Thanks very much Andreia, yes this does look like what I want. I haven't had a chance to test it yet but it does indeed appear to answer my question. Thanks to those that have offered answers, to clarify, I did indeed mean the surface area of the pial surface rather than the white/grey boundary.

Will

On Wed, Sep 3, 2014 at 1:12 AM, <_andreia_@sapo.pt> wrote:

Hi Will,

I use the following commands to get surface area from the pial surface:


In the subject label dir:

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab SUBJ lh pial

mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab SUBJ rh pial
 

Then run aparcstats2table using aparc.pial instead of aparc (only because I called this new parcellation aparc.pial)



To get the total surface area of each hemisphere I use:

In the subject stats dir:

mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total_pial.stats -b SUBJ lh pial

mris_anatomical_stats -l ../label/rh.cortex.label -f rh.total_pial.stats -b SUBJ rh pial

Then run aparcstats2table using total_pial instead of aparc (again, only because I called this new parcellation total_pial. You may call it whatever you'd like)

Just remeber to leave the specified dirs when creating the tables. If you dont't I think they will be created in the current dir.

I use FS 5.0.

Is this what you want?


Best,
Andreia

Citando will brown <willbrown1987@gmail.com>:

Hi all,

 

I messed up this question recently so just want to clarify and try again. We want to know the cortical gray matter surface area of our subjects but are unclear about how to get this info.

 

?.aparc.stats reports:

 

Measure Cortex, WhiteSurfArea, White Surface Total Area, XXXX, mm^2

 

How about the gray matter?

 

Thanks,

Will