From axelt at drcmr.dk Wed Sep 2 16:47:14 2020 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 2 Sep 2020 16:47:14 +0200 Subject: [Simnibs-discuss] manual correction In-Reply-To: References: <2392cc26e2e34ee5a6c4e8f63bea1f94@dtu.dk> Message-ID: Hi Witold, regarding your question 1: correct regarding your question 2: You cannot use SimNIBS to automatically optimize electrode position for TI. However, I added a matlab function? and an example on how to calculate and visualize the TI envelop amplitude, so that you can manually test and optimize the montages: https://github.com/simnibs/simnibs/blob/master/simnibs/matlab/get_maxTI.m https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TI.m Best regards, Axel On 8/28/2020 10:20 PM, w.tomasz at sensusmed.pl wrote: > Hi Oula, > > Thanks for your answers and suggestions. > 1)If I understand correctly, the final headform in the B and B + > ranges will be sufficient to calculate the optimal stimulation if I > first check with Freesurfer for large deviations in bone and skin > mapping ? > > 2)Is it possible to use software to calculate appropriate electrode > placement for transcranial temporal interference stimulation? > Of course also to visualize the distribution of the electric field. > For example, for fields with a frequency of 200 and 210 Hz. > The area of interest is the L-amygdala. > > Best regards, > Witold > W dniu 2020-08-19 13:36, Oula Puonti napisa?(a): >> Hi Witold, >> >> 1) When using CAT the cortical and white matter surfaces are not >> generated from the volume files (.nii.gz), but rather the surface >> files stored in the mask_prerp folder. Thus editing the volume files >> >> will have no effect on the cortical or white matter surfaces in the >> final headmodel. You can, however, edit the CSF, skull, and scalp >> masks and these edits are propagated to the final head model. >> >> If you want to edit the GM and WM masks, please disable CAT12 >> (--no-cat flag). After that the edits on the WM and GM masks will also >> change the final headmodel. >> >> 2) We have not studied this systematically, but in my experience CAT12 >> does a good job even if the grade it assigns is B. That being said, >> you should still inspect the resulting segmentation for large errors >> using the >> >> headreco check call. >> >> 3 & 4) I'm not that experienced with manual edits and the little >> experience I have is limited to freeview. I've heard people >> succesfully using ITK snap, but if you find it too difficult, I would >> consider using freeview through the windows subsystem for linux. It's >> a bit trickier, but the instructions here are quite clear: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport >> >> Best, >> Oula >> ------------------------- >> >> From: Simnibs-discuss > > on behalf of >> w.tomasz at sensusmed.pl >> > >> Sent: Tuesday, August 18, 2020 5:37:11 PM >> To: Guilherme B Saturnino >> Cc: discuss at simnibs.org >> Subject: [Simnibs-discuss] manual correction >> >> Hello, >> >> I had the pleasure of talking to you for a while at the April webinar >> on brain modeling after stroke. >> I am currently researching the use of stimulation in a person with >> tinnitus with personalized stimulation. >> I have a question about the manual correction of the brain model (the >> model created from the t1_mprage_sag and t2_space_dark_fluid_sag_p2 >> images) in the automatic model creation in the CAT report gets results >> on the B and B + levels. >> I'm a beginner when it comes to modeling (I am more concerned with >> NIBS in clinical applications), sorry if my questions are trivial : >> >> 1. on the SIMNIBS website, it says that it is not possible to do CAT >> cuttings, whether in such a system we use "m2m_ernie \ mask_prep \ >> MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual editing. >> Does a manual correction make sense in such a situation? >> >> 2. From your and your team's experience, how big are the differences >> in electric field distributions between the B / B + and A-level >> models? >> >> 3.I wanted to use ITK-SNAP for the correction proposed on one of your >> toutorials but I am a beginner I have a hard time figuring out how to >> check if (how exactly) the surface contours follow the tissue shapes >> in the T1w image, with more masks than one . >> >> 4. Could you suggest a program other than FS to evaluate the created >> model? Since I'm a Windows 10 and FS user, it's more complicated here. >> >> Thank you very much for your help and your time! >> Best regards, >> -- >> >> ??????????Witold Tomasz >> >> ?psycholog, psychoterapeuta, terapeuta tDCS >> >> ??????????O?rodek psychoterapii i neurorehabilitacji >> >> ??????????Sensusmed Witold Tomasz >> >> ??????????p: >> ??????????504288040 ?m: 789335047 >> >> ??????????a: >> ??????????Krak?w 30-303 >> >> ??????????ul.Madali?skiego 3/1 >> >> ??????????w: >> www.sensusmed.pl [1 >> ] ?e: w.tomasz at sensusmed.pl >> >> >> >> >> Links: >> ------ >> [1] http://www.sensusmed.pl > > -- > > Witold Tomasz > /psycholog, psychoterapeuta, terapeuta tDCS > / > O?rodek psychoterapii i neurorehabilitacji > *Sensusmed Witold Tomasz* > p: 504288040 m: 789335047 > a: Krak?w 30-303 > ul.Madali?skiego 3/1 > w: www.sensusmed.pl e: > w.tomasz at sensusmed.pl > > > _______________________________________________ > 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 laurent.torlay at univ-grenoble-alpes.fr Thu Sep 17 15:36:31 2020 From: laurent.torlay at univ-grenoble-alpes.fr (LAURENT TORLAY) Date: Thu, 17 Sep 2020 15:36:31 +0200 (CEST) Subject: [Simnibs-discuss] [tACS] multi electrodes montage Message-ID: <586040752.55784415.1600349791180.JavaMail.zimbra@univ-grenoble-alpes.fr> Hi, Thank you fo developping SimNibs software ! I have a newbie question about tACS (I already did tDCS simulations and experiments). First, I use Neuroelectrics (NE) device and, with their software, I have the possibility to have several "input" electrodes with different phases and only one return electrode if needed. In Simnibs, the GUI is designed fo tDCS but I understood that the results can be extrapolated to tACS for low frequencies (that's our case : around 10 Hz). So the question is : if I am happy with the result of a 2 + 1 montage by using CP3 and P5 (at -1 mA) and P1 (at +2mA) with PI electrodes in a tDCS perspective...how to translate this in terms of tACS parameters ? For example, can I manage this with phase difference but with same amplitude or half ? What is exactly the role of return electrodes in tACS ? Thanks in advance, Laurent -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Mon Sep 21 20:15:33 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Mon, 21 Sep 2020 18:15:33 +0000 Subject: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 Message-ID: Hi all, I'm having some issues getting the latest version of SIMNIBS set up. After initial troubleshooting, I followed the Install Using Conda (Advanced) instructions for MacOS. In attempting to pip install from github, I get the following error: [cid:c25f0a91-78f3-410b-adf0-6c74e2a0f7cf] Any advice? I've also tried this same process on Windows with no luck. Thank you! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 14956 bytes Desc: image.png URL: From axelt at drcmr.dk Mon Sep 21 20:25:35 2020 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 21 Sep 2020 20:25:35 +0200 Subject: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 In-Reply-To: References: Message-ID: <9eebae6f-52bb-e693-ae6f-b067f5c6ef03@drcmr.dk> Hi Dan, can you please clarify whether you had also trouble with the installers (if yes, please send the error message etc), or whether you only tried the "Advanced" version. Thank you! Best, Axel On 9/21/2020 8:15 PM, Mccalley, Daniel wrote: > Hi all, > > I'm having some issues getting the latest version of SIMNIBS set up. > > After initial troubleshooting, I followed the Install Using Conda > (Advanced) instructions for MacOS. > > In attempting to pip install from github, I get the following error: > > > > Any advice? I've also tried this same process on Windows with no luck. > > Thank you! > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 14956 bytes Desc: not available URL: From fangc at drcmr.dk Tue Sep 22 12:40:25 2020 From: fangc at drcmr.dk (fangc) Date: Tue, 22 Sep 2020 12:40:25 +0200 Subject: [Simnibs-discuss] Fwd: Re: Trouble updating/installing SIMNIBS v3.2 In-Reply-To: References: Message-ID: Hi Dan, Could you please send us your log file? It should be in the folder that you choose to install Simnibs, and if you choose the default settings, you can find it here: \Users\YourName\SimNIBS-3.2\install.log Regards, Fang On 2020-09-22 09:32, Axel Thielscher wrote: > -------- Forwarded Message -------- > > SUBJECT: > Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 > > DATE: > Mon, 21 Sep 2020 18:35:45 +0000 > > FROM: > Mccalley, Daniel > > TO: > Axel Thielscher > > Hi Axel, > > The installer actually worked for my MacOS install > > Here's the error message that comes up for my Windows install > > Thank you again! > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------- > > FROM: Axel Thielscher > SENT: Monday, September 21, 2020 2:25 PM > TO: Mccalley, Daniel ; discuss at simnibs.org > > SUBJECT: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS > v3.2 > > CAUTION: External > > Hi Dan, > > can you please clarify whether you had also trouble with the > installers (if yes, please send the error message etc), or whether you > only tried the "Advanced" version. Thank you! > > Best, > > Axel > > On 9/21/2020 8:15 PM, Mccalley, Daniel wrote: > >> Hi all, >> >> I'm having some issues getting the latest version of SIMNIBS set >> up. >> >> After initial troubleshooting, I followed the Install Using Conda >> (Advanced) instructions for MacOS. >> >> In attempting to pip install from github, I get the following >> error: >> >> Any advice? I've also tried this same process on Windows with no >> luck. >> >> Thank you! >> >> Best, >> >> Dan McCalley >> Medical University of South Carolina >> College of Graduate Studies, Neuroscience >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss [1] > > -- > Dr. Axel Thielscher > Associate Professor > Danish Research Center for Magnetic Resonance > Copenhagen University Hospital Hvidovre > DK-2650 Hvidovre, Denmark > www.drcmr.dk [2] > & > Department of Health Technology > Technical University of Denmark > DK-2800 Kgs. Lyngby > http://www.healthtech.dtu.dk/ [3] > > > Links: > ------ > [1] > https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhOHb9EJm$ > [2] > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhBDYZGgL$ > [3] > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhNoYfxWL$ From axelt at drcmr.dk Tue Sep 22 15:42:22 2020 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 22 Sep 2020 15:42:22 +0200 Subject: [Simnibs-discuss] [tACS] multi electrodes montage In-Reply-To: <586040752.55784415.1600349791180.JavaMail.zimbra@univ-grenoble-alpes.fr> References: <586040752.55784415.1600349791180.JavaMail.zimbra@univ-grenoble-alpes.fr> Message-ID: <3280c0ec-7ac9-ba47-4d16-8022dd16977a@drcmr.dk> Dear Laurent: > So the question is : if I am happy with the result of a 2 + 1 montage > by using CP3 and P5 (at -1 mA) and P1 (at +2mA) with PI electrodes in > a tDCS perspective...how to translate this in terms of tACS parameters ? Opposite signs in TDCS translate to a 180? phase shift in TACS. So here you will have currents with the opposite phase in P1 versus CP3 and P5. I suggest that you look at the normal component of E on the cortex (see also https://simnibs.github.io/simnibs/build/html/faq.html for an explanation fo the normal component): All positions that have opposite signs have a 180? phase shift to each other. You can tell Simnibs to calculate the normal component in the simulation options. For more details, please see also https://www.biorxiv.org/content/10.1101/500314v1 and https://pubmed.ncbi.nlm.nih.gov/28919407/ Best regards, Axel On 9/17/2020 3:36 PM, LAURENT TORLAY wrote: > Hi, > Thank you fo developping SimNibs software ! > I have a newbie question about tACS (I already did tDCS simulations > and experiments). > First, I use Neuroelectrics (NE) device and, with their software, I > have the possibility to have several "input" electrodes with different > phases and only one return electrode if needed. > In Simnibs, the GUI is designed fo tDCS but I understood that the > results can be extrapolated to tACS for low frequencies (that's our > case : around? 10 Hz). > So the question is : if I am happy with the result of a 2 + 1 montage > by using CP3 and P5 (at -1 mA) and P1 (at +2mA) with PI electrodes in > a tDCS perspective...how to translate this in terms of tACS parameters ? > For example, can I manage this with phase difference but with same > amplitude or half ? What is exactly the role of return electrodes in > tACS ? > Thanks in advance, > Laurent > > _______________________________________________ > 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 sasan_kvz at yahoo.com Tue Sep 22 22:20:05 2020 From: sasan_kvz at yahoo.com (sasan keshavarz) Date: Tue, 22 Sep 2020 20:20:05 +0000 (UTC) Subject: [Simnibs-discuss] glError messages when opening the GUI References: <996463021.4922780.1600806005875.ref@mail.yahoo.com> Message-ID: <996463021.4922780.1600806005875@mail.yahoo.com> hello ?I have problem in opening the GUI. my video drivers are updated and i cant find the reson. please help me to solve it. i need SimNIBS for my final Bsc project. install.log is attached. kind regardssasan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From sasan_kvz at yahoo.com Tue Sep 22 22:20:54 2020 From: sasan_kvz at yahoo.com (sasan keshavarz) Date: Tue, 22 Sep 2020 20:20:54 +0000 (UTC) Subject: [Simnibs-discuss] glError messages when opening the GUI In-Reply-To: <996463021.4922780.1600806005875@mail.yahoo.com> References: <996463021.4922780.1600806005875.ref@mail.yahoo.com> <996463021.4922780.1600806005875@mail.yahoo.com> Message-ID: <1594185265.4923844.1600806054805@mail.yahoo.com> On Tuesday, September 22, 2020, 11:50:05 PM GMT+3:30, sasan keshavarz wrote: hello ?I have problem in opening the GUI. my video drivers are updated and i cant find the reson. please help me to solve it. i need SimNIBS for my final Bsc project. install.log is attached. kind regardssasan? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: install.log Type: application/octet-stream Size: 855577 bytes Desc: not available URL: From mccalled at musc.edu Thu Sep 24 18:53:32 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Thu, 24 Sep 2020 16:53:32 +0000 Subject: [Simnibs-discuss] Fwd: Re: Trouble updating/installing SIMNIBS v3.2 In-Reply-To: References: , Message-ID: Hi all, Sorry for the delay! The log file is attached I cc'd Dr. Kaur as well as she is trying to setup SIMNIBS on her PC Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: fangc Sent: Tuesday, September 22, 2020 6:40 AM To: Mccalley, Daniel Cc: Axel Thielscher ; discuss at simnibs.org Subject: Re: Fwd: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 CAUTION: External Hi Dan, Could you please send us your log file? It should be in the folder that you choose to install Simnibs, and if you choose the default settings, you can find it here: \Users\YourName\SimNIBS-3.2\install.log Regards, Fang On 2020-09-22 09:32, Axel Thielscher wrote: > -------- Forwarded Message -------- > > SUBJECT: > Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 > > DATE: > Mon, 21 Sep 2020 18:35:45 +0000 > > FROM: > Mccalley, Daniel > > TO: > Axel Thielscher > > Hi Axel, > > The installer actually worked for my MacOS install > > Here's the error message that comes up for my Windows install > > Thank you again! > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------- > > FROM: Axel Thielscher > SENT: Monday, September 21, 2020 2:25 PM > TO: Mccalley, Daniel ; discuss at simnibs.org > > SUBJECT: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS > v3.2 > > CAUTION: External > > Hi Dan, > > can you please clarify whether you had also trouble with the > installers (if yes, please send the error message etc), or whether you > only tried the "Advanced" version. Thank you! > > Best, > > Axel > > On 9/21/2020 8:15 PM, Mccalley, Daniel wrote: > >> Hi all, >> >> I'm having some issues getting the latest version of SIMNIBS set >> up. >> >> After initial troubleshooting, I followed the Install Using Conda >> (Advanced) instructions for MacOS. >> >> In attempting to pip install from github, I get the following >> error: >> >> Any advice? I've also tried this same process on Windows with no >> luck. >> >> Thank you! >> >> Best, >> >> Dan McCalley >> Medical University of South Carolina >> College of Graduate Studies, Neuroscience >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNIVRLhEK$ [1] > > -- > Dr. Axel Thielscher > Associate Professor > Danish Research Center for Magnetic Resonance > Copenhagen University Hospital Hvidovre > DK-2650 Hvidovre, Denmark > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNDVXVYHG$ [2] > & > Department of Health Technology > Technical University of Denmark > DK-2800 Kgs. Lyngby > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNJlsmr1i$ [3] > > > Links: > ------ > [1] > https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhOHb9EJm$ > [2] > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhBDYZGgL$ > [3] > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhNoYfxWL$ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: install.log Type: application/octet-stream Size: 878697 bytes Desc: install.log URL: From axelt at drcmr.dk Thu Sep 24 19:05:23 2020 From: axelt at drcmr.dk (Axel Thielscher) Date: Thu, 24 Sep 2020 19:05:23 +0200 Subject: [Simnibs-discuss] Fwd: Re: Trouble updating/installing SIMNIBS v3.2 In-Reply-To: References: Message-ID: <9dda5d6b-746e-7e35-ceb8-6204161c6119@drcmr.dk> Hi Dan, thanks for sharing the log file. It seems that downloading the additional coil files did not work due to an internet problem (some firewall blocking the connection or similar). Please install without selecting the download of the coil files. This should work. Afterwards, download them manually from https://github.com/simnibs/simnibs-coils (use Code --> Download ZIP). After unzipping, move them into the "ccd-files" subfolder of the simnibs installaltion. Best, Axel On 9/24/2020 6:53 PM, Mccalley, Daniel wrote: > Hi all, > > Sorry for the delay! The log file is attached > > I cc'd Dr. Kaur as well as she is trying to setup SIMNIBS on her PC > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------------------------------------------------------ > *From:* fangc > *Sent:* Tuesday, September 22, 2020 6:40 AM > *To:* Mccalley, Daniel > *Cc:* Axel Thielscher ; discuss at simnibs.org > > *Subject:* Re: Fwd: Re: [Simnibs-discuss] Trouble updating/installing > SIMNIBS v3.2 > CAUTION: External > > Hi Dan, > > Could you please send us your log file? It should be in the folder that > you choose to install Simnibs, and if you choose the default settings, > you can find it here: > > \Users\YourName\SimNIBS-3.2\install.log > > Regards, > Fang > > > > > On 2020-09-22 09:32, Axel Thielscher wrote: > > -------- Forwarded Message -------- > > > >?????????????? SUBJECT: > >?????????????? Re: [Simnibs-discuss] Trouble updating/installing > SIMNIBS v3.2 > > > >?????????????? DATE: > >?????????????? Mon, 21 Sep 2020 18:35:45 +0000 > > > >?????????????? FROM: > >?????????????? Mccalley, Daniel > > > >?????????????? TO: > >?????????????? Axel Thielscher > > > >? Hi Axel, > > > >? The installer actually worked for my MacOS install > > > >? Here's the error message that comes up for my Windows install > > > >? Thank you again! > > > >? Best, > > > > Dan McCalley > > Medical University of South Carolina > > College of Graduate Studies, Neuroscience > > > > ------------------------- > > > > FROM: Axel Thielscher > > SENT: Monday, September 21, 2020 2:25 PM > > TO: Mccalley, Daniel ; discuss at simnibs.org > > > > SUBJECT: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS > > v3.2 > > > >? CAUTION: External > > > > Hi Dan, > > > > can you please clarify whether you had also trouble with the > > installers (if yes, please send the error message etc), or whether you > > only tried the "Advanced" version. Thank you! > > > > Best, > > > > Axel > > > > On 9/21/2020 8:15 PM, Mccalley, Daniel wrote: > > > >> Hi all, > >> > >> I'm having some issues getting the latest version of SIMNIBS set > >> up. > >> > >> After initial troubleshooting, I followed the Install Using Conda > >> (Advanced) instructions for MacOS. > >> > >> In attempting to pip install from github, I get the following > >> error: > >> > >> Any advice? I've also tried this same process on Windows with no > >> luck. > >> > >> Thank you! > >> > >> Best, > >> > >> Dan McCalley > >> Medical University of South Carolina > >> College of Graduate Studies, Neuroscience > >> > >> _______________________________________________ > >> Simnibs-discuss mailing list > >> Simnibs-discuss at drcmr.dk > >> > https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNIVRLhEK$ > [1] > > > > -- > > Dr. Axel Thielscher > > Associate Professor > > Danish Research Center for Magnetic Resonance > > Copenhagen University Hospital Hvidovre > > DK-2650 Hvidovre, Denmark > > > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNDVXVYHG$ > [2] > > & > > Department of Health Technology > > Technical University of Denmark > > DK-2800 Kgs. Lyngby > > > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNJlsmr1i$ > [3] > > > > > > Links: > > ------ > > [1] > > > https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhOHb9EJm$ > > [2] > > > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhBDYZGgL$ > > [3] > > > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhNoYfxWL$ -- 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 nkaur at wakehealth.edu Thu Sep 24 19:47:03 2020 From: nkaur at wakehealth.edu (Navneet Kaur) Date: Thu, 24 Sep 2020 17:47:03 +0000 Subject: [Simnibs-discuss] Fwd: Re: Trouble updating/installing SIMNIBS v3.2 In-Reply-To: <9dda5d6b-746e-7e35-ceb8-6204161c6119@drcmr.dk> References: <9dda5d6b-746e-7e35-ceb8-6204161c6119@drcmr.dk> Message-ID: It worked. Thank you! Navneet Kaur, Ph.D. Research Fellow Clinical Neuromodulation Laboratory Department of Cancer Biology Wake Forest University School of Medicine nkaur at wakehealth.edu From: Axel Thielscher Sent: Thursday, September 24, 2020 1:05 PM To: Mccalley, Daniel Cc: fangc ; discuss at simnibs.org; Navneet Kaur Subject: [EXTERNAL] Re: Fwd: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 Hi Dan, thanks for sharing the log file. It seems that downloading the additional coil files did not work due to an internet problem (some firewall blocking the connection or similar). Please install without selecting the download of the coil files. This should work. Afterwards, download them manually from https://github.com/simnibs/simnibs-coils [github.com] (use Code --> Download ZIP). After unzipping, move them into the "ccd-files" subfolder of the simnibs installaltion. Best, Axel On 9/24/2020 6:53 PM, Mccalley, Daniel wrote: Hi all, Sorry for the delay! The log file is attached I cc'd Dr. Kaur as well as she is trying to setup SIMNIBS on her PC Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience ________________________________ From: fangc Sent: Tuesday, September 22, 2020 6:40 AM To: Mccalley, Daniel Cc: Axel Thielscher ; discuss at simnibs.org Subject: Re: Fwd: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 CAUTION: External Hi Dan, Could you please send us your log file? It should be in the folder that you choose to install Simnibs, and if you choose the default settings, you can find it here: \Users\YourName\SimNIBS-3.2\install.log Regards, Fang On 2020-09-22 09:32, Axel Thielscher wrote: > -------- Forwarded Message -------- > > SUBJECT: > Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS v3.2 > > DATE: > Mon, 21 Sep 2020 18:35:45 +0000 > > FROM: > Mccalley, Daniel > > TO: > Axel Thielscher > > Hi Axel, > > The installer actually worked for my MacOS install > > Here's the error message that comes up for my Windows install > > Thank you again! > > Best, > > Dan McCalley > Medical University of South Carolina > College of Graduate Studies, Neuroscience > > ------------------------- > > FROM: Axel Thielscher > SENT: Monday, September 21, 2020 2:25 PM > TO: Mccalley, Daniel ; discuss at simnibs.org > > SUBJECT: Re: [Simnibs-discuss] Trouble updating/installing SIMNIBS > v3.2 > > CAUTION: External > > Hi Dan, > > can you please clarify whether you had also trouble with the > installers (if yes, please send the error message etc), or whether you > only tried the "Advanced" version. Thank you! > > Best, > > Axel > > On 9/21/2020 8:15 PM, Mccalley, Daniel wrote: > >> Hi all, >> >> I'm having some issues getting the latest version of SIMNIBS set >> up. >> >> After initial troubleshooting, I followed the Install Using Conda >> (Advanced) instructions for MacOS. >> >> In attempting to pip install from github, I get the following >> error: >> >> Any advice? I've also tried this same process on Windows with no >> luck. >> >> Thank you! >> >> Best, >> >> Dan McCalley >> Medical University of South Carolina >> College of Graduate Studies, Neuroscience >> >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNIVRLhEK$ [1] > > -- > Dr. Axel Thielscher > Associate Professor > Danish Research Center for Magnetic Resonance > Copenhagen University Hospital Hvidovre > DK-2650 Hvidovre, Denmark > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNDVXVYHG$ [2] > & > Department of Health Technology > Technical University of Denmark > DK-2800 Kgs. Lyngby > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!VQOptFev3bA75t2pMiWbtSbShedriUBXxSQ3d1rCSMXigJN3GhaYbq1KNJlsmr1i$ [3] > > > Links: > ------ > [1] > https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhOHb9EJm$ > [2] > https://urldefense.com/v3/__http://www.drcmr.dk__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhBDYZGgL$ > [3] > https://urldefense.com/v3/__http://www.healthtech.dtu.dk/__;!!Ab1_Rw!T_Kc8hSOQUhC1N354NSsaQoGlM4HXrOBdiToISbtPQMbNcXYnk1tMSLUhNoYfxWL$ -- Dr. Axel Thielscher Associate Professor Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk [drcmr.dk] & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ [healthtech.dtu.dk] -------------- next part -------------- An HTML attachment was scrubbed... URL: