krista kelly wrote:

I'm looking at both cortical thickness and surface area differences between two groups. I've been using mris_anatomical_stats to retrieve values but had a few questions:

1. Do I need to do separate mris_anatomical_stats using different

thickness files (bolded below) to get cortical thickness and surface area measures. For example:

cortical thickness - mris_anatomical_stats -l lh.v1.label -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh surface area - mris_anatomical_stats -l lh.v1.label -t *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh

Or, since the output files include all of these measures, is it fine to just run one of the two?

Just run the first one.

2. The output files for both analyses run above (with different

thickness files) have identical values for everything except for tray matter volume. Using lh.thickness file - grayvol = 8082; using lh.area file - grayvol = 4029. Can anyone clarify why this happens?

It computes the gray matter volume by thickness*area. If you pass it "area" as the "thickness", then you are probably getting area*area. Though I'm surprised that the "thickness" values are correct.

3. The default surface area values are for the white matter surface.

How do I run mri_anatomical_stats to get the pial surface? I've tried mris_anatomical_stats -l lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats BV01 lh but I get identical values for everything (except grayvol).

Try adding "pial" to the end of the command line (and use lh.thickness) doug

Thanks! Krista

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