[Simnibs-discuss] Network Optimisation Avoid Tissues

Axel Thielscher axelt at drcmr.dk
Wed Feb 17 14:41:28 CET 2021


the weights in the eyes are set to zero for TDCS network optimization as 
standard. There is currently no option to include the eyes into the 
optimization. Its a good point, and we will try to add it in the future. 
For now, we can only offer you a hacking solution. In the 
*opt_struct.py* file in the simnibs installation on your computer, 
*lines 2258 ff *(see 

         # setting values in eyes to zero
         if np.any(self.mesh.elm.tag1 == 1006):
             logger.info('setting target values in eyes to zero')
             if self.lf_type == 'node':
eye_nodes=np.unique(self.mesh.elm.node_number_list[self.mesh.elm.tag1 == 
                 eye_nodes = eye_nodes[eye_nodes>0]
*field[eye_nodes-1] = 0.0 # node indices in mesh are 1-based*
             elif self.lf_type == 'element':
*field[self.mesh.elm.tag1 == 1006] = 0.0*

Replace the 0.0 in the bold lines by some negative weights. You will 
have to manually step through a few values to see which one work well 
for you.



On 2/12/2021 1:21 PM, Kaiser, Max (Stud. FPN / Alumni FPN) wrote:
> Hi SimNIBS Team,
> I wanted to use the tDCS network optimisation function for a tACS experiment.
> When I run the optimization, the electrodes are clustered around the frontal areas, stimulating the eyes substantially.
> However, the avoid.tissue function only worked for „single-target“ but not for the network-targeted optimisation.
> Is there a possibility to implement the avoid function for the network optimisation?
> Thank you in advance!
> Kind regards,
> Max.
> _______________________________________________
> 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
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby

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