Hi Beatriz,

Thanks for the reply. So, I just re-ran the analysis with fewer subjects to make troubleshooting easier (3 patients and 3 controls). This time the slicer GUI says the status is completed but the MRML files still did not create.

1)I've checked and all the output data has been created for all the input files and I can view them in Slicer using "File -> add data .." I opened the files created in Mesh/SPHARM/
2) I also typed MeshMath --help and I get the help message prompt so seems to be working.

Any other suggestions greatly appreciated!!

Thanks,
Cathy