headreco reconstructs a tetrahedral head mesh from T1- and T2-weighted structural MR images. It runs also with only a T1w image, but it will achieve more reliable skull segmentations when a T2w image is supplied.
headreco requires a MATLAB. Linux and MacOSX users might need to configure MATLAB for usage with headreco, please see the see here for more information.
Open a terminal and go to the
ernie/folder of the example data set.
Run the reconstruction:
headreco all ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz
alltells headreco to run all reconstruction steps including volume meshing. The subject ID (subID)
ernieis given next. Headreco will create a mesh named
ernie.msh, and a folder
m2m_ernie/that contains the segmentation results and the files needed for volume meshing. The input images are given as final arguments (first the T1, then the T2).
Alternatively, the reconstruction can be run with only the T1w image as input, but this will result in a less accurate skull region:headreco all ernie org/ernie_T1.nii.gz
You can also run headreco without using CAT12 by calling.headreco all --no-cat ernie org/ernie_T1.nii.gz
Segmentations without CAT12 will run faster, but will have a poorer reconstruction of the cortical gray and white matter.
Check the results:
headreco check ernie
This will show the reconstructed surfaces overlaid over the MR images using freeview. A second freeview will show the subject T1 registered to the MNI template for visual inspection of the accuracy of the registration. In addition, you should have a look at the tetrahedral head mesh by loading it into Gmsh. In case freeview is not available, the spm viewer will be opened to allow for a basic check of the results.
Mesh resolution can be controlled using the -v option, which allows setting the vertex density (nodes per mm²) of the surface meshes. As a standard,
headrecouses 0.5 nodes per mm², resulting in head meshes with around 4 million tetrahedra.
After the head mesh creation, temporary files are deleted to save disk space. Adding
Manual editing: Edit one or more of the binary masks stored in
m2m_subID/mask_prep/. Then run
headreco surfacemesh subIDand
headreco volumemesh subIDto re-create the head mesh based on the edited masks. Add
--no-catto the surfacemesh step in case you did nott use CAT12. Note: When using CAT12, surfaces instead of voxel masks will be stored for GM and WM in the
mask_prep/folder. For now, these surfaces cannot be manually improved.
Transformation from and to MNI space: Both positions and results such as the electric field can be transformed between MNI and subject space. Please see below for a description of the corresponding command line programs. The transformation is based on a non-linear whole-head registration of the T1 of the subject to the MNI template that is determined during the SPM12 segmentation procedure. The transformations are stored in the
m2m_subID/toMNI/directory. Subject space is defined by the qform set in the
m2m_subID/subID_T1fs_conform.nii.gz, which can be found in the same folder as the head mesh.
When something goes wrong, you can check the