# Create a tempate for amygdala

**URL:** <https://discourse.slicer.org/t/create-a-tempate-for-amygdala/1037>\
**Category:** SlicerSALT\
**Created:** [September 11, 2017, 8:33pm UTC](https://discourse.slicer.org/t/create-a-tempate-for-amygdala/1037 "2017-09-11T20:33:16Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![bpaniagua](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bpaniagua/32/20_2.png) [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Post date:** [September 11, 2017, 8:33pm UTC](https://discourse.slicer.org/t/create-a-tempate-for-amygdala/1037/1 "2017-09-11T20:33:16Z")

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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

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**Author:** ![bpaniagua](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/bpaniagua/32/20_2.png) [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Post date:** [September 11, 2017, 8:38pm UTC](https://discourse.slicer.org/t/create-a-tempate-for-amygdala/1037/2 "2017-09-11T20:38:46Z")

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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](https://www.slicer.org/wiki/Documentation/Nightly/Extensions/SpharmPdm) now incorporates a module to do the flip of the parameterizations easily. Also, see the [new documentation here](https://github.com/NIRALUser/SPHARM-PDM/blob/master/Doc/SPHARM-PDM-Tutorial.pdf).

There is thread [here](https://discourse.slicer.org/t/group-analysis-with-spharm-pdm/885) in which we discussed (among other things) how to create average meshes in SlicerSALT-SPHARM.

I hope this helps.  
Best,

Bea