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-... 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
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 CautionHi 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-... 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
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 CautionHi 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-... 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
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 CautionHi 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.... 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
did it include the update to mri_tessellate?
On 11/13/18 6:33 PM, Baxter P. Rogers wrote:
External Email - Use CautionI 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 CautionHi 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.... 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.mgzIteration 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.nofixERROR: 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
External Email - Use Caution
Ah - looking deeper, I think not. I'm not building it locally - I downloaded today's available compiled version (commit 8abd50c judging by the build stamp) and it looks like the relevant fix was later, in commit 2720b25. Is there a way to tell what commit is available at the dev download URL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ ?
Anyway, I will try again in a day or two assuming the dev binaries update, and let you know how it goes.
Thanks much, Baxter
Greve, Douglas N.,Ph.D. wrote:
did it include the update to mri_tessellate?
On 11/13/18 6:33 PM, Baxter P. Rogers wrote:
External Email - Use CautionI 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 CautionHi 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.... 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.mgzIteration 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.nofixERROR: MRISalloc: nvertices=-1879047998< 0
No such file or directory
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mg...
freesurfer@nmr.mgh.harvard.edu
-
Baxter P. Rogers -
Bruce Fischl -
Greve, Douglas N.,Ph.D.