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: 2002-11-01 Time: 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: 72312 vertices, 72739 faces > >> slice 130: 82849 vertices, 83231 faces > >> slice 140: 93501 vertices, 93872 faces > >> slice 150: 102733 vertices, 103030 faces > >> slice 160: 110701 vertices, 110956 faces > >> slice 170: 117496 vertices, 117707 faces > >> slice 180: 123160 vertices, 123326 faces > >> slice 190: 127019 vertices, 127145 faces > >> slice 200: 128240 vertices, 128242 faces > >> slice 210: 128240 vertices, 128242 faces > >> slice 220: 128240 vertices, 128242 faces > >> slice 230: 128240 vertices, 128242 faces > >> slice 240: 128240 vertices, 128242 faces > >> slice 250: 128240 vertices, 128242 faces > >> > >> Command Finished > >> /softwares/freesurfer/freesurfer_alpha/bin/Linux/mri_tessellate >/home/chxc/freesurfer-data/subjects/sheng_new/mri/filled 255 >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.orig > >> slice 40: 248 vertices, 295 faces > >> slice 50: 3879 vertices, 4046 faces > >> slice 60: 10443 vertices, 10680 faces > >> slice 70: 18507 vertices, 18838 faces > >> slice 80: 28264 vertices, 28592 faces > >> slice 90: 37793 vertices, 38136 faces > >> slice 100: 48335 vertices, 48706 faces > >> slice 110: 60833 vertices, 61269 faces > >> slice 120: 73737 vertices, 74149 faces > >> slice 130: 84812 vertices, 85205 faces > >> slice 140: 95460 vertices, 95812 faces > >> slice 150: 104054 vertices, 104330 faces > >> slice 160: 112226 vertices, 112503 faces > >> slice 170: 118749 vertices, 118937 faces > >> slice 180: 123555 vertices, 123692 faces > >> slice 190: 126742 vertices, 126817 faces > >> slice 200: 127470 vertices, 127470 faces > >> slice 210: 127470 vertices, 127470 faces > >> slice 220: 127470 vertices, 127470 faces > >> slice 230: 127470 vertices, 127470 faces > >> slice 240: 127470 vertices, 127470 faces > >> slice 250: 127470 vertices, 127470 faces > >> > >> Command Finished > >> /softwares/freesurfer/freesurfer_alpha/bin/Linux/mris_smooth -n 10 >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.orig >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.smoothwm > >> smoothing for 10 iterations > >> smoothing surface tessellation for 10 iterations... > >> smoothing complete - recomputing first and second fundamental forms... > >> writing smoothed curvature to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.curv > >> writing smoothed area to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.area > >> > >> Command Finished > >> /softwares/freesurfer/freesurfer_alpha/bin/Linux/mris_smooth -n 10 >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.orig >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.smoothwm > >> smoothing for 10 iterations > >> smoothing surface tessellation for 10 iterations... > >> smoothing complete - recomputing first and second fundamental forms... > >> writing smoothed curvature to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.curv > >> writing smoothed area to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.area > >> > >> Command Finished > >> /softwares/freesurfer/freesurfer_alpha/bin/Linux/mris_inflate -n 10 -dist 0.1 >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.smoothwm >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.inflated > >> niterations = 10 > >> l_dist = 0.100 > >> avg radius = 44.6 mm, total surface area = 70437 mm^2 > >> tol=1.0e-04, host=DELL-, nav=16, nbrs=2, l_spring_norm=1.000, l_dist=0.100 > >> mom=0.90, dt=0.90 > >> desired rms height=0.015 > >> writing inflated surface to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.inflated > >> writing sulcal depths to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.sulc > >> inflation took 6.4 minutes > >> inflating to desired rms height = 0.015 > >> 000: dt: 0.0000, rms height=0.159, avgs=16 > >> 005: dt: 0.9000, rms height=0.117, avgs=16, l_dist=0.40 > >> 010: dt: 0.9000, rms height=0.085, avgs=16, l_dist=0.40 > >> 015: dt: 0.9000, rms height=0.070, avgs=8, l_dist=0.28 > >> 020: dt: 0.9000, rms height=0.058, avgs=8, l_dist=0.28 > >> 025: dt: 0.9000, rms height=0.050, avgs=4, l_dist=0.20 > >> 030: dt: 0.9000, rms height=0.042, avgs=4, l_dist=0.20 > >> 035: dt: 0.9000, rms height=0.036, avgs=2, l_dist=0.14 > >> 040: dt: 0.9000, rms height=0.032, avgs=2, l_dist=0.14 > >> 045: dt: 0.9000, rms height=0.029, avgs=1, l_dist=0.10 > >> 050: dt: 0.9000, rms height=0.027, avgs=1, l_dist=0.10 > >> 055: dt: 0.9000, rms height=0.025, avgs=0, l_dist=0.00 > >> 060: dt: 0.9000, rms height=0.024, avgs=0, l_dist=0.00 > >> > >> inflation complete. > >> writing curvature file /home/chxc/freesurfer-data/subjects/sheng_new/surf/rh.sulc > >> > >> Command Finished > >> /softwares/freesurfer/freesurfer_alpha/bin/Linux/mris_inflate -n 10 -dist 0.1 >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.smoothwm >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.inflated > >> niterations = 10 > >> l_dist = 0.100 > >> avg radius = 44.4 mm, total surface area = 69956 mm^2 > >> tol=1.0e-04, host=DELL-, nav=16, nbrs=2, l_spring_norm=1.000, l_dist=0.100 > >> mom=0.90, dt=0.90 > >> desired rms height=0.015 > >> writing inflated surface to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.inflated > >> writing sulcal depths to >/home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.sulc > >> inflation took 6.2 minutes > >> inflating to desired rms height = 0.015 > >> 000: dt: 0.0000, rms height=0.160, avgs=16 > >> 005: dt: 0.9000, rms height=0.118, avgs=16, l_dist=0.40 > >> 010: dt: 0.9000, rms height=0.085, avgs=16, l_dist=0.40 > >> 015: dt: 0.9000, rms height=0.068, avgs=8, l_dist=0.28 > >> 020: dt: 0.9000, rms height=0.058, avgs=8, l_dist=0.28 > >> 025: dt: 0.9000, rms height=0.050, avgs=4, l_dist=0.20 > >> 030: dt: 0.9000, rms height=0.042, avgs=4, l_dist=0.20 > >> 035: dt: 0.9000, rms height=0.035, avgs=2, l_dist=0.14 > >> 040: dt: 0.9000, rms height=0.031, avgs=2, l_dist=0.14 > >> 045: dt: 0.9000, rms height=0.028, avgs=1, l_dist=0.10 > >> 050: dt: 0.9000, rms height=0.026, avgs=1, l_dist=0.10 > >> 055: dt: 0.9000, rms height=0.025, avgs=0, l_dist=0.00 > >> 060: dt: 0.9000, rms height=0.024, avgs=0, l_dist=0.00 > >> > >> inflation complete. > >> writing curvature file /home/chxc/freesurfer-data/subjects/sheng_new/surf/lh.sulc > >> > >> Command Finished > >> > >> > >> ########### > >> Medit Log > >> ########### > >> > >> > >> > > > > > >. > > ========= End Of Original Message ========= > >
