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 <willbrown1...@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, <_andre...@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 <willbrown1...@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 >> >> >> >> >> >> >> > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
