katjaq / volume

tool to work with volume data

volume

A command-line tool to work with volume data.

-i str	input volume
-o str	output volume
-selectVolume int	selects the n-th volume in a nifti file with many volumes
-largest6con	largest 6 connected component
-dilate int	dilate(size)
-erode int	erode(size)
-compress float str	cosinus transform compress rate coeff_file
-hist int	hist(#bins)
-matchHist str	matchHistogram(another_mri)
-stats	stats, returns mean, std, min, max
-tiff str str str float	write slice as tiff file. Args: path, cmap, ori {x, y, z}, slice
-info	information: dimensions, data type, pixel size
-threshold float int	threshold(level,direction)
-volume	calculate volume
-new	create a new volume with dimx,dimy,dimz,pixx,pixy,pixz,offx,offy,offz
-zigzag	print volume values in zigzag order
-decompose str	decompose(basename) a volume with many values into volumes with one single value
-strokeMesh str	set the surface of the mesh (text format) at input path to value=max+1; mesh needs to be in voxel coordinates
-surfaceNets level path	extract isosurface from the volume at the indicated level using the surface nets algorithm, save at the indicated path
-sampleMesh str1 str2	sampleMesh(mesh_path, result_path) save the volume values at the vertices of the mesh pointed by the file path to the result path