In my research project, I have analyzed 100 MRI-scans using freesurfer for both baseline and longitudinal comparison between groups.

It is very good to measure differences in area, volume and cortical thickness.

But it would be very interesting to do some shape-analysis; if this can be done in an automatic or semi-automatic way.


Setup:
* Freesurfer 5.3.0 is running on a Centos6-based workstation.
* I have installed two versions of 3D-slicer: 3.6.3 and 4.2.x.
* The Spharm-PDM toolbox have succesfully into 3d-slicer 3.6.3, and I can see the shape-analysis module.

At first I would like to analyze hippocampal shape between groups; and I have been reading some of the tutorials.

But it seems, that i need hippocampus-data in *.gz-format to implement these into the *.csv-file? Is this correct?

In 3D-slicer I can produce 3D-models of the different subcortical structures based on the freesurfer "aseg.mgz"; but these models can only be saved in either *.vtk or -stl format?


Can I use SPARHM-PDM toolbox to perform the shape analysis on the freesurfer-based 3D-models in 3D-slicer?