Hi Ajay-

I believe that Rick and I were under the impression that you were doing functional MRI with SUMA. Based on your goals of doing anatomical analysis with both 1) cortical thickness and 2) subcortical structures, I would recommend sticking to a more Freesurfer based pipeline. That way there's considerably more documentation. If you're still interested in mapping fMRI data, I can talk more about this, but I think for what you want, the following is more relevant:

A while back, I wrote up a tutorial for doing cortical thickness analysis in SUMA tools and how it matches the Freesurfer results here. In this example I'm using the Freesurfer smoothed files (generated with adding -qcache to the end of a recon-all command or using mris_preproc) instead of using the SUMA tool SurfSmooth. For subcortical analysis in Freesurfer, it is standard practice to use the statistics files that Freesurfer generates (and you can get at using asegstats2table). You'll probably want to read more on the Freesurfer list for best practices on both of these analyses (like covarying out ICV).

I would be very hesitant at submitting all of your normalized subjects into Freesurfer for doing morphometry analysis. If you want to do VBM analyses with nonlinear warps on subcortical, then you could look into one of the following: FSL VBM, FSL_anat, or SPM (with VBM toolbox) solutions. Of course once you have the data preprocessed and setup using any of these pipelines, you can do the Group analysis using AFNI tools (e.g. 3dttest++) because the results are just NIFTI files.

-Peter



Edited 5 time(s). Last edit at 12/02/2015 05:12PM by Peter Molfese.