Hi Lucas,


I am glad to hear that the documentation, the forum and the papers have helped you process your data.
This project does not have dedicated funding for new tool releases. We are maintaining it and solving bugs with small funds from other projects that only allow us to keep the current version of spharm in good working order but not adding new functionality. We have been making a lot of efforts to gather new funding and we hope to be able to obtain the resources we need soon to develop and release a new tool that can replace mancova, but for now older versions of mancova is what is available for analysis.

Yes, there is a fix for that but you will have to run the last spharm step manually. When you run ParaToSPHARMMesh you can enforce a certain flip (8 possible flips in each 3D axis and all the combinations), and choose the flip that makes your data match well. There are several ways to do it. You could use some comparison metric between the input binary map and the output PDM, and use the spharm degree and subdivision that give you an acceptable error level (they wont be the absolute same). In Slicer, for example you can look at volume values from a label map as well as a 3D surface, and you could use that value to compare both representations. Yes, that is correct, those are parameters only affecting the computation of the mean latitude axis. The number of theta iterations define how many points you will have along the axis, and the number of phi iterations define how many points along the surface you will use to compute the mean point for a latitude. Para out is to write out the parameterization values as scalar maps that can be loaded into the pdm or the unit sphere, it does not have anything to do with the alignment template. If you do not select "use mean as template" the first case in the list will be the template for the paramterization pose correction and the other additional alignment options (ellalign and procalign), if you use mean as template it will do one round of computation of spharm representations for all cases to them compute a mean. In a second round of computation, the mean will be used as template and new files will be writen out for all cases (mtemplate). It has to do with the procrustes registration. As any other registration problems involves an optimization, and those are parameters relating to the optimization process. Procrustes alignment tries to optimize the positions of one or more surface meshes points to have the least error between them as possible. This only is important if you use an output folder with files computed inside it. SPHARM by default will not compute again files that already exist in a certain output folder, unless the overwrite option is specified.



I hope that helps!
Best regards,


Beatriz