Re: Re: Re: Re: Re: Question on segmentation
it looks fine. Does the filled volume have your editing changes in it? On Fri, 1 Nov 2002, Xiangchuan Chen wrote: It is as follows. Thanks, Xiangchuan ## csurf0.9: log ending: Fri Nov 1 00:07:13 EST 2002 ## # Command Log # /home/chxc/softwares/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat /home/chxc/freesurfer-data/subjects/sheng_new/mri/wm /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat... updating initial cc seed to (127, 136, 128) corpus callosum seed point found at (127, 137, 132), TAL: (1.0, 4.0, -9.0) corpus callosum: cutting at slice 7, area 1671, (127, 137, 132) putative pons found at (110, 174) -- (127, 174, 111) pons seed point found at (125, 174, 114), TAL: (3.0, -14.0, -46.0) pons: cutting at slice 8, area 496, (125, 173, 114) rh seed point at (109, 137, 132): 5 neighbors on. searching for lh wm seed...found at (146, 138, 132) lh seed point at (146, 138, 132): 5 neighbors on. filling left hemisphere... total of 485249 voxels filled... total of 16224555 voxels filled... total of 0 holes filled total of 486104 voxels filled... total of 0 holes filled filling right hemisphere... total of 485249 voxels filled... total of 16224555 voxels filled... total of 0 holes filled total of 486104 voxels filled... total of 0 holes filled filling degenerate left hemisphere surface locations... 1075 voxels filled 16 voxels filled 1 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 1075 voxels filled 16 voxels filled 1 voxels filled 0 voxels filled combining hemispheres... using variable coefficient diffusion to correct hemispheric overlap... 26: 486732 ambiguous voxels remaining 9: 40255 ambiguous voxels remaining 8: 15694 ambiguous voxels remaining 7: 5290 ambiguous voxels remaining 6: 1624 ambiguous voxels remaining 5: 607 ambiguous voxels remaining 4: 229 ambiguous voxels remaining 3: 76 ambiguous voxels remaining 2: 18 ambiguous voxels remaining 1: 0 ambiguous voxels remaining writing output to /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled... filling took 5.8 minutes Command Finished Start Of Original Message Date: 2002-11-01Time: 17:04:00 From: Bruce Fischl ([EMAIL PROTECTED]) To: freesurfer ([EMAIL PROTECTED]) Subject: Re: Re: Re: Re: Question on segmentation can you send it with the neighbor threshold at it's default value (1). thanks, Bruce On Fri, 1 Nov 2002, Xiangchuan Chen wrote: Hi Bruce, The content of the log file is listed below. Thanks for your help. Xiangchuan ## csurf0.9: log ending: Wed Oct 30 16:59:25 EST 2002 ## # Command Log # /softwares/freesurfer/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 8 -L /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat /home/chxc/freesurfer-data/subjects/sheng_new/mri/wm /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat... reading input volume...done. searching for cutting planes...done. filling left hemisphere... filling volume: pass 1 of 3...total of 483589 voxels filled... filling volume: pass 2 of 3...total of 16226171 voxels filled... filling volume: pass 3 of 3...total of 240285 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 483589 voxels filled... filling volume: pass 2 of 3...total of 16226171 voxels filled... filling volume: pass 3 of 3...total of 238617 voxels filled...done. filling degenerate left hemisphere surface locations... 275 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 315 voxels filled 0 voxels filled combining hemispheres... writing output to /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled... filling took 3.8 minutes Command Finished /softwares/freesurfer/freesurfer_alpha/bin/Linux/mri_tessellate /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled 80 /home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.orig slice 50: 2661 vertices, 2850 faces
Re: Re: Re: Re: Re: Question on segmentation
It is as follows. Thanks, Xiangchuan ## csurf0.9: log ending: Fri Nov 1 00:07:13 EST 2002 ## # Command Log # /home/chxc/softwares/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 1 -L /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat /home/chxc/freesurfer-data/subjects/sheng_new/mri/wm /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat... updating initial cc seed to (127, 136, 128) corpus callosum seed point found at (127, 137, 132), TAL: (1.0, 4.0, -9.0) corpus callosum: cutting at slice 7, area 1671, (127, 137, 132) putative pons found at (110, 174) -- (127, 174, 111) pons seed point found at (125, 174, 114), TAL: (3.0, -14.0, -46.0) pons: cutting at slice 8, area 496, (125, 173, 114) rh seed point at (109, 137, 132): 5 neighbors on. searching for lh wm seed...found at (146, 138, 132) lh seed point at (146, 138, 132): 5 neighbors on. filling left hemisphere... total of 485249 voxels filled... total of 16224555 voxels filled... total of 0 holes filled total of 486104 voxels filled... total of 0 holes filled filling right hemisphere... total of 485249 voxels filled... total of 16224555 voxels filled... total of 0 holes filled total of 486104 voxels filled... total of 0 holes filled filling degenerate left hemisphere surface locations... 1075 voxels filled 16 voxels filled 1 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 1075 voxels filled 16 voxels filled 1 voxels filled 0 voxels filled combining hemispheres... using variable coefficient diffusion to correct hemispheric overlap... 26: 486732 ambiguous voxels remaining 9: 40255 ambiguous voxels remaining 8: 15694 ambiguous voxels remaining 7: 5290 ambiguous voxels remaining 6: 1624 ambiguous voxels remaining 5: 607 ambiguous voxels remaining 4: 229 ambiguous voxels remaining 3: 76 ambiguous voxels remaining 2: 18 ambiguous voxels remaining 1: 0 ambiguous voxels remaining writing output to /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled... filling took 5.8 minutes Command Finished Start Of Original Message Date: 2002-11-01Time: 17:04:00 From: Bruce Fischl ([EMAIL PROTECTED]) To: freesurfer ([EMAIL PROTECTED]) Subject: Re: Re: Re: Re: Question on segmentation can you send it with the neighbor threshold at it's default value (1). thanks, Bruce On Fri, 1 Nov 2002, Xiangchuan Chen wrote: Hi Bruce, The content of the log file is listed below. Thanks for your help. Xiangchuan ## csurf0.9: log ending: Wed Oct 30 16:59:25 EST 2002 ## # Command Log # /softwares/freesurfer/freesurfer_alpha/bin/Linux/mri_fill -lval 255 -rval 80 -ccmask -T 8 -L /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat /home/chxc/freesurfer-data/subjects/sheng_new/mri/wm /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled using 255 as fill val for left hemisphere. using 80 as fill val for right hemisphere. not using corpus callosum to mask possible location of pons. logging cutting plane coordinates to /home/chxc/freesurfer-data/subjects/sheng_new/mri/tmp/ponscall.dat... reading input volume...done. searching for cutting planes...done. filling left hemisphere... filling volume: pass 1 of 3...total of 483589 voxels filled... filling volume: pass 2 of 3...total of 16226171 voxels filled... filling volume: pass 3 of 3...total of 240285 voxels filled...done. filling right hemisphere... filling volume: pass 1 of 3...total of 483589 voxels filled... filling volume: pass 2 of 3...total of 16226171 voxels filled... filling volume: pass 3 of 3...total of 238617 voxels filled...done. filling degenerate left hemisphere surface locations... 275 voxels filled 0 voxels filled filling degenerate right hemisphere surface locations... 315 voxels filled 0 voxels filled combining hemispheres... writing output to /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled... filling took 3.8 minutes Command Finished /softwares/freesurfer/freesurfer_alpha/bin/Linux/mri_tessellate /home/chxc/freesurfer-data/subjects/sheng_new/mri/filled 80 /home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.orig slice 50: 2661 vertices, 2850 faces slice 60: 9074 vertices, 9312 faces slice 70: 17008 vertices, 17337 faces slice 80: 26619 vertices, 26946 faces slice 90: 36923 vertices, 37283 faces slice 100: 47136 vertices, 47487 faces slice 110: 60042 vertices, 60440 faces slice 120
Re: Re: Re: Re: Re: Re: Question on segmentation
If the neighbor threshold is 1, it has; if the threshold is 8, it misses some added voxels. Xiangchuan Start Of Original Message Date: 2002-11-01Time: 17:36:00 From: Bruce Fischl ([EMAIL PROTECTED]) To: freesurfer ([EMAIL PROTECTED]) Subject: Re: Re: Re: Re: Re: Question on segmentation it looks fine. Does the filled volume have your editing changes in it? = End Of Original Message =
