Dear FS,

I just started reanalyzing my data using FS5.3 (based on your feedback) after experiencing problems in the 5.0 version.

Here however, I'm having a new problem: the pial surface of a number of subjects is missing only for the right hemisphere, while the white matter surface looks perfect. Similar to http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29628.html

See the pictures below.

https://www.dropbox.com/s/fr4ve5mb0ioy1o2/no_pial_coronal.tiff

https://www.dropbox.com/s/s36o8y0hkfw0gix/no_pial_surface.tiff

I checked the brainmasks, and these were all ok. To be sure I reran the recon-all process for these subjects, but unfortunately this didn't solve my problems.

However, I do get an error after autorecon2, yet the commandline responsible for the error is part of autorecon3:

#@# ASeg Stats Mon Sep 9 17:31:53 CEST 2013

/home/cedric/data/Anatomy_BD/freesurfer/FS5.3/CREA/CREA_915_12_1

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --

in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject CREA_915_12_1

ERROR: Option --euler unknown

-----------

Full log for 2 subjects, though similar errors:

https://www.dropbox.com/s/jzbp2vpzfb12wsu/recon-all.o128590

https://www.dropbox.com/s/so5jfd7wuo19ax6/recon-all.o128591

Do you have any idea what might be causing this? And of course, how to fix this?

Many thanks!

Cheers,

Cédric

------------------------------------------------------------

P.C.M.P. Koolschijn (Cédric), PhD

Dutch Autism & ADHD Research Center

Brain and Cognition

Weesperplein 4; Room 3.07

1018 XA Amsterdam

The Netherlands

E P.C.M.P.Koolschijn@uva.nl

T +31-20-525-2427

W http://www.dutcharc.nl