Re: Re: Re: Re: Re: Question on segmentation

2002-11-01 Thread Xiangchuan Chen 
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

2002-11-01 Thread Xiangchuan Chen 
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  =

Question on segmentation

2002-10-30 Thread Xiangchuan Chen 
Hi all,

I found that the segmentation of the white matter near the occipital pole of my data 
was not quite accurate. I tried to add some voxels to the wm volume there, but the 
FreeSurfer didn't take them into account. Then, how can I improve the segmentation at 
this part of brain?

Thanks,
Xiangchuan Chen

Questions on tkregister

2002-04-12 Thread Xiangchuan Chen 

Hi,

I am trying to register a 2D anatomical volume to a T1 volume with tkregister for 
functional overlapping. The 2D volume is in AFNI .BRIK format. There are some 
questions on this registration process:

1. It is said in the manual that tkregister can input .BRIK dataset as moveable 
volume, but I can not make it be done correctly. I have edited the analyse.dat and 
register.dat according to the .BRIK's voxel dimension (FOV=20cm, 256x256 voxels in 
plane, 5mm slice thickness). Then, are there any tricks to have it work?

2. Since the 2D volume has a lower resolution across slices than T1 volume, it may 
look blurry when rotated. In this case, the registration may become inaccurate. Can I 
set T1 volume as moveable one, and 2D volume as target one to get a register.dat file, 
and then transform it to the register.dat file that can be used for functional 
overlapping?

Any suggestion is greatly appreciated.

Xiangchuan Chen