External Email - Use Caution I am still getting the same error with today's build of freesurfer-linux-centos7_x86_64-dev.tar.gz SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c
Thanks, Baxter Greve, Douglas N.,Ph.D. wrote: > I just fixed it > > On 11/12/2018 09:35 PM, Bruce Fischl wrote: >> 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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Ffreesurfer-linux-centos7_x86_64-dev.tar.gz&data=02%7C01%7Cbaxter.rogers%40vanderbilt.edu%7Cb8badf76061748e9ae8d08d6497fa6e2%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C636777209944764060&sdata=iSBzhEBA1CVRe5r1LhhR%2FI2fYcdyyY5nU%2F9t9uYUjto%3D&reserved=0 >>> 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
