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

Wed Jul 15 18:39:21 CEST 2020

Great, thank you all so much for the help!

Best,

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

________________________________
From: Guilherme B Saturnino <guilhermebs at drcmr.dk>
Sent: Wednesday, July 15, 2020 1:57 AM
To: Mccalley, Daniel <mccalled at musc.edu>; Oula Puonti <oupu at dtu.dk>; discuss at simnibs.org <discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp

CAUTION: External

Hi Dan,

This transformation is embedded inside the NifTi files. It's often called the "affine". Normally the X axis corresponds to left/right, Y to posterior/anterior and Z to bottom/top, but it can vary depending on how the image was acquired and how the subject was positioned inside the scanner, so it is not so reliable. However, the co-register images, located in the m2m_{subID}/toMNI folder, are sure to follow this convention, if the co-registration worked (it generally does). We also use the co-registrations to calculate the 10-10 EEG positions, including FP1, which are stored in m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv.

Best Regards,

Guilherme

On 14/07/2020 23.12, Mccalley, Daniel wrote:
Hi all,

Thanks again for the help!

Oula, would you be able to point me toward the header file that may have information on the voxel-to-world transformation? It would be useful to know which direction is up/down, left/right, forward/backward if X Y and Z aren't always accurate

Best,

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

________________________________
From: Oula Puonti <oupu at dtu.dk><mailto:oupu at dtu.dk>
Sent: Monday, July 13, 2020 2:44 AM
To: Mccalley, Daniel <mccalled at musc.edu><mailto:mccalled at musc.edu>; Guilherme B Saturnino <guilhermebs at drcmr.dk><mailto:guilhermebs at drcmr.dk>; discuss at simnibs.org<mailto:discuss at simnibs.org> <discuss at simnibs.org><mailto:discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp

CAUTION: External

Hi Daniel,

Thanks for the clarification.

I could see two problems:

1) The Nz coordinate from SimNIBS is not correctly placed. This can happen due to segmentation/registration errors. You should open the MRI scan in a viewer, for example freeview, and check that the Nz coordinate that SimNIBS outputs matches the nasion location on the scan.

2) The header, i.e., voxel-to-world transformation, of the MRIs is different between subjects. If you always substract the X and Y distances you might end up moving in a different direction than intended.

Best,

Oula

________________________________
From: Mccalley, Daniel <mccalled at musc.edu><mailto:mccalled at musc.edu>
Sent: Friday, July 10, 2020 6:43:03 PM
To: Oula Puonti; Guilherme B Saturnino; discuss at simnibs.org<mailto:discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp

Hi all,

Thank you so much for the fast replies!

Let me clear up a few things about our experiment --

When our participants come in, the experimenter measures the individual's head (nasion to inion, tragus to tragus, circumference). Each person's measurements are of course different and there is some amount of error/rounding made by the experimenter in each measurement. Our participants are never fitted with an EEG cap to locate our cortical target (FP1).

Instead, starting at Nz, we take 10% of the distance for Nz to Inion (generally ranges from 2-4 cm, I referred to this as Y in my initial example) and move up and we take 5% of the total head circumference and move that distance left (towards FP1, I referred to this as X in my initial example). The experimenter makes a mark on the persons head with sharpie, but unfortunately we did not use a fiducial for this study.

Given that the FP1 location is determined in a patient-tailored manner and we expect some degree of experimenter error in making these measurements, I'd like to as closely as possible recreate an e-field at the site of stimulation for each person using these measurements. Thus far, I have used the coordinates for Nz that SIMNIBs produces and made adjustments from there based on X and Y displacement for each subject. This almost always produces a result close to FP1, but in some instances it seems the result remains near the eye or in entirely unexpected head locations

Does that information help?

Thank you all again for your help!

Best,

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

________________________________
From: Oula Puonti <oupu at dtu.dk><mailto:oupu at dtu.dk>
Sent: Friday, July 10, 2020 3:35 AM
To: Guilherme B Saturnino <guilhermebs at drcmr.dk><mailto:guilhermebs at drcmr.dk>; Mccalley, Daniel <mccalled at musc.edu><mailto:mccalled at musc.edu>; discuss at simnibs.org<mailto:discuss at simnibs.org> <discuss at simnibs.org><mailto:discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] Targeting subject specific locations on the scalp

CAUTION: External

Hi,

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.

Best,

Oula

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

Hello,

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://urldefense.com/v3/__https://simnibs.github.io/simnibs/build/html/tutorial/gui.html__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBSlfQpNA$>, which loads it automatically, or in  scripts (MATLAB example<https://urldefense.com/v3/__https://github.com/simnibs/simnibs/blob/v3.1.2/simnibs/examples/simulations/TMS.m__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBXnVXhnJ$>)

2) Using the eeg_positions<https://urldefense.com/v3/__https://simnibs.github.io/simnibs/build/html/documentation/command_line/eeg_positions.html__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBd53sE1Z$> command line tool with the Nz, LPA, RPA and Iz as an input

Those two were compared and validated here<https://urldefense.com/v3/__https://link.springer.com/chapter/10.1007/978-3-030-21293-3_1__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBSy4FP92$>.

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,

Guilherme

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/<https://urldefense.com/v3/__http://clinicalresearcher.org/F3/__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBcP0FOvN$>) 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!

Best,

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

_______________________________________________
Simnibs-discuss mailing list
Simnibs-discuss at drcmr.dk<mailto:Simnibs-discuss at drcmr.dk>
https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss<https://urldefense.com/v3/__https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBfqFDV5E$>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20200715/a4a29d73/attachment-0001.html>