[Simnibs-discuss] Targeting subject specific locations on the scalp

Oula Puonti oupu at dtu.dk
Fri Jul 10 09:35:45 CEST 2020


Just to add to what Guilherme said: Are you locating the nasion manually or using coordinates that SimNIBS outputs automatically? If the latter, please check that the fiducial placements look correct.



From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Guilherme B Saturnino <guilhermebs at drcmr.dk>
Sent: Friday, July 10, 2020 9:31:07 AM
To: Mccalley, Daniel; discuss at simnibs.org
Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp


SimNIBS 3 offers two ways of getting 10/10 EEG positions out of the box.

1) Use the eeg positions calculated using MNI transformations, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. Those can also be accessed in the GUI<https://simnibs.github.io/simnibs/build/html/tutorial/gui.html>, which loads it automatically, or in  scripts (MATLAB example<https://github.com/simnibs/simnibs/blob/v3.1.2/simnibs/examples/simulations/TMS.m>)

2) Using the eeg_positions<https://simnibs.github.io/simnibs/build/html/documentation/command_line/eeg_positions.html> command line tool with the Nz, LPA, RPA and Iz as an input

Those two were compared and validated here<https://link.springer.com/chapter/10.1007/978-3-030-21293-3_1>.

I'm not sure why it is not working in your case though, might be due to head size, as you are moving by constant amounts?

Best Regards,


On 09/07/2020 19.48, Mccalley, Daniel wrote:
Hi all,

Our lab targets the FP1 with TMS. We use a simple measurement system (http://clinicalresearcher.org/F3/) to locate exactly where we want to place the coil for each subject. Typically, we measure the subject's head, and then, starting from nasion, we'll move up Y mm and left X mm (where X and Y are determined from each subject's given head size).

Ideally, we'd like to create an electric field model for each subject that accounts for the TMS parameters as well as the exact location used. To implement this in SIMNIBS, I've tried the following:

1) Open a subjects m2m file and find the coordinates for nasion (say, for example, that these coordinates are X= -2.78, Y= 117.59, Z= -20.63).

2) Determine Y and X used to locate FP1 for the given subject (say, for example, that starting from nasion, we moved 37 mm in the Y direction, and over 32 mm in the X direction).

3) Subtract the displacements in the Y and X directions from the original nasion coordinates, resulting in X= -34.78 and Y=80.69

4) Add a new position wherein the reference coordinates match the original nasion coordinates (and the Define Reference Coordinates box is checked) and the coordinates calculated in step 3 are input in the position fields (Z is left blank for SIMNIBs to calculate)

5) Adjust for coil orientation and TMS parameters

This seems to have worked well for 90-95% of our subjects, however there are a few subjects in which the resulting coil placement appears to be over the eye (Note: Ordinarily I'd attach examples of the working and not-working subjects, but I'm not sure if the skin reconstruction of our participants falls under PHI).

Am I going about this the wrong way? Could this reflect a problem with segmentation/meshing? Or maybe a problem with the experimenter measurements of the subjects head? Any advice would be greatly appreciated. Thank you all so much!


Dan McCalley
Medical University of South Carolina
College of Graduate Studies, Neuroscience

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