E-field Dosing

Dependencies and where to download them

• SimNIBS and any additional dependencies (depending on version): https://simnibs.github.io/simnibs/build/html/installation/simnibs_installer.html
  • The SimNIBS example dataset is found at https://simnibs.github.io/simnibs/build/html/dataset.html
• FreeSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
  • For Windows users, it is possible to download and use FreeSurfer through the Linux subsystem by following the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl

Checking the FreeSurfer integration with SimNIBS 4

1. In the Linux subsystem / Terminal, navigate to the folder where the NifTI files are located in the SimNIBS example dataset
2. In the Linux subsystem / Terminal, run recon-all -subjid ernie -all -i org/ernie_T1.nii.gz -T2 org/ernie_T2.nii.gz
   1. This should generate a fs_ernie folder in the SUBJECTS_DIR you specified during the FreeSurfer Installation
   2. If you get a permission denied error, add export SUBJECTS_DIR=<path to acceessable folder> to the same file you added source $FREESURFER_HOME/SetUpFreeSurfer.sh while setting up freesurfer
3. In the Linux subsystem / Terminal, run charm ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz --fs-dir <path to fs_ernie folder>

Checking the TAP installation

1. In MATLAB, Open “run_subj.m”
2. In MATLAB, change the filepaths between %%%%% CHANGE TAP PARAMETER HERE: Begin %%%%% and %%%%% CHANGE TAP PARAMETER HERE: End %%%%% as needed
   1. Set Scale_Efield_to_Value to the desired E-field value in V/m (can use 100 to test)
   2. If not running on a Linux cluster, comment out the line starting with setenv
3. Change subjects/Ernie_charm or the subjects subfolder corresponding to the appropriate pipeline to subjects/ernie and copy the ernie folder from the example dataset to subjects/ernie
4. Copy M1_mask_TMS_target.nii.gz from TAP/subjects/Ernie_headreco into “subjects/ernie”
5. In MATLAB, run run_subj('ernie', 'subjects', 'M1', 'M1_mask_TMS_target.nii.gz', 1)
   1. This should generate a ernie_M1 folder, a ernie_M1_scirun folder, and at least one M1_HTX.X folder

Quality control

1. For the SimNIBS head mesh, see https://simnibs.github.io/simnibs/build/html/tutorial/advanced/fix_affine_registration.html for quality control
2. Open subjects/ernie/M1_HT0.0/ernie_TMS_optimize_MagVenture_Cool-B65.msh
   1. Check that the target is at the expected location
   2. Check that the coil is oriented such that the primary E-field induced by the coil points into the target gyrus
      • Many coils have arrows on them indicating the current direction
      • For monophasic pulses, the primary E-field points in the opposite direction as the current
      • For biphasic pulses, the primary E-field points in the same direction as the current

TAP: TMS_Targeting_And_Analysis_Pipeline

Custom MATLAB code to determine an optimal scalp placement of a TMS coil on the computational model of the subject's head. (1) Optimal coil placement is chosen based on maximizing the TMS-induced electric field in a brain region of interest which is derived from individual fMRI peak activity and computed prospectively for neuronavigation-supported TMS experiments. (2) The code's functionality allows also for accuracy assessment of the coil placement recorded during and analyzed after a TMS session.

Dependencies:

• SimNIBS 3.2.X
• 'Tools for NIfTI and ANALYZE image' for loading structural MRI data sets (nii files) version 1.27.0.0 (from MATHWORKS MATLAB Central)

For SimNIBS version < 3.2.5 users, the option to control the smoothness of the scalp surface (scalp_normals_smoothing_steps) to allow changing the scalp tangential plane from MATLAB is not available. However, there is a simple patch you can do yourself and described here: simnibs/simnibs#42 and change smooth=1 to smooth=20 for example.