From guilhermebs at drcmr.dk Mon May 4 09:53:48 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Mon, 4 May 2020 09:53:48 +0200 Subject: [Simnibs-discuss] Animations In-Reply-To: References: Message-ID: Hi Ane, The important thing to keep in mind is that the /spread/ of the field is kept the exact same over time, just the scale changes over time. The change is proportional to the time derivative of the coil input current (dI/dt). This is explained a little better here: https://simnibs.github.io/simnibs/build/html/faq.html#what-is-the-di-dt-in-tms-simulations As for how to do animations, I have never tried it so I can't give you much help there. But the tip above gives you a way of generating frames without having to run new simulations, and instead just re-scaling an existing one. Best Regards, Guilherme On 30/04/2020 11.17, Ane Miren Guti?rrez wrote: > Dear developers. > > Can we do animated simulations with SimNIBS (e.g. rTMS theta burst > protocol simulation).?If so, which are critical parameters and how can > we solve it? > > Thank you very much for your time, I look forward to hearing from?you. > > ------------------------------------------------------------------------ > > Ane Miren Guti?rrez Muto > Responsable de Calidad > Direcci?n: Carretera M-501, KM 17,900 - 28690 Brunete, Madrid > Tel?fono: (+34) 91 546 00 94 > www.inntegra.es > > ------------------------------------------------------------------------ > > Antes de imprimir este mensaje, por favor compruebe que es necesario. > Una tonelada de papel implica la tala de 15 ?rboles, y el consumo de > 250.000 litros de agua. > El Medio Ambiente es cuesti?n de TODOS. > > Este mensaje se dirige exclusivamente a su destinatario. Contiene > informaci?n CONFIDENCIAL sometida a secreto profesional o cuya > divulgaci?n est? prohibida por Ley. Si ha recibido este mensaje por > error, debe saber que su lectura, copia y uso est?n prohibidos. Le > rogamos nos lo comunique inmediatamente por esta misma v?a o por > tel?fono y proceda a su destrucci?n. El correo electr?nico v?a > Internet no permite asegurar la confidencialidad de los mensajes que > se transmiten ni su integridad o correcta recepci?n. INNTEGRA no asume > responsabilidad por estas circunstancias. Si el destinatario de este > mensaje no consintiera la utilizaci?n del correo electr?nico v?a > Internet y la grabaci?n de los mensajes, rogamos lo ponga en nuestro > conocimiento de forma inmediata. > > En cumplimiento de la Ley Org?nica 15/1999, de 13 de diciembre, de > Protecci?n de Datos de Car?cter Personal le informamos de que sus > datos personales y de empresa pasar?n a formar parte de un fichero > registrado ante la Agencia Espa?ola de Protecci?n de Datos. Los datos > personales que existen en nuestro poder est?n protegidos por nuestra > Pol?tica de Privacidad. Usted puede ejercitar sus derechos de acceso, > rectificaci?n, cancelaci?n y oposici?n dirigi?ndose por escrito > a?INNTEGRA (info at inntegra.es ) > > > _______________________________________________ > 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 mrsnicolson at gmail.com Thu May 7 18:48:53 2020 From: mrsnicolson at gmail.com (Valerie Nicolson) Date: Thu, 7 May 2020 09:48:53 -0700 Subject: [Simnibs-discuss] mri2mesh error Message-ID: Hello, I am a new simnibs user on a Mac running Catalina 10.15.4. After installation (and verifying the simnibs gui using ernie) I tried creating a mesh using mri2mesh using ernie's T1 only mri2mesh --all ernie org/ernie_T1.nii.g After many hours and lots of output it crashes. This is the last of the output: meshfix subcortical_FS.stl ERROR- fseek /Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed.exiting mri2mesh after error I checked, and subcortical_FS.stl exists and is definitely longer than 80 (this seems to be the fseek call in io.cpp that is failing). I've also tried running meshfix on other .stl files and get the same error, so I'm getting the idea that meshfix is trying to open some other file). Any ideas of how to fix this or what file might be missing from my installation? Thanks, Valerie Cardenas Nicolson -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Thu May 7 19:05:36 2020 From: axelt at drcmr.dk (Axel Thielscher) Date: Thu, 7 May 2020 19:05:36 +0200 Subject: [Simnibs-discuss] mri2mesh error In-Reply-To: References: Message-ID: Dear Valerie, thanks for contacting us. It seems that we might have to update meshfix to work with Catalina. We'll come back to you. In the meantime, could you quickly check whether subcortical_FS.stl looks "normal" (i.e. is a closed surface) when you open it in gmsh? (gmsh is also part of simnibs). Otherwise, please let us know. Best, Axel On 5/7/2020 6:48 PM, Valerie Nicolson wrote: > Hello, > > I am a new simnibs user on a Mac running Catalina 10.15.4. After > installation (and verifying the simnibs gui using ernie) I tried > creating a mesh using mri2mesh using ernie's T1 only > > mri2mesh --all ernie org/ernie_T1.nii.g > > > After many hours and lots of output it crashes. This is the last of > the output: > > meshfix subcortical_FS.stl > > > ERROR- fseek > /Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 > failed.exiting mri2mesh after error > > > > I checked, and subcortical_FS.stl exists and is definitely longer than > 80 (this seems to be the fseek call in io.cpp that is failing). I've > also tried running meshfix on other .stl files and get the same error, > so I'm getting the idea that meshfix is trying to open some other > file). Any ideas of how to fix this or what file might be missing from > my installation? > > > Thanks, > > > Valerie Cardenas Nicolson > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Associate Professor 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 1155138422 at link.cuhk.edu.hk Sat May 23 07:26:17 2020 From: 1155138422 at link.cuhk.edu.hk (TI, Chun Hang Eden) Date: Sat, 23 May 2020 05:26:17 +0000 Subject: [Simnibs-discuss] Enquiries about a error on TDCSLEADFIELD Message-ID: Dear Sir/Madam, I am trying to use simnibs for optimizing electrode montage. When I set the anisotropy type as 'vn', and run the tdcs leadfield, I got the following message. [cid:1fce48c1-fded-45b9-96ec-abe91a56fcdc] I have run dwi2cond on my head models, and it can identify the path of my tensors. I tried to search the documentation but I cannot find this attribute. How could I solve this? Look forward to your reply, and thanks a lot. Best regards, Ti Chun Hang Eden PhD, Department of Biomedical Engineering The Chinese University of Hong Kong Email: 1155138422 at link.cuhk.edu.hk -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 3835 bytes Desc: image.png URL: From guilhermebs at drcmr.dk Mon May 25 10:31:35 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Mon, 25 May 2020 10:31:35 +0200 Subject: [Simnibs-discuss] Enquiries about a error on TDCSLEADFIELD In-Reply-To: References: Message-ID: <46ff07a2-36cd-da88-cce5-eed4ecd815fb@drcmr.dk> Hello, Thanks for letting us know. There is a bug in version 3.1.2 which does not let you use DTI-based conductivity maps to build leadfields. It has now been fixed for the next release. Best Regards, Guilherme On 23/05/2020 07.26, TI, Chun Hang Eden wrote: > Dear Sir/Madam, > > I am trying to use simnibs for optimizing electrode montage. When I > set the anisotropy type as 'vn', and run the tdcs leadfield, I got the > following message. > > > I have run dwi2cond on my head models, and it can identify the path of > my tensors. I tried to search the documentation but I cannot find this > attribute. How could I solve this? > > Look forward to your reply, and thanks a lot. > > Best regards, > > *Ti Chun Hang Eden* > PhD, Department of Biomedical Engineering > The Chinese University of Hong Kong > Email: 1155138422 at link.cuhk.edu.hk > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 3835 bytes Desc: not available URL: