open-discussion > Some question about the shape align process
Showing 1-2 of 2 posts
Mar 24, 2016 06:03 AM | xiaoguang li
Some question about the shape align process
Hello SPHARM experts,
I am a beginner of SPHARM and want to use this software building liver shape model.I run the SPHARM in 3dSlicer.After Testing,I found a question that all the shapes have no change in scaling factor.So i want to know is there has a parameter in SPHARM can add the scaling factor in aligning process,or I need scale the shapes by myself.
I am a beginner of SPHARM and want to use this software building liver shape model.I run the SPHARM in 3dSlicer.After Testing,I found a question that all the shapes have no change in scaling factor.So i want to know is there has a parameter in SPHARM can add the scaling factor in aligning process,or I need scale the shapes by myself.
Mar 25, 2016 02:03 PM | Martin Styner
RE: Some question about the shape align process
Hi Xiaoguang
Yes, by default our shape tools do not change the scale of the objects, as that is commonly the desired thing to do when analyzing biological structures (as scale is an important part of shape of such objects). Of course, there are settings in which scaling normalization is needed.
The ShapeAnalysisModule though does not provide (yet) an option to enable the scaling normalization in the alignment process and you would need to do that yourself. I would run the module as is and then scale the final surfaces at the end. In the distribution, you also get a module called MeshMath (it is in the Extension folder SPHARM-PDM/lib/Slicer-4.3/ExternalBin/MeshMath) which allows you to do Procrustes alignment with scaling via the "-alignMesh" option that allows you to enable "-scalingOn".
Hope this helps
Martin
Yes, by default our shape tools do not change the scale of the objects, as that is commonly the desired thing to do when analyzing biological structures (as scale is an important part of shape of such objects). Of course, there are settings in which scaling normalization is needed.
The ShapeAnalysisModule though does not provide (yet) an option to enable the scaling normalization in the alignment process and you would need to do that yourself. I would run the module as is and then scale the final surfaces at the end. In the distribution, you also get a module called MeshMath (it is in the Extension folder SPHARM-PDM/lib/Slicer-4.3/ExternalBin/MeshMath) which allows you to do Procrustes alignment with scaling via the "-alignMesh" option that allows you to enable "-scalingOn".
Hope this helps
Martin