Changelog

4.1.0

  • Tetrahedral quality of the meshes was increased substantially to improve numerical accuracy of the FEM calculations and remove outliers in the calculated electric fields

  • Option added to use white matter and pial surfaces from FreeSurfer for more accurate representation of smaller sulci in the head meshes

  • I/O functions for neuronavigation data have been updated to support new Brainsight version 2.5.3

NOTES & Known issues: see 4.0.0

4.0.1

  • changed Brainsight position import/export to support only NIfTI:Aligned (to avoid ambiguities)

  • small bug fixes

4.0.0

  • New head segmentation and meshing pipeline charm with improved accuracy and robustness

  • Many new TMS coil models

  • New head models with additional tissue types, in particular spongy bone and large blood vessels

  • New flexible meshing approach to simplify manual editing and inclusion of custom tissue types in the head mesh

  • New command line tool meshmesh to support meshing of custom geometries

  • Support of Nx1 center-surround montages in python and Matlab

  • Added python examples for temporal interference simulations using pre-calculated leadfields for speed

  • Added basic I/O functions for neuronavigation data in python

  • Update to python 3.9

  • Major code cleanup and restructuring under the hood

  • Tested on Windows 10, Linux and Macs with Intel and Apple Silicon

  • Headreco and mri2mesh are deprecated.

NOTE: Simnibs 4 is NOT backwards compatible. Head models created with charm cannot be used in older versions. Head models from older versions need to be converted using the command line tool convert_3_to_4 for use with SimNIBS 4.

Known issues:

  • Installation fails on paths with non-standard characters, such as backslash, chinese characters, … (workaround: provide another path)

  • simnibs_gui does not start on some linux systems, e.g. with wayland (workaround: ld preloading of libstdc++.so.6 seems to help; example: export LD_PRELOAD=/usr/lib/libstdc++.so.6 - path needs to be adjusted according to library path on local system)

  • The PARDISO solver (available as option for the FEM calculations) does not work on Apple Silicon

3.2.6

  • fixed a bug causing headreco to fail on MacOS

  • Note: On Apple M1s using .ccd coil files does not yet work, please use niftis instead.

3.2.5

  • added skin smoothing options for TMS optimization

  • more informative matlab error messages

  • small bug fixes

3.2.4

  • Small bug fix related to gmsh options.

3.2.3

  • Gmsh version changed to avoid issues with Big Sur (only MacOS)

  • Headreco bug fixes to make meshing more stable in the eye region and air cavities

  • Added a Nx1 example for a center-surround electrode montage

3.2.2

  • Added matlab and python examples for TACSchallenge

  • Added matlab examples to calculate TI amplitudes

  • TMS optimization now prints optimal position in log file

  • Added reading of leadfields in mesh_load_hdr5.m

  • Added work-around to enable installation on Mac OS 11 Big Sur; NOTE: If you attempted to install a previous version of SimNIBS 3.2, you have to wipe the installation folder (in “/Users/username/Applications/SimNIBS-3.2” before attempting to install again; NOTE: This work-around is temporary and will be removed once the issues in the underlying python packages have been resolved

  • Changed the skin smoothing iterations in headreco from 5 to 20, which should result in a smoother skin surface. Note: this changes the standard behavior of headreco, so results might differ slightly.

  • Per default, headreco does not print the cat summary pdf anymore. The –cat_no_print flag was removed; Instead, use –cat_print now in case you need the summary.

Bug fixes:

  • TDCS Network Optimization: Fixed bugs to accept images with NaNs, binary images, and images of size NxMxKx1; weights of eyes are now set to 0.

  • Added buffered read for gmsh v2 files in python to resolve speed issue on clusters

  • Resolved a bug causing some points of the individual middle gm surface to be falsely interpreted as outside gm when interpolating results to individual gm surface

  • Further small fixes across the code

  • Fixed electrode meshing that sometimes caused some parts of the electrodes to be detached.

Known issues:

  • mri2mesh does not work with Freesurfer 7; please use Freesurfer 6 for now

  • SimNIBS is so far not tested on Macs with Apple Silicon, and is likely to give errors on those machines

3.2

  • Added Auxiliary Dipole Method (ADM) TMS optimization (contributed by Luis Gomez)

  • Added TES magnetic field calculations for MRCDI/MREIT (contributed by Hassan Yazdanian)

  • Added TES optimization with field strength

  • Added TES optimization for brain network targeting

  • FMM-based coil A field calculations from .ccd files

  • Refactoring of optimization code

  • Calculating coil-cortex distances during TMS simulations

  • New installers

3.1

  • Added TDCS and TMS Optimization

  • Added support to the MKL PARDISO solver

  • Minor bug fixes

3.0

  • Major update to SimNIBS

  • New integrated solver based on PETSc and Hypre with huge speed ups!

  • New installation procedure

  • Changed headreco call (-d no-conform and CAT12 now standard)

  • New coil models

  • Moved to Python 3.7

  • Updated documentation

  • Uncertainty quantification support

  • Improved results visualizations

  • SimNIBS is now installable as a python package

2.1.2

  • This upgrade focused on the MATLAB library for SimNIBS

  • The MATLAB library can be found in in the matlab/functions/ folder in the simnibs directory

  • The MATLAB examples have been expanded to show the new features

  • We also made a few bug fixes to get_fields_at_coordinates and the graphical user interface

2.1.1

  • This upgrade focused on usability of SimNIBS

  • Simnibs is now shipped with spm12 and cat12. Installing those separately is no longer necessary to run heareco. When you have Matlab installed, you’re ready to go after the SimNIBS installation.

  • Added features for automatically calculate eeg positions and easily using them to set-up simulations in the GUI. Added a script called get_eeg_positions in order to use the new features on head models ran with SimNIBS 2.1.0

  • Improved Matlab and python scripting. Examples can be fount in $SIMNIBSDIR/matlab/examples and $SIMNIBSDIR/python_examples

  • Changed the sign of the normals when interpolating to the cortical surface

  • the SimNIBS python installation no longer requires scikit-image

2.1.0

  • 2.1.0 is a major update of SimNIBS 2

  • New head segmentation script headreco

  • New post-processing options to transform fields to NIfTI volumes, MNI space, FreeSurfer overlays and FsAverage space

  • New scripts to calculate EEG 10-10 positions

  • New MATLAB library, including example scripts e.g. to set up simulations for ring electrodes

  • New example data sets, including an extended MNI template

  • Major refactoring under the hood, for a cleaner experience and quicker future updates

  • Head segmentations and simulation files created with SimNIBS 2.0 are incompatible with SimNIBS 2.1

2.0.1g

  • More fixes to the GUI

  • Changes address to Miniconda during installation procedure

  • Changed bug in simnibs.py where it would look for files that didn’t exist

2.0.1f

  • Changed 3dcalc wrapper in Linux

  • Fixed bugs in the GUI related to the PySide->PyQt changes

2.0.1e

  • Changed from PySide to PyQt

  • Changed getopt in osx to a wrapper script which will call getopt_o adjusting DYLD_LIBRARY_PATH

  • Changed scalp color on GUI

2.0.1d

  • Fixed the intallation of qt on mac

  • Fixed an installation bug that occurred when reinstalling simnibs without starting a new terminal window

2.0.1c

  • freeglut is no longer required

  • now a local verision of libXp, libXpm and libXmu is provided. This should make the installation easier

  • solved bug in the anisotropic conductivity calculations that would happen if there was a “.” in the path

2.0.1b

  • Now SimNIBS gui gives out a warning if there are any spaces in the file path

  • The installation procedure will now install freeglut on Linux

2.0.1a

  • support of conductivity tensors for gray and white matter added to GUI

  • script dwi2cond added to estimate conductiviy tensors from diffusion MRI

  • automatic installation procedure changed to use miniconda

  • bug in mri2mesh fixed which prevented it to use the T2 image to reconstruct the skull

  • Changed standard colors in GUI

  • The GUI now lets you set TMS coil distances

  • Removed deprecated post processing options

  • Added new TMS coil files

  • Fixed bug where the electrode thickness would change every time the electrode edition window opened

  • Fixed bug where every simulation would use the same conductivities

  • GUI now supports advanced electrode modeling

  • ATTENTION old .simnibs files maybe incompatible with the new version