[Simnibs-discuss] Basic simNIBS questions

Catriona Scrivener Catriona.Scrivener at mrc-cbu.cam.ac.uk
Mon Sep 20 12:30:35 CEST 2021

Dear simNIBS,

Thank you for creating such a great tool! I am new to simNIBS and have a few basic questions:

1) I have run segmentation using headreco, which I read should preserve the original coordinates of the structural file. Is it sensible to use target co-ordinates derived using SPM as coordinates for a TMS target in simNIBS? I am hoping that a real world xyz coordinate in SPM is the same as an xyz coordinate in simNIBS.

2) The .txt files created by simNIBS' normalisation to MNI space (e.g. MNI2conform_6DOF) look very different to the normalisation parameters created by SPM12 (e.g. s*seg_sn.mat). Is this expected? In particular, values in the fourth column from SPM range up to ~200, but only up to ~10 from simNIBS. Is there a relationship between these files or should I not attempt to equate them?

3) we want to run simulations for a TMS-fMRI experiment. Are there existing coil files for the MagVenture 'MRi-B91 Air Cooled coil', or should I use one of the others provided?

4) for using the dwi2cond function, does a phase direction of '-y' correspond to an AP direction?

5) is it possible to extract the co-ordinates of EEG electrodes projected from the scalp down onto the brain? i.e. can you extract the co-ordinates of the brain region 'closest' to each electrode?

Kind regards,


Catriona Scrivener

Research Associate

MRC Cognition and Brain Sciences Unit

University of Cambridge

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