It is a little tricky because you don't want to use different masks for different subjects. I recommend using CVS where I've created a subcoritcal mask in 2mm space (mri.2mm). So the idea would be that you map your subcortical MG map to CVS space, then smooth it (mri_fwhm) specifying the subcortical mask in $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm. You can then concatenate the different subjects together to do your group analysis

Dear Dr Greve,

Thank you so much for the quick response. 

Just to confirm that I understood the procedure correctly. The analysis is volume based (i.e. voxel-wise) for the subcortical structures using mask created by freesurfer's "mri_binarize" for these regions.

Correct?

-------- Original Message --------

On January 18, 2018 4:34 PM, John Anderson <John.anderso@protonmail.com> wrote:

It is volume-based for subcortical

 

On 1/12/18 8:17 AM, John Anderson wrote:

Dear Dr Greeve,

I interestingly read the manuscript "Different partial volume correction methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank you for publishing this data.

I understood from this paper that he recommended stream for PVC is to correct the PET images using Muller-Gartner method then feed the corrected maps into three group level analyses: surface based for left and right hemispheres then for subcortical regions..

My question is about the subcortical analysis: To describe this analysis, is it a volumetric analysis for subcortical gray matter, or surface based?

I am sorry if my questions is basics, I don't have good experience in freesurfer so I want to be sure that I am using the correct terms.

Thanks you for any advice!

John

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