The 'msh2nifti' function converts a .msh file that was output from a simNIBS simulation run back into a .nii.gz file. Users can specify a specific View (1=WM, 2=GM, 3=CSF, 4=Skull, 5=Head), a specific Field (E,normE,J,normJ), and a specific voxel size (1,2,..).
This allows users to use the simulated fields seamlessly with structural/functional nifti files collected during real TMS/tDCS experimentation.
- Uninstall current simNIBS application:
- run 'sudo rm -r -f $SIMNIBSDIR' (add 'sudo' at beginning if you get an error)
- run 'sed -i.bak '/SIMNIBS/d' ~/.bash_profile'
- Download simNIBS tar file again from the website http://simnibs.de/version2/installation
- move folder wherever you want... doesnt matter
- Uncompress folder by double clicking or run 'tar -zxvf simnibs_X.X.X.tar.gz'
- copy msh2nifti.py file to simnibs_X.X.X/fem_efield/src_pythonmsh2nifti.py
- copy install_simnibs_NCC.sh to simnibs_X.X.X/install_simnibs_NCC.sh
- go to uncompressed simnibs directory (e.g. run 'cd ~/downloads/simnibs_X.X.X'
- run './install_simnibs_NCC.sh'
- if you get an error about permissions, run
chmod u+x install_simnibs_NCC.sh
- Follow the rest of the simnibs instructions.. It installs exactly as before.
usage: msh2nifti [-h] -mesh MESH -t1 T1 [-view VIEW] [-field FIELD] [-voxel VOXEL] [-out OUT] [--verbose]
optional arguments:
-h, --help show this help message and exit
-mesh MESH mesh file from simNIBS simulation filepath
-t1 T1 reference T1 conform image filepath
-view VIEW integer from 1-5 -> which volume/surface to use (default = 2)
-field FIELD string -> simulation field values to use (default='normE')
-voxel VOXEL integer -> resolution of voxelized image (default=1)
-out OUT filepath to resulting output nifti image
--verbose whether to print status
msh2nifti -mesh /Users/user-name/desktop/testfiles/mymeshfile.msh
-t1 /Users/ncullen/desktop/testfiles/T1_conform.nii.gz
-view 2
-field normE
-voxel 1
-out /Users/user-name/desktop/testfiles/myniftifile.nii.gz
--verbose