimNIBS Team, > > I found some negative values in my nifti volume for normE in MNI > space, and I thought something must have gone awry during the > segmentation process for my head mesh (created using headreco (with > cat) on a MNI152 T1-weighted image).? However, the head mesh looks > okay when I checked it with gmsh. The headreco_log doesn't seem to > indicate any issues either - at least not to my untrained eye. I do > not have access to freeview, and couldn't do a proper check via headreco. > > I'm also wondering if it might be due to normE not being very accurate > as a result of registration to the MNI template? > > Your suggestions would be greatly appreciated. I am happy to provide > my head mesh and segmentation results if that would be of any help. > > best regards, > Jane > > > > > > > Best regards, > > > Jane > > > ** > ** > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Thu Mar 19 11:32:35 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Thu, 19 Mar 2020 11:32:35 +0100 Subject: [Simnibs-discuss] normE values in MNI space In-Reply-To: References: Message-ID: Which SimNIBS version are you using? In 3.1 we switched to using linear interpolation, so these artifacts should not happen anymore. Best Regards, Guilherme On 19/03/2020 10.31, Jane Tan wrote: > Hi Guilherme, > > Thanks for the reply. There are a good number of negative values (~22.5%). > Do you have any suggestions on what I can do to attenuate the > artifacts? My main aim is to get the mean e-field for specific ROIs. > For instance, would you recommend the use of normJ instead? I notice > that there are fewer negative values for normJ, and notably none in > the ROIs I am interested in. > > best regards, > Jane > ------------------------------------------------------------------------ > *From:* Guilherme B Saturnino > *Sent:* Thursday, 19 March 2020 4:08 PM > *To:* Jane Tan ; discuss at simnibs.org > > *Subject:* Re: [Simnibs-discuss] normE values in MNI space > > Dear Jane, > > > > How many negative values are there? This is likely an artifact due to > spline interpolation of the electric field from the original space to > MNI space. > > > Best Regards, > > Guilherme > > > On 19/03/2020 06.06, Jane Tan wrote: >> Hi SimNIBS Team, >> >> I found some negative values in my nifti volume for normE in MNI >> space, and I thought something must have gone awry during the >> segmentation process for my head mesh (created using headreco (with >> cat) on a MNI152 T1-weighted image).? However, the head mesh looks >> okay when I checked it with gmsh. The headreco_log doesn't seem to >> indicate any issues either - at least not to my untrained eye. I do >> not have access to freeview, and couldn't do a proper check via headreco. >> >> I'm also wondering if it might be due to normE not being very >> accurate as a result of registration to the MNI template? >> >> Your suggestions would be greatly appreciated. I am happy to provide >> my head mesh and segmentation results if that would be of any help. >> >> best regards, >> Jane >> >> >> >> >> >> >> Best regards, >> >> >> Jane >> >> >> ** >> ** >> >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jane.Tan at murdoch.edu.au Thu Mar 19 10:31:17 2020 From: Jane.Tan at murdoch.edu.au (Jane Tan) Date: Thu, 19 Mar 2020 09:31:17 +0000 Subject: [Simnibs-discuss] normE values in MNI space In-Reply-To: References: , Message-ID: Hi Guilherme, Thanks for the reply. There are a good number of negative values (~22.5%). Do you have any suggestions on what I can do to attenuate the artifacts? My main aim is to get the mean e-field for specific ROIs. For instance, would you recommend the use of normJ instead? I notice that there are fewer negative values for normJ, and notably none in the ROIs I am interested in. best regards, Jane ________________________________ From: Guilherme B Saturnino Sent: Thursday, 19 March 2020 4:08 PM To: Jane Tan ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] normE values in MNI space Dear Jane, How many negative values are there? This is likely an artifact due to spline interpolation of the electric field from the original space to MNI space. Best Regards, Guilherme On 19/03/2020 06.06, Jane Tan wrote: Hi SimNIBS Team, I found some negative values in my nifti volume for normE in MNI space, and I thought something must have gone awry during the segmentation process for my head mesh (created using headreco (with cat) on a MNI152 T1-weighted image). However, the head mesh looks okay when I checked it with gmsh. The headreco_log doesn't seem to indicate any issues either - at least not to my untrained eye. I do not have access to freeview, and couldn't do a proper check via headreco. I'm also wondering if it might be due to normE not being very accurate as a result of registration to the MNI template? Your suggestions would be greatly appreciated. I am happy to provide my head mesh and segmentation results if that would be of any help. best regards, Jane Best regards, Jane _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jane.Tan at murdoch.edu.au Thu Mar 19 15:25:58 2020 From: Jane.Tan at murdoch.edu.au (Jane Tan) Date: Thu, 19 Mar 2020 14:25:58 +0000 Subject: [Simnibs-discuss] normE values in MNI space In-Reply-To: <00cab8790fb24f51a6a2627a574844e1@SYBPR01MB5243.ausprd01.prod.outlook.com> References: , <00cab8790fb24f51a6a2627a574844e1@SYBPR01MB5243.ausprd01.prod.outlook.com> Message-ID: Hi Guilherme, Ah I see. I have been using v.3.0.6. I will update accordingly. with thanks, Jane ________________________________ From: Guilherme B Saturnino Sent: Thursday, 19 March 2020 6:32 PM To: Jane Tan ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] normE values in MNI space Which SimNIBS version are you using? In 3.1 we switched to using linear interpolation, so these artifacts should not happen anymore. Best Regards, Guilherme On 19/03/2020 10.31, Jane Tan wrote: Hi Guilherme, Thanks for the reply. There are a good number of negative values (~22.5%). Do you have any suggestions on what I can do to attenuate the artifacts? My main aim is to get the mean e-field for specific ROIs. For instance, would you recommend the use of normJ instead? I notice that there are fewer negative values for normJ, and notably none in the ROIs I am interested in. best regards, Jane ________________________________ From: Guilherme B Saturnino Sent: Thursday, 19 March 2020 4:08 PM To: Jane Tan ; discuss at simnibs.org Subject: Re: [Simnibs-discuss] normE values in MNI space Dear Jane, How many negative values are there? This is likely an artifact due to spline interpolation of the electric field from the original space to MNI space. Best Regards, Guilherme On 19/03/2020 06.06, Jane Tan wrote: Hi SimNIBS Team, I found some negative values in my nifti volume for normE in MNI space, and I thought something must have gone awry during the segmentation process for my head mesh (created using headreco (with cat) on a MNI152 T1-weighted image). However, the head mesh looks okay when I checked it with gmsh. The headreco_log doesn't seem to indicate any issues either - at least not to my untrained eye. I do not have access to freeview, and couldn't do a proper check via headreco. I'm also wondering if it might be due to normE not being very accurate as a result of registration to the MNI template? Your suggestions would be greatly appreciated. I am happy to provide my head mesh and segmentation results if that would be of any help. best regards, Jane Best regards, Jane _______________________________________________ Simnibs-discuss mailing list Simnibs-discuss at drcmr.dk https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: