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
neurolabusc
commented
1 week ago
The upcoming commit (v1.0.20240817) introduces two new operations.
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).niimath imgin-close 0.5 3 6 imgoutniimath imgin -close $iso $dx1 $dx2 imgoutis an accelerated alias forniimath imgin -thr $iso -binv -edt -thr $dx1 -binv -edt -thr $dx2 -bin -mul $iso -max imgin imgout