[Simnibs-discuss] First steps into Simnibs

[Quentin Mesnildrey]

Dear all,

please find the very basic simulation I tried to run and the associated 
error message.

Note that the same code works when I add a TMS section.

Best

Quentin





Le 29/03/2022 à 09:44, Axel Thielscher a écrit :
> Dear Quentin,
>
> can you please send the matlab script where the error occured?
>
> Best,
>
> Axel
>
>
> On 3/25/2022 4:54 PM, Quentin Mesnildrey wrote:
>> Dear community,
>>
>> I am just beginning to run simulations using simnibs so I apologize 
>> in advance if my question has been answered in the past. If so, 
>> please redirect me to a previous discussion.
>>
>> I have managed to run tDCS simulation using the GUI. My next step is 
>> to run it using matlab scripts. I started using the tutorial script 
>> provided on the website. Everything seems to work well when I do not 
>> change anything but when I remove the TMS component (which I am not 
>> interested in), I end up with the following error message :
>>
>> **************
>> if PL['type'][0] == 'TMSLIST':
>> IndexError: only integers, slices (`:`), ellipsis (`...`), 
>> numpy.newaxis (`None`) and integer or boolean arrays are
>> valid indices
>> **************
>> Which seems to indicate that not having the TMS is problematic.
>>
>> I would deeply appriciate any advice on this (beginner) issue.
>>
>> Best regards,
>>

-- 
Quentin Mesnildrey
Chef de projet R&D  - CorStim
quentin.mesnildrey at corstim.com
+33688875685
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Error using run_simnibs (line 30)
There was an error running SimNIBS:
 Traceback (most recent call last):
  File "C:\Users\quent\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\run_simnibs.py", line
  29, in <module>
    main()
  File "C:\Users\quent\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\run_simnibs.py", line
  25, in main
    run_simnibs(args.simnibs_file, args.cpus)
  File
  "C:\Users\quent\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\simulation\run_simnibs.py",
  line 23, in run_simnibs
    p = read_mat(simnibs_struct)
  File "C:\Users\quent\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\utils\matlab_read.py",
  line 80, in read_mat
    structure = SESSION(matlab_struct=mat)
  File "C:\Users\quent\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\simulation\sim_struct.py",
  line 116, in __init__
    self.read_mat_struct(matlab_struct)
  File "C:\Users\quent\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\simulation\sim_struct.py",
  line 362, in read_mat_struct
    if PL['type'][0] == 'TMSLIST':
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or
boolean arrays are valid indice
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clear 
p=genpath('C:\Users\quent\SimNIBS-3.2\'); 
addpath(p)
% Initialize a session
s = sim_struct('SESSION');
% Name of head mesh
s.fnamehead = 'ernie.msh';
% Output folder
s.pathfem = 'testsimu/';
S.map_to_surf = true;
S.open_in_gmsh = true;

num_elecs = 2;

% Initialize a tDCS simulation
s.poslist{num_elecs} = sim_struct('TDCSLIST');
% Set currents
s.poslist{num_elecs}.currents = [1e-3 -1e-3];

%% STIM1
s.poslist{num_elecs}.electrode(1).channelnr = 1;
% Electrode dimension
s.poslist{num_elecs}.electrode(1).dimensions = [20 20];
% Rectangular shape
s.poslist{num_elecs}.electrode(1).shape = 'ellipse';
% 5mm thickness
s.poslist{num_elecs}.electrode(1).thickness = 5;
% Electrode Position
s.poslist{num_elecs}.electrode(1).centre = 'AFz';
% Electrode direction
s.poslist{num_elecs}.electrode(1).pos_ydir = 'Cz';

%% STIM2
s.poslist{num_elecs}.electrode(2).channelnr = 2;
% Electrode dimension
s.poslist{num_elecs}.electrode(2).dimensions = [20 20];
% shape
s.poslist{num_elecs}.electrode(2).shape = 'ellipse';
% 5mm thickness
s.poslist{num_elecs}.electrode(2).thickness = 5;
% Electrode Position
s.poslist{num_elecs}.electrode(2).centre = 'POz';
% Electrode direction
s.poslist{num_elecs}.electrode(2).pos_ydir = 'Cz';

%% run 
run_simnibs(s)