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
_______________________________________________
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.
