Mesh geometry tools. Several commands can be chained together, with the same operation appearing many times in the same command line. They are processed sequentially.
Compiling: bash compile.sh
In Linux, you may need to install the freeglut3 and libmesa libraries first: apt-get update apt install freeglut3-dev apt install mesa-common-dev
| I/O commands | Description |
|---|---|
| -iformat format_name | Force input format (needs to precede imesh) |
| -oformat format_name | Force output format (needs to precede omesh) |
| -i filename | Input file (also accepts -imesh) |
| -o filename | Output file (also accepts -omesh) |
| -odata filename | Output data |
| Geometry measurement | Description |
|---|---|
| -absgi | Compute absolute gyrification index |
| -area | Surface area |
| -checkOrientation | Check that normals point outside |
| -centre | Move the mesh's barycentre to the origin |
| -euler | Print Euler characteristic |
| -foldLength | Compute total fold length |
| -size | Display mesh dimensions |
| -tris | Display number of triangles |
| -verts | Display number of vertices |
| -volume | Compute mesh volume |
| -curv | Compute curvature |
| -depth | Compute sulcal depth |
| -areaMap | Compute surface area per vertex |
| -icurv number_of_iterations | Integrated curvature (warning: icurv changes the geometry of the mesh) |
| -isolatedVerts | Count the number of isolated vertices in the mesh |
| Geometry modification | Description |
|---|---|
| -add filename | Add mesh at filename to the current mesh |
| -average n_meshes path1 path2 ... pathn | Compute an average of n_meshes all of the same topology |
| -barycentricProjection reference_mesh | Print barycentric coordinates for each vertex in reference_mesh |
| -fixFlip | Detect flipped triangles and fix them |
| -fixSmall | Detect triangles with an angle >160 |
| -flip | Flip normals degrees and fix them |
| -laplaceSmooth lambda number_of_iterations | Laplace smoothing |
| -level level_value | Adds new vertices (and triangles) to the edges that cross level_value in the vertex data (f.ex., mean curvature) |
| -normalise | Place all vertices at distance 1 from the origin |
| -randverts number_of_vertices | Generate homogeneously distributedrandom vertices over the mesh |
| -relax filename | Relax current mesh to mesh at filename (both meshes have the same topology) |
| -resample smooth_mesh reference_mesh | Resample the mesh to match the vertices and the topology of the argument mesh |
| -removeIsolatedVerts | Removes isolated vertices in the mesh (if present) |
| -rotate x y z | Rotate with angles x, y and z (in degrees) |
| -scale scale_value | Multiply each vertex by 'scale' |
| -sortTriangles | Sort the triangles in the mesh file along the x axis |
| -stereographic | Stereographic projection |
| -subdivide | Subdivide the mesh with one iteration of Kobbelt's sqrt(3) algorithm |
| -taubinSmooth lambda mu number_of_iterations | Taubin Smoothing |
| -translate x y z | Translate mesh by x, y, and z. |
| -lissencephalic | Smooth valleys and hills, not the coast |
| -normal | Mesh normal vectors |
| Data measurement | Description |
|---|---|
| -countClusters value | Count clusters in texture data |
| -max | Maximum data value |
| -mean | Mean data value |
| -min | Minimum data value |
| Data modification | Description |
|---|---|
| -addVal | Add value data |
| -subVal | Subtract value from data |
| -multVal | Multiply data time value |
| -divVal | Divide data by value |
| -clip min max | Clip data values to the interval [min,max]\n\ |
| -smoothData lambda number_of_iterations | Laplace smoothing of data, lambda=0 -> no smoothing, lambda=1 -> each vertex value to neighbour's average |
| -threshold value 0:down/1:up | Threshold texture data |
| Other | Description |
|---|---|
| -drawSurface colourmap path | draw surface in tiff format, colormap is 'grey' or 'rainbow' |
| -v | Verbose mode |
| -h | Help |
Meshgeometry can read and write several formats, based on the file extension:
| Extension | Description |
|---|---|
| .orig, .pial, .white, .inflated, .sphere, .reg | Freesurfer meshes |
| .curv, .sulc, .sratio | Freesurfer data |
| .mesh | BrainVisa mesh |
| .txt | RT's mesh plain text format |
| .float | Raw float data |
| .txt1 | RT's data format |
| .bin | n-e-r-v-o-u-s system web binary mesh |
| .wrl, .obj, .ply, .stl, .smesh, .off, .vtk, .gii | Other mesh formats |