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:
- 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.
- 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.
- 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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