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 =========
