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

Sky