You can try

imorph, Morphome3cs II, PAST or R

R package geomorph, Morpho

Many thanks

https://sites.google.com/site/hymsfme/morphologikadisclaimer

Morphologika was quite helpful for me.

Our Checkpoint software (below) can help you collect landmark points as well as perform some 3D shape analysis on the collected points, including PCA, Procrustes, and more.

https://www.stratovan.com/products/checkpoint?utm_source=rg&utm_medium=ans&utm_campaign=gmm1

Many thanks I already used Stratovan it was very helpful.

IMP8:

http://www3.canisius.edu/~sheets/IMP%208.htm

CVA, PCA, Regression, PLS,.... and an utility that converts .pts format files from LandMark to tps format.

SlicerMorph (a customized version of 3D Slicer for landmark-based geometric morphometrics with GPA + PCA decomposition and real-time 3D visualization)

http://download.slicermorph.org