Hi Baxter we are seeing this locally as well. Probably a bug introduced into the last day or two. We will post a fix soon
cheers Bruce On Mon, 12 Nov 2018, Baxter P. Rogers wrote: > External Email - Use Caution > > Hi all - I'm having a problem with recon-all in the current dev version > of Freesurfer. It is failing somewhere in the surface creation steps. I > get an error during mris_extract_main_component: > > ERROR: MRISalloc: nvertices=-1879047998 < 0 > No such file or directory > > The filled left and right white matter images look reasonable but I > can't load the lh.orig.nofix surface in Freeview. > > More info below. Thanks much for any help, > Baxter > > > > ----------------------------------------------------------------------------- > FREESURFER VERSION: > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-linux-centos7_x86_64-dev.tar.gz > Downloaded 2018-11-12 > SHA256 792a0e90ec6b4cfd3a530c3e5b4c9aead575dbb45217756e66931bb5d118e89d > > > ----------------------------------------------------------------------------- > SYSTEM INFORMATION: > > CentOS 7.5.1804 > Running in Docker on OS X El Capitan with 1 CPU, 6.5 GB RAM > > # df -h > Filesystem Size Used Avail Use% Mounted on > overlay 74G 30G 40G 43% / > tmpfs 64M 0 64M 0% /dev > tmpfs 3.2G 0 3.2G 0% /sys/fs/cgroup > osxfs 465G 438G 27G 95% /wkdir > /dev/sda1 74G 30G 40G 43% /etc/hosts > shm 3.0G 0 3.0G 0% /dev/shm > > # cat /proc/meminfo > MemTotal: 6616764 kB > MemFree: 4934288 kB > MemAvailable: 6134084 kB > ... > > > ----------------------------------------------------------------------------- > ATTEMPT TO VIEW SURFACE IN FREEVIEW: > > Failed to load Surface .../surf/lh.orig.nofix > > # ls -l lh.orig.nofix > -rw-rw-r-- 1 root root 4320024 Nov 11 23:02 lh.orig.nofix > > > ----------------------------------------------------------------------------- > LATER PORTIONS OF recon-all.log > > > > mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz > > Iteration Number : 1 > pass 1 (xy+): 49 found - 49 modified | TOTAL: 49 > ... > pass 1 (-+): 0 found - 0 modified | TOTAL: 0 > > Total Number of Modified Voxels = 1264 (out of 703656: 0.179633) > binarizing input wm segmentation... > Ambiguous edge configurations... > > mri_pretess done > > > > > mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta > -segmentation aseg.presurf.mgz wm.mgz filled.mgz > > logging cutting plane coordinates to ../scripts/ponscc.cut.log... > ... > 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 ... > > > > mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz > ../mri/filled-pretess255.mgz > > Iteration Number : 1 > pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 > ... > pass 1 (-+): 0 found - 0 modified | TOTAL: 0 > > Total Number of Modified Voxels = 15 (out of 347364: 0.004318) > Ambiguous edge configurations... > > mri_pretess done > > > > > mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix > > $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ > $Id$ > slice 30: 1553 vertices, 1720 faces > ... > slice 250: 179904 vertices, 180024 faces > using the conformed surface RAS to save vertex points... > writing ../surf/lh.orig.nofix > using vox2ras matrix: > -1.00000 0.00000 0.00000 128.00000; > 0.00000 0.00000 1.00000 -128.00000; > 0.00000 -1.00000 0.00000 128.00000; > 0.00000 0.00000 0.00000 1.00000; > > rm -f ../mri/filled-pretess255.mgz > > mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix > > ERROR: MRISalloc: nvertices=-1879047998 < 0 > > No such file or directory > > > > _______________________________________________ > 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
