[Simnibs-discuss] Coil position _question modified

[Axel Thielscher]

Dear Mana:

On 1/22/2021 12:03 AM, Mana Biabani wrote:
> Hi again!
>
> I apologise for the additional email. I would like to modify my 
> question below regarding the coil position.
>
> Would appreciate if you could ignore my previous email and help me 
> with the points below:
>
>> I am using SimNIBS to simulate TMS-induced e-field and had two 
>> questions :
>>
>> 1- Is there any method to measure the exact distance between the coil 
>> and scalp surface? The 4mm default distance is not appropriate for my 
>> experiment; as the participants have EEG cap on and also there is a 
>> foam between the coil and the cap. Also, I’d like to account for the 
>> differences in the hair volume, etc.  I was thinking to measure the 
>> minimum euclidean distance between the coil centre and the scalp 
>> coordinates but as far as I understood the coil centre is actually a 
>> scalp position. So, it shouldn’t work.

When you have measured the distance physically during your experiment or 
can estimate it otherwise, you can update the distance used by SimNIBS 
by the proper value. See "distance" on 
https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html

Example : pos.distance = 10

--> 10 mm distance to skin

Note that you can also enter coordinates instead of electrode positions 
for the centre and pos_ydir.

>>
>> 2- My second question was about the coil orientation (in a more 
>> accurate way than choosing a reference electrode …). I am using 
>> Brainsight to get the information about the coil position, but not 
>> sure which outputs represent coil angels around different axes. I 
>> guess I can use [m0n0 m0n1 m0n2;  m1n0 m1n1 m1n2; m2n0 m2n1 m2n2 ] 
>> from Brainsight to make the transformation matrix, is that correct? 
>> If so, could you please let me know how I should modify them to be 
>> compatible with the coil axes in SimNIBS.

When you have neuronavigation positions, you can directly set the 
*matsimnibs *(also see 
https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html.)

Please also see 
https://simnibs.github.io/simnibs/build/html/_downloads/f0b89a9aa2f494cfe8e4dfd5d455e80e/coil_axesorientation.pdf 
for a visualizatoin of the coil coordinate system used by SimNIBS.

I think that you can use Lox X, Loc Y & Loc Z and the m0n0 m0n1 m0n2, 
m1n0 ...... to directly set up the matsimnibs, but you will likely have 
to exchange some of axes (i.e. m0 might not correspond to px, but maybe 
-pz or so, depending on how the convention in Brainsight is).

Hope this helps.

Best regards,

Axel


>>
>
> Kind regards,
> Mana
>
>
>
> ---
> *MANA BIABANI*
> Research Fellow
>
> *Turner Institute for Brain and Mental Health*
> Monash University
> 18 Innovation Walk
> Clayton VIC 3800
> Australia
>
> E: mana.biabanimoghadam at monash.edu 
> <mailto:mana.biabanimoghadam at monash.edu>
>
>
>
>
>> On 21 Jan 2021, at 4:19 pm, Mana Biabani 
>> <mana.biabanimoghadam at monash.edu 
>> <mailto:mana.biabanimoghadam at monash.edu>> wrote:
>>
>> Hi,
>>
>> I am using SimNIBS to simulate TMS-induced e-field and had two 
>> questions :
>>
>> 1- Is there any method to measure the exact distance between the coil 
>> and scalp surface? The 4mm default distance is not appropriate for my 
>> experiment; as the participants have EEG cap on and also there is a 
>> foam between the coil and the cap. Also, I’d like to account for the 
>> differences in the amount of hair, etc.  I was thinking to measure 
>> the minimum euclidean distance between the coil centre and the scalp 
>> but as far as I understood the coil centre coordinates are actually 
>> scalp positions. So, it shouldn’t work.
>>
>> 2- My second question was about coil angle. I am using the angles 
>> that Brainsight provides to make the transformation matrix as below :
>>
>> [ m0n0-m0n1m0n2 coil.center(1)
>>  m1n0-m1n1m1n2coil.center(2)
>>  m2n0-m2n1m2n2coil.center(3)] .
>>
>> Could you please confirm if this matrix is correct.  My understanding 
>> is that I need to inverse the y axis in Brainsight and it does not 
>> need any transformations (like MNI to subject space). Is that correct?
>>
>> Greatly appreciate your help in advance!
>>
>> Kind Regards,
>> Mana
>>
>>
>> ---
>> *MANA BIABANI*
>> Research Fellow
>>
>> *Turner Institute for Brain and Mental Health*
>> Monash University
>> 18 Innovation Walk
>> Clayton VIC 3800
>> Australia
>>
>> E: mana.biabanimoghadam at monash.edu 
>> <mailto:mana.biabanimoghadam at monash.edu>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>
> _______________________________________________
> 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: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20210126/a6f3513b/attachment-0001.html>