Christian, Updated mri_segstats and mris_wm_volume executables for centos 32/64bit can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable Nick On Wed, 2008-08-20 at 10:57 +0200, [EMAIL PROTECTED] wrote: > Dear freesurfers, > > I get an error message while running recon-all on two on my subjects (on > both version 4.02 and 4.05 on a CentOS linux station). It seems to be the > same error that is described earlier this summer by Sky Raptentsetsang. > > The error message is: > MrisComputeWhiteVolume: src (14, 721, 277) maps to src (14, 721, 277) - OBB > > Recon-all does finish, but it takes a lot longer than usual. The error > message is repeated thousands of times and the error log is massive as Sky > also describes below. > > Is there some way to fix these errors? > > best regards, > Christian Tamnes > > > > > > 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? > > > > #-------------------------------------------- > [EMAIL PROTECTED] 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. > #-------------------------------------------- > [EMAIL PROTECTED] 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
