Yup this is a known issue with the mri_segstats binary. Please go to the following page and download the mri_segstats file that corresponds to your version of freesurfer (see contents of $FREESURFER_HOME/build-stampt.txt file to determine your version). Replace the version of mri_segstats in your $FREESURFER_HOME/bin directory with the one you download from the following link. Also, it would be good to backup the version you currently have.
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ -Zeke On 05/01/2015 05:02 PM, Krieger, Donald N. wrote: > I have completed runs of recon-all -autorecon1 and recon-all > –autorecon2-volonly per your suggested sequence: > > recon-all -s subj -autorecon1 > > recon-all -s subj -autorecon2-volonly > > recon-all -s subj -autorecon2-perhemi -hemi rh -log recon-all-hemi > rh.log -notify rh-done.log -openmp 4 & > > recon-all -s subj -autorecon2-perhemi -hemi lh -log > recon-all-hemi-lh.log -notify lh-done.log -openmp 4 & > > while (rh-done.log AND lh-done.log do not both exist) > > do > > sleep 1 > > end loop > > recon-all -s -autorecon3 > > recon-all –s subj –autorecon2-volonly is completing but with an error. > > I’ve included below my signature the last 50 lines or so of > recon-all.log (file attached). > > It looks like it’s completing execution of mri_fill successfully and > then going on to execute mri_segstats out of order. > > In the log for a standard run on this same image set, i.e. recon-all > –all, that mri_segstats cmd doesn’t appear to occur till 3000 lines > later in the log file. And as the log file shows, no ribbon.mgz can be > found and inspection of the directories shows that surf is empty. > > It looks like something is missing between recon-all –autorecon2-volonly > and recon-all –autorecon2-perhemi > > What do you think? > > Thanks, > > Don > > Don Krieger, Ph.D. > > Department of Neurological Surgery > > Universityof Pittsburgh > > mri_pretess done > > #-------------------------------------------- > > #@# Fill Fri May 1 12:28:01 PDT 2015 > > /home/donkri/Contrib/freesurfer/subjects/173_9sh_lr/mri > > mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta > -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz > > logging cutting plane coordinates to ../scripts/ponscc.cut.log... > > INFO: Using transforms/talairach.lta and its offset for Talairach volume ... > > using segmentation aseg.auto_noCCseg.mgz... > > reading input volume...done. > > searching for cutting planes...voxel to talairach voxel transform > > 0.964 -0.026 -0.002 8.591; > > 0.022 1.002 0.185 -15.064; > > -0.012 -0.183 0.940 20.634; > > 0.000 0.000 0.000 1.000; > > voxel to talairach voxel transform > > 0.964 -0.026 -0.002 8.591; > > 0.022 1.002 0.185 -15.064; > > -0.012 -0.183 0.940 20.634; > > 0.000 0.000 0.000 1.000; > > reading segmented volume aseg.auto_noCCseg.mgz... > > Looking for area (min, max) = (350, 1400) > > area[0] = 2029 (min = 350, max = 1400), aspect = 0.86 (min = 0.10, max = > 0.75) > > need search nearby > > using seed (128, 110, 91), TAL = (0.0, -37.0, 18.0) > > talairach voxel to voxel transform > > 1.037 0.026 -0.003 -8.449; > > -0.025 0.963 -0.190 18.642; > > 0.009 0.188 1.027 -18.439; > > 0.000 0.000 0.000 1.000; > > segmentation indicates cc at (128, 110, 91) --> (0.0, -37.0, 18.0) > > done. > > writing output to filled.mgz... > > filling took 0.5 minutes > > talairach cc position changed to (0.00, -37.00, 18.00) > > Erasing brainstem...done. > > seed_search_size = 9, min_neighbors = 5 > > search rh wm seed point around talairach space:(18.00, -37.00, 18.00) > SRC: (108.24, 104.54, 96.63) > > search lh wm seed point around talairach space (-18.00, -37.00, 18.00), > SRC: (145.58, 103.65, 96.94) > > compute mri_fill using aseg > > Erasing Brain Stem and Cerebellum ... > > Define left and right masks using aseg: > > Building Voronoi diagram ... > > Using the Voronoi diagram to separate WM into two hemispheres ... > > Find the largest connected component for each hemisphere ... > > #-------------------------------------------- > > #@# ASeg Stats Fri May 1 12:28:33 PDT 2015 > > INFO: mri_segstats will not calculate Supratentorial > > due to missing ribbon.mgz file > > INFO: ?h.white surfaces not available to mri_segstats. > > /home/donkri/Contrib/freesurfer/subjects/173_9sh_lr > > 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 --subcortgray --in mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --etiv --ctab /ho > > me/donkri/Contrib/freesurfer/ASegStatsLUT.txt --subject 173_9sh_lr > > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > > cwd > > cmdline 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 --subcortgray --in mri/norm.mgz > --in-intensity-name norm --in-intensity-units MR --etiv --c > > tab /home/donkri/Contrib/freesurfer/ASegStatsLUT.txt --subject 173_9sh_lr > > sysname Linux > > hostname comet-08-01.sdsc.edu > > machine x86_64 > > user donkri > > UseRobust 0 > > atlas_icv (eTIV) = 1971942 mm^3 (det: 0.987912 ) > > MRISread(/home/donkri/Contrib/freesurfer/subjects/173_9sh_lr/surf/lh.white): > could not open file > > Loading mri/aseg.mgz > > Getting Brain Volume Statistics > > No such file or directory > > Linux comet-08-01.sdsc.edu 3.10.73-1.el6.elrepo.x86_64 #1 SMP Thu Mar 26 > 16:28:30 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 173_9sh_lr exited with ERRORS at Fri May 1 12:28:33 PDT 2015 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. 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