Hi Martin and others, 

I have followed the steps in this thread using the general three steps:
1. run ParaToSPHARMMeshCLP separately for each subject without specifying flip or registration templates to get vtk files having correspondance (*_surfSPHARM.vtk)
2. use MeshMath -avgMesh to create study-specific average using the *_surfSPHARM.vtk files
3. rerun ParaToSPHARMMeshCLP while specifying both the flip and registration templates

I have successfully run steps 1 and 2 and have run into a wall with step 3. 

Here's what I ran for step 3 specifically:

ParaToSPHARMMeshCLP --regTemplate [template_directory]/average_SPHARM_template.vtk --regTemplateFileOn --flipTemplate [template_directory]/[randomsubj]_Lhipp_surfSPHARM.coef flipTemplateOn --medialMesh --paraOut --phiIteration 100 --thetaIteration 100 --spharmDegree 12 --subdivLevel 20 [subjid]_Lhipp_para.vtk [subjid]_Lhipp_surf.vtk [subjid]_Lhipp_surf_round2

The specific error message I'm getting is:

PARSE ERROR: Argument: [subjid]_Lhipp_surf_round2
Couldn't find match for argument

(note that where I typed [subjid] in this post, I insert actual subject id number)
Also, in the above command, [subjid]_Lhipp_para.vtk and [subjid]_Lhipp_surf.vtk = output vtk files from step 1; [template_directory]/average_SPHARM_template.vtk = the average study template I made with MeshMath; [randomsubj]_Lhipp_surfSPHARM.coef is a coefficient file that I pulled from a subject at random following step #1.

Any feedback on where I'm going wrong is greatly appreciated!
Lara