[Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure

[Axel Thielscher]

Hi,

you could adjust the dI/dt when setting up the simulations to realistic 
values (the standard in the GUI is 1 A/mue_s, which is very low; values 
exceeding ~70 A/Mue_s would be realistic for standard coils). You will 
then also have to adjust the threshold in the script to a more realistic 
value for a e-field strength that would result in neural excitation. You 
can try ~60 V/m, for example. However, as long as the dI/dt of both 
simulations is the same, the outcome will be identical to that of the 
original script when selecting the threshold accordingly (as setting the 
dI/dt only linearly scales the simulated fields) - the selected 
threshold is somewhat arbitrary as the exact cortical excitation 
thresholds are not fully known and just determines how large the overlap 
region is.

When you don't use the same stimulation intensity for both stimulations, 
then it would be for sure important to set the dI/dt values, as this 
will then also shift the position of the overlap region.

Best regards,

Axel


On 6/10/2021 11:58 AM, Dantas, A (MW) wrote:
>
> Dear Axel,
>
> One more question: What about the stimulation intensities? Can we 
> adjust the intensity to check if the overlap is influenced by it?
>
> Kind regards,
>
> *Aline Dantas *
>
> /PhD candidate/
>
> /Human Decision and Policy Design/
>
> /Departments of Marketing and Supply Chain Management (SBE) and 
> Cognitive Neurosciences (FPN)/
>
> Room F2.02. Tongersestraat 53, 6211 LM
>
> Room 2.018. Oxfordlaan 55, 6229 EV
>
> *From:*Dantas, A (MW)
> *Sent:* Wednesday, 2 June 2021 15:10
> *To:* 'Axel Thielscher' <axelt at drcmr.dk>; discuss at simnibs.org; 
> jonas.persson at neuro.uu.se
> *Cc:* Ébner, Nancy (Stud. FHML / Alumni UCV) 
> <n.ebner at student.maastrichtuniversity.nl>
> *Subject:* RE: [Simnibs-discuss] SimNIBS simulation - TMS study - 
> Overlap figure
>
> Thank you very much! I’ll try this solution.
>
> Kind regards,
>
> Aline Dantas
>
> *From:*Axel Thielscher <axelt at drcmr.dk <mailto:axelt at drcmr.dk>>
> *Sent:* Wednesday, 2 June 2021 14:50
> *To:* Dantas, A (MW) <a.dantas at maastrichtuniversity.nl 
> <mailto:a.dantas at maastrichtuniversity.nl>>; discuss at simnibs.org 
> <mailto:discuss at simnibs.org>; jonas.persson at neuro.uu.se 
> <mailto:jonas.persson at neuro.uu.se>
> *Cc:* Ébner, Nancy (Stud. FHML / Alumni UCV) 
> <n.ebner at student.maastrichtuniversity.nl 
> <mailto:n.ebner at student.maastrichtuniversity.nl>>
> *Subject:* Re: [Simnibs-discuss] SimNIBS simulation - TMS study - 
> Overlap figure
>
> Hi,
>
> for determining an overlap, you will have to set a threshold to then 
> show the regions where both TMS fields exceed this threshold.  In the 
> attached example code , I've used 0.75 as threshold, please adjust 
> this according to your needs.
>
> Regions where the first stimulation exceeds the threshold are coded as 
> 1, regions where the second stimulation exceeds the threshold are 
> coded as 2, the overlap is coded as 3.
>
> Best regards,
>
> Axel
>
> On 5/26/2021 2:33 PM, Dantas, A (MW) wrote:
>
>     Dear all,
>
>     My student Nancy Ébner got in touch with you recently about the
>     need for a Magventure double cone coil simulation using SimNIBS.
>
>     We ran the simulations successfully, so first of all I would like
>     to thank you!
>
>     We have an experiment deactivating the VMPFC vs. deactivating the
>     right DLPFC. So far, we managed to run both simulations, but it
>     would be great if we could the overlap image of stimulating these
>     two areas. We tried to make it but did not succeed.
>
>     Do you think you could help me to build that?
>
>     Thank you!
>
>     Kind regards,
>
>     Aline Dantas
>
>     _______________________________________________
>
>     Simnibs-discuss mailing list
>
>     Simnibs-discuss at drcmr.dk <mailto:Simnibs-discuss at drcmr.dk>
>
>     https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>     <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 <http://www.drcmr.dk>
> &
> Department of Health Technology
> Technical University of Denmark
> DK-2800 Kgs. Lyngby
> http://www.healthtech.dtu.dk/ <http://www.healthtech.dtu.dk/>

-- 
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: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20210624/01fa2081/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 661752 bytes
Desc: not available
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20210624/01fa2081/attachment-0001.png>