Create a tempate for amygdala

Hi Beatriz

I am a Msc student in Neuroscience in Ege University, Turkey. I am doing shape analysis for amygdala. I could not find a template for amygdala. So,I would like to create template.

I have 30 amygdala in my population. First I run all the steps in SPHARM-PDM (SegPostProcess, GenParaMesh and ParaToSPHARMMesh).

After SegPostProcess I end up having 30 *_SegPost.nii files.

After GenParaMesh I end up having 30 *_para.vtk and 30 *_surp.vtk files.

After ParaToSPHARMMesh I end up having 30 *_MedialAxisScalars.csv, 30 *_SPHARM.coef, 30 *_SPHARM.vtk, 30 *_SPHARM_ellalign.coef, 30 *_SPHARM_ellalign.vtk and 30 *_SPHARMMedialAxis.vtk files.

I need a regTemplate and a flipTemplate. How can I create these two templates and which outcome files can I use while creating these templates?

best regards,

Gozde Kizilates

Hi Gozde,

Thank you for your email.

The choice of regTemplates and flipTemplates is up to you. Some people generate an average of the whole population after running the whole SPHARM-PDM pipeline once, some other people just randomly choose a single mesh of the population representative of the anatomy to be the regTemplate/flipTemplate.

For the flipTemplate is worth mentioning that the new SPHARM-PDM extension now incorporates a module to do the flip of the parameterizations easily. Also, see the new documentation here.

There is thread here in which we discussed (among other things) how to create average meshes in SlicerSALT-SPHARM.

I hope this helps.