From zhen.li.dada at gmail.com Tue Dec 7 10:12:56 2021 From: zhen.li.dada at gmail.com (Zhen Li) Date: Tue, 7 Dec 2021 10:12:56 +0100 Subject: [Simnibs-discuss] (no subject) Message-ID: Dear researchers, I have got a head model on a Mac laptop using normal T1 and T2 nii, but it looks so weird. I have no idea what the problem is. [image: ??2021-12-07 10.11.55.png] Can anybody explain that? Thank you in advance. Best, Zhen -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ??2021-12-07 10.11.55.png Type: image/png Size: 462006 bytes Desc: not available URL: From hasyaz at dtu.dk Tue Dec 21 14:26:49 2021 From: hasyaz at dtu.dk (Hassan Yazdanian) Date: Tue, 21 Dec 2021 13:26:49 +0000 Subject: [Simnibs-discuss] Question about BCs and getting nodal potentials Message-ID: <75e1c793cfdc4331b38fa35aff48172b@dtu.dk> Hello, I am trying y to compare the result obtained by SimNIBS with that one calculated by FEniCS (https://fenicsproject.org/) for a tDCS simulation. For this purpose, I have imported .msh file generated by a SimNIBS simulation into FEniCS. I have used the spherical model provided in SimNIBS dataset. Now, I have two questions: 1- How can I get the electrical potentials of nodes and corresponding nodal coordinates? In earlier versions of SimNIBS, I used "v = fem.tdcs_getdp". I was wondering if there is a similar command in SimNIBS 3.2. 2- About applying boundary condition, as I understood, SimNIBS uses a constant potential on electrodes (Say -1 on Cathode and 0 on Anode). After solving the FEM system of equations, then potentials are scaled to reach the given current set for electrodes ( I mean we know the potential on 2101 and 1501 surfaces, both side of Anode, and we know the conductivity of the electrode, 29.4 S/m, then we can determine the current passing through the electrode). Am I right? Merry Christmas and Happy new year in advance! Best wishes, -Hassan -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Tue Dec 21 19:29:25 2021 From: mccalled at musc.edu (Mccalley, Daniel) Date: Tue, 21 Dec 2021 18:29:25 +0000 Subject: [Simnibs-discuss] Details about coil-to-cortex measurement Message-ID: Hi all, Could you provide some more information on the coil-to-cortex distance that is provided during efield modeling? Does this distance represent a) the distance between the modeled stimulation site and the nearest point on the cortex directly under that site, or b) the shortest distance between the stimulation and the nearest point on the cortex near the stimulation site? In other words, does this distance come from drawing a straight line under the coil until the cortex is reached, or is the line a diagonal such that the distance to a closer, neighboring part of the cortex is measured? Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience (he/him) -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Tue Dec 21 19:43:55 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 21 Dec 2021 19:43:55 +0100 Subject: [Simnibs-discuss] Details about coil-to-cortex measurement In-Reply-To: References: Message-ID: <880beacb-0e71-33de-ad57-19dbb857eafa@drcmr.dk> Hi Dan, it is option b). Best, Axel On 12/21/2021 7:29 PM, Mccalley, Daniel wrote: > Hi all, > > Could you provide some more information on the coil-to-cortex distance > that is provided during efield modeling? > > Does this distance represent a) the distance between the modeled > stimulation site and the nearest point on the cortex directly under > that site, or b) the shortest distance between the stimulation and the > nearest point on the cortex near the stimulation site? > > In other words, does this distance come from drawing a straight line > under the coil until the cortex is reached, or is the line a diagonal > such that the distance to a closer, neighboring part of the cortex is > measured? > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > (he/him) > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Tue Dec 21 19:50:03 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 21 Dec 2021 19:50:03 +0100 Subject: [Simnibs-discuss] Question about BCs and getting nodal potentials In-Reply-To: <75e1c793cfdc4331b38fa35aff48172b@dtu.dk> References: <75e1c793cfdc4331b38fa35aff48172b@dtu.dk> Message-ID: Hi Hassan, please see below. On 12/21/2021 2:26 PM, Hassan Yazdanian wrote: > > Hello, > > I am trying y to compare the result obtained by SimNIBS with that one > calculated by FEniCS (https://fenicsproject.org/) for a tDCS > simulation. For this purpose, I have imported .msh file generated by a > SimNIBS simulation into FEniCS. I have used the spherical model > provided in SimNIBS dataset. Now, I have two questions: > > 1-How can I get the electrical potentials of nodes and corresponding > nodal coordinates? In earlier versions of SimNIBS, I used ?v = > fem.tdcs_getdp?. I was wondering if there is a similar command in > SimNIBS 3.2. > You can add a 'v' to the 'fields' attribute when defining the simulation: https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/session.html The potential will then be added as node_data to the results mesh. The nodal positions are stored under the "nodes" parameter: https://simnibs.github.io/simnibs/build/html/documentation/python_lib/auto/simnibs.Msh.html#simnibs.Msh > 2-About applying boundary condition, as I understood, SimNIBS uses a > constant potential on electrodes (Say -1 on Cathode and 0 on Anode). > After solving the FEM system of equations, then potentials are scaled > to reach the given current set for electrodes ( I mean we know the > potential on 2101 and 1501 surfaces, both side of Anode, and we know > the conductivity of the electrode, 29.4 S/m, then we can determine the > current passing through the electrode). Am I right? > Yes, that's correct. Merry Christmas and a good start into the new year to you, too! Best, Axel > Merry Christmas and Happy new year in advance! > > Best wishes, > > -Hassan > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Wed Dec 22 16:04:11 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 22 Dec 2021 16:04:11 +0100 Subject: [Simnibs-discuss] Adding tumour tissue to mesh In-Reply-To: References: Message-ID: Hi, sorry for following up on these topics rather late. Regarding Alzheimer or MCI, I don't think that specific adjustments are needed for the electric field calculations. The structural differences (atrophy) will be reflected in the segmentation results when generating headmodels from MR data of these patients, and thus be taken into account during the e-field simulations. Obviously, e-field simulations do not provide information about disease-related physiological changes that might alter the response to brain stimulation, for which other information is required in addition. Regarding the addition of tumor tissues, the short answer is that SimNIBS is not good in dealing with this so far, but will get much better next year. Best regards, Axel On 9/20/2021 9:18 AM, Utkarsh Pancholi wrote: > Hi, > > Indeed a great question from Stephen. I would also like to ask a > similar?question. Is there any way to include pathological > abnormalities like in Alzheimer's disease and MCI (Loss of Neural > tissue mass)?? How we can relate the generated E-field for validation > and their effects on physiological/ neuronal/ functional changes > within the target area. > ----------------------------------------------------------------------------------------------------- > UTKARSH V. PANCHOLI > > > > On Mon, Sep 20, 2021 at 12:34 PM Stephen Hogg > wrote: > > Hi, > > Thanks for making SimNIBS, it's a great program. I was wondering > if I could ask a few questions about including pathologies in the > outputs. Specifically, I have a region of the brain that I want to > overwrite with a tissue type not produced by SimNIBS itself (e.g. > tumour tissue). In order to include the tumour tissue in the > meshes, do I need to add an extra .nii file in the mask_prep > directory after updating the existing masks? If so, are there any > considerations I should be aware of? How is the new tissue type > incorporated in mesh generation? Hope this isn't a bother, would > greatly?appreciate any light you could shed on this. > > Regards, > Stephen > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From 872244656 at qq.com Mon Dec 27 17:30:53 2021 From: 872244656 at qq.com (=?utf-8?Q?bingo=E7=B3=8A=E6=B6=82?=) Date: Tue, 28 Dec 2021 00:30:53 +0800 Subject: [Simnibs-discuss] ***Suspected SPAM*** Can not installer Message-ID: ? Windows ????? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: simnibs_install_log.txt URL: