From Debby.Klooster at UGent.be  Fri May  6 20:53:53 2022
From: Debby.Klooster at UGent.be (Deborah Klooster)
Date: Fri, 6 May 2022 18:53:53 +0000
Subject: [Simnibs-discuss] How to define matsimnibs?
Message-ID: <0D4AAF06-F101-4348-B098-7BCA88E197DD@ugent.be>

Dear simNIBS experts,
I would like to run a simulation (so no actual stimulation performed yet!) of TMS induced electric field after DLPFC stimulation, targeting particular MNI coordinates within the gray matter, with the coil positioned tangentially to the scalp with the handle pointing backwards in a 45-degrees angle with the A-P line. Specifically, I have three questions about how I can define my position and orientation properly (or in other words: what is the best way to define my matsimnibs?):

1.     I know my stimulation target in the gray matter and I know simnibs has an ?project on scalp? function built in. I assume that this basically seeks the nearest point on the scalp? Can we get the information (i.e., coil position on the scalp based on gray matter position input) somewhere out of the code? It must be in there somewhere but I failed to find it?

2.     I am struggling with the left-upper 3x3 part of the affine transformation matrix. I know the rotation around the z-axis is 45 degrees but I am not sure how to define the rotation around x and y (in order to keep the coil tangentially to the scalp). I could derive these rotations from a vector normal to the scalp (I think this would just be an extension of the projection from the gray matter point to the scalp position?). Should I derive this normal vector from curvature data from freesurfer or is it possible to retrieve this info in a simpler way?

3.     Assuming that, at some point, I will manage to define matsimnibs, is there a proper way to visualize this (preferable in the simnibs GUI) such that I can verify if my matrix, and hence my subsequent simulation, is correct? What is the relation between the matsimnibs and the reference coordinates that need to be put in the simnibs GUI as direction reference?
Thank you very much in advance!
Kind regards,
Debby
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From nb18104 at shibaura-it.ac.jp  Thu May 12 11:23:40 2022
From: nb18104 at shibaura-it.ac.jp (Manami, Kanamaru)
Date: Thu, 12 May 2022 18:23:40 +0900
Subject: [Simnibs-discuss] Regarding the positional relationships between
 the elements of each body tissues
Message-ID: <CALLX+0SDtEAG75Hwiz_-vs5kMRkxj9c6k-xkRke2SRa5AND1ZA@mail.gmail.com>

Dear Sir/ Madam,

I am working on the simulation when the eyeballs are stimulated with the
electrodes placed on the facial skin. The simulation using SimNIBS is
working well, but I have a problem as stated in the title.
In order to consider the electric current path, I would like to use the A*
algorithm. The electric conductivities would be used for the cost, and the
coordinates of each element would be used for the node of the A* algorithm.
However, I have no idea which elements are nearby. I have already found the
coordinates' information stored in the module "mesh_load_gmsh4". There are
"triangles" and "nodes" in "mesh_load_gmsh4", each of them has the nodes
number that consists of the triangles, and the coordinates of the nodes.
However, I could not understand the positional relationship of each
element. How can I know which nodes are next to the specific node? And If I
don't extract specific tissue using the code stated below, can I get the
coordinates of all of the nodes in the human head model?

m=mesh_extract_regions(m, 'region_idx', [6 1006]);

I would appreciate it if you could give me any ideas on that.

Best regards,
Manami


<nb18104 at shibaura-it.ac.jp>
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From barnaghosh19 at gmail.com  Wed May 18 19:38:09 2022
From: barnaghosh19 at gmail.com (Barna)
Date: Wed, 18 May 2022 23:38:09 +0600
Subject: [Simnibs-discuss] Extra Coils Files is not downloading
Message-ID: <5B6CEBB6-A574-4104-A134-FFBD089361AD@hxcore.ol>

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From martin.bardhi at ucalgary.ca  Wed May 18 19:51:19 2022
From: martin.bardhi at ucalgary.ca (Martin Bardhi)
Date: Wed, 18 May 2022 17:51:19 +0000
Subject: [Simnibs-discuss] Adding Tissues in the leadfield question
Message-ID: <QB1PR01MB27716E052F1E1D1F814DA025F7D19@QB1PR01MB2771.CANPRD01.PROD.OUTLOOK.COM>

Hello,
My name is Martin B and I am a university student researched using simNibs tDCS optimization feature for my project. When testing some of the functionality of the optimization scripts I found that if I include different tissues in the leadfield (CSF and skull surfaces for example (1003,1004) ) the resulting optimization will have different electrode placements (even when I then exclude these tissues from target.tissues().
I am a little confused as to what including these tissues in the leadfield does, as I initially thought it just meant that electric field would be recorded there but I have now found that it changes the optimization in some way. So, my question is: what does including different tissues in the leadfield do. And if I wanted to obtain an optimization that would be best reflective of real-world results, what tissues should I include (if any)?

Thanks,

Martin

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From andres.carvallo-pecci at umontpellier.fr  Fri May 20 10:57:27 2022
From: andres.carvallo-pecci at umontpellier.fr (Andres Carvallo Pecci)
Date: Fri, 20 May 2022 10:57:27 +0200 (CEST)
Subject: [Simnibs-discuss] Helmoltz-Like Coil_Simnibs Modelisation
Message-ID: <1420317107.653702.1653037047817.JavaMail.zimbra@umontpellier.fr>

Hello, 

I'm trying to model helmoltz-like coil (A-field) in matlab and then transfer it to simnibs in the form of a compressed Nifti file. 

I did a discretization 2.5 mm as suggested in the "Deng_Brain_Stim_2013" document (attached). My questions are the following: 

1) The A-field is calculated with a electric current equal to 1A? 
2) In the simnibs program, where is the origin coordinate with respect to the brain? 

My magnetic exposure is a helmoltz-like coil, stimulating the entire brain, but it seems that in my simnibs simulation, I am doing something wrong given that the simulated induced E-field is localized in Cz. 
Thank you for your help. 
Andres 
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From axelt at drcmr.dk  Tue May 24 11:49:12 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 24 May 2022 11:49:12 +0200
Subject: [Simnibs-discuss] Adding Tissues in the leadfield question
In-Reply-To: <QB1PR01MB27716E052F1E1D1F814DA025F7D19@QB1PR01MB2771.CANPRD01.PROD.OUTLOOK.COM>
References: <QB1PR01MB27716E052F1E1D1F814DA025F7D19@QB1PR01MB2771.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <42755ac3-4123-83d2-8549-bb3439db68af@drcmr.dk>

Hi Martin,


in general terms, the tdcs optimization tries to focus the currents on 
the target region(s) while avoiding all the rest (the "rest" is 
determined as all surfaces except the target regions). By including CSF 
and skull into the leadfield, you basically ask the optimization to 
avoid those surfaces as well, and this then will cause changes in your 
optimization results.


Best regards,

Axel


On 18-05-2022 19:51, Martin Bardhi wrote:
> Hello,
> My name is Martin B and I am a university student researched using 
> simNibs tDCS optimization feature for my project. When testing some of 
> the functionality of the optimization scripts I found that if I 
> include different tissues in the leadfield (CSF and skull surfaces for 
> example (1003,1004) ) the resulting optimization will have different 
> electrode placements (even when I then exclude these tissues from 
> target.tissues().
> I am a little confused as to what including these tissues in the 
> leadfield does, as I initially thought it just meant that electric 
> field would be recorded there but I have now found that it changes the 
> optimization in some way. So, my question is: what does including 
> different tissues in the leadfield do. And if I wanted to obtain an 
> optimization that would be best reflective of real-world results, what 
> tissues should I include (if any)?
>
> Thanks,
>
> Martin
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> 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
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/
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From axelt at drcmr.dk  Tue May 24 11:59:08 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 24 May 2022 11:59:08 +0200
Subject: [Simnibs-discuss] Helmoltz-Like Coil_Simnibs Modelisation
In-Reply-To: <1420317107.653702.1653037047817.JavaMail.zimbra@umontpellier.fr>
References: <1420317107.653702.1653037047817.JavaMail.zimbra@umontpellier.fr>
Message-ID: <7e84247f-a7d1-6bc9-98e2-bc3c868601ad@drcmr.dk>

Hi,

yes, it's for a current flow of 1A. The origin and coil orienations are 
defined by the header information in the nifti (the qform/sform matrices 
- please keep them identical to avoid weird behaviors). It's a 6 DoF 
transformation between voxel indices and real world coordinates (in mm).


Best regards,

Axel


On 20-05-2022 10:57, Andres Carvallo Pecci wrote:
> Hello,
>
> I'm trying to model helmoltz-like coil (A-field) in matlab and then 
> transfer it to simnibs in the form of a compressed Nifti file.
>
> I did a discretization 2.5 mm as suggested in the 
> "Deng_Brain_Stim_2013" document (attached). My questions are the 
> following:
>
> 1) The A-field is calculated with a electric current equal to 1A?
> 2) In the simnibs program, where is the origin coordinate with respect 
> to the brain?
>
> My magnetic exposure is a helmoltz-like coil, stimulating the entire 
> brain, but it seems that in my simnibs simulation, I am doing 
> something wrong given that the simulated induced E-field is localized 
> in Cz.
> Thank you for your help.
> Andres
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> 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
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/
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