New operations - Githubissues

The upcoming commit (v1.0.20240817) introduces two new operations.

fastsurfer and freesurfer conform. For example, niimath t1 -conform ct1. Like FSL, the upper intensity threshold is 2% (0.98), while the freesurfer/fastsurfer default is 0.999. The more liberal outlier rejection is useful for T1 scans with flow artifacts (e.g. T1 scans from 7T scanners).
- morphological close operation. This combines dilation and erosion and is useful for creating meshes to fill small cavities. Below shows an input and resulting image with the call niimath imgin-close 0.5 3 6 imgout The operation takes three arguments, the isosurface threshold, the initial dilation amount (in mm) and the final erosion amount (in mm). Note that niimath imgin -close $iso $dx1 $dx2 imgout is an accelerated alias for niimath imgin -thr $iso -binv -edt -thr $dx1 -binv -edt -thr $dx2 -bin -mul $iso -max imgin imgout

rordenlab / niimath