Dear list,
I'm trying to extract vertex-level measures of thickness, area, etc, for all of my subjects. I ran recon-all -all on all subjects as normal, then ran:
recon-all -s {subject} -qcache
where {subject} is the subject ID. This was followed by `mris_convert` to make the values human-readable:
mris_convert -c {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.mgh {fsavg_dir}/surf/lh.sphere {subj_dir}/surf/{hem}.{meas}.fwhm25.fsaverage.asc
I did this for each subject, hemisphere, and measure (thickness, area, sulc). Many of the vertices in the left hemisphere always produce values of 0, for every subject, and for every measure. The first offending vertex is #9. So if I head a randomly chosen file, I get:
[sm2286@grace0 surf]$ head lh.area.fwhm25.fsaverage.asc 000 0.00000 0.00000 100.00000 0.43150 001 27.64000 -85.07000 44.72000 0.39083 002 89.44000 0.00000 44.72000 0.33804 003 27.64000 85.07000 44.72000 0.81910 004 -72.36000 52.57000 44.72000 0.41731 005 -72.36000 -52.57000 44.72000 0.37795 006 -27.64000 -85.07000 -44.72000 0.77490 007 72.36000 -52.57000 -44.72000 0.49643 008 72.36000 52.57000 -44.72000 0.00000 <--- this value
This is a different subject:
[sm2286@grace0 surf]$ head lh.sulc.fwhm25.fsaverage.asc 000 0.00000 0.00000 100.00000 0.00692 001 27.64000 -85.07000 44.72000 -0.45451 002 89.44000 0.00000 44.72000 0.38711 003 27.64000 85.07000 44.72000 0.17178 004 -72.36000 52.57000 44.72000 -0.54163 005 -72.36000 -52.57000 44.72000 -0.01465 006 -27.64000 -85.07000 -44.72000 -0.07269 007 72.36000 -52.57000 -44.72000 0.46408 008 72.36000 52.57000 -44.72000 0.00000 <--- this value
Bizarrely this also happens when I switch the target of qcache to fsaverage5. The right hemisphere is never affected. Does anyone have any clue what's going one here?
-- Samuel R. Mathias, Ph.D. Associate Research Scientist (ARS) Neurocognition, Neurocomputation and Neurogenetics (n3) Division Yale University School of Medicine 40 Temple Street, Room 694 New Haven CT 06511 http://www.srmathias.com