meshgeometry

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