did it include the update to mri_tessellate? On 11/13/18 6:33 PM, Baxter P. Rogers wrote: > 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
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