Thanks Andreia, this does appear to have worked. Please forgive my ignorance but I do just want to double check two things;
1) The first commands you have given provide the stats for the two hemispheres of the cerebral cortex only based on the pial surface, whereas the second set of commands provide the pial boundary stats for the whole brain rather than just cortex?
2) The surface area value that I am looking for (grey matter surface area at the grey/pial boundary) is listed in the new stats table next to: *# Measure Cortex, WhiteSurfArea, White Surface Total Area,* ?
Thanks again, Will
On Tue, Sep 9, 2014 at 5:36 PM, will brown willbrown1987@gmail.com wrote:
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