Hi Sky,

this means that the aseg voxel that corresponds to the interior of the ?h.white surface has been computed to be outside the aseg volume, which definitely means something is wrong. Can you tar up one subject like this (without the 6G of error messages!) and we'll take a look?

thanks,
Bruce


On Fri, 27 Jun 2008, Sky Raptentsetsang wrote:

This is a very strange and amusing issue that is occurring with a
population of subjects that I ran previously on version 3.0.5 and am now
rerunning on version 4.0.4. The subjects are finishing recon-all with no
errors after substantially longer than usual, because the mri_segstats
script appears to be looking for WM volumes that are not there, and the
error is printed out over a 106 million times but still manages to finish
recon-all....amazing. Below I have pasted the lines before the repeating
errors. In blue is the repeating portion. In short these files seem to be
anywhere from 3GB to 6GB and is managing to filling up our memory
resources. :)
Is there a flag that I can invoke that will skip this seemingly needless
error loop?

#--------------------------------------------
#@# Inflation2 rh Wed Jun 25 22:25:25 PDT 2008
/cind/00/FCDv4/Freesurfer/subjects/FCD009-1/scripts
 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
avg radius = 43.6 mm, total surface area = 69264 mm^2
writing inflated surface to ../surf/rh.inflated
writing sulcal depths to ../surf/rh.sulc
step 030: RMS=0.029 (target=0.015) 
step 060: RMS=0.016 (target=0.015) 
inflation complete.
inflation took 1.5 minutes
 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10
../surf/rh.inflated
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
276 vertices thresholded to be in k1 ~ [-0.22 0.26], k2 ~ [-0.11 0.05]
total integrated curvature = 0.565*4pi (7.101) --> 0 handles
ICI = 1.4, FI = 7.8, variation=135.859
144 vertices thresholded to be in [-0.01 0.02]
writing Gaussian curvature to ../surf/rh.inflated.K...thresholding
curvature at 99.90% le
vel
curvature mean = 0.000, std = 0.001
122 vertices thresholded to be in [-0.13 0.12]
done.
writing mean curvature to ../surf/rh.inflated.H...curvature mean =
-0.018, std = 0.022
done.
#--------------------------------------------
#@# ASeg Stats Wed Jun 25 22:29:01 PDT 2008
/cind/00/FCDv4/Freesurfer/subjects/FCD009-1
 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
--excludeid 0 -
-brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz
--in-intensity-name n
orm --in-intensity-units MR --etiv --subject FCD009-1 --surf-wm-vol
--ctab /opt/freesurfe
r4.0.4/ASegStatsLUT.txt
MRIScomputeWhiteVolume: src (0, 279, 274) maps to (104, -12, 235) - OOB
atlas_icv = 1.19127e+06
Loading mri/aseg.mgz
Getting Cerebral WM volumes from surface
No such file or directory
MRIScomputeWhiteVolume: src (0, 279, 275) maps to (104, -12, 235) - OOB
No such file or directory
MRIScomputeWhiteVolume: src (0, 280, 273) maps to (104, -13, 236) - OOB
No such file or directory
MRIScomputeWhiteVolume: src (0, 280, 274) maps to (104, -12, 236) - OOB
No such file or directory
.
.
.
.
.

Hopefully you can save us a HUGE amount of disk space and maybe get a
laugh out of it as we did.
Sky

Sky Raptentsetsang

Staff Research Associate
CIND, San Francisco VAMC
Department of Radiology, UCSF
4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M
San Francisco, CA 94121
Phone 415.221.4810 ext. 4186
Fax 415.386.3954