[no subject]

[orphoebe]

Hi,

I got the following problems when using the latest version of freesurfer 
(fsa-20020521) downloaded from the surfer site:

1) Segmentation fault when trying to check the registration using tkregister:

[phoebe@taz rnnmean]$ tkregister local
tkregister: starting register
register: cwd scan = subject's T1/COR's
register:   reg image transform matrix: 
1.171900 0.00 0.00 0.00 
0.00 1.50 0.00 99.00 
0.00 0.00 1.171900 0.00 
0.00 0.00 0.00 1.00 
register: done reading target COR images
register: input file type: bshort (x,y,t: prefixz.bshort)
First slice read: s_000.bshort
Last slice read:  s_123.bshort
register: done reading to-be-registered images
register: no slice offset (default centered z bounding box)
Segmentation fault (core dumped)

2)The settings of the directory for minc tools are weird.  I got the bin and 
lib directory directly under mni_tools.  In the previous versions, there is no 
problem in this setting.  However, in the current version, a subdirectory 
Linux is defined in the middle.  Do you know where can I change this?

Setting up enviroment for FreeSurfer/FS-FAST
$Id: FreeSurferEnv.csh,v 1.2 2002/05/17 21:40:03 greve Exp $
FREESURFER_HOME /home/phoebe/bin/freesurfer_alpha
FSFAST_HOME /home/phoebe/bin/freesurfer_alpha/fsfast
AFNI_DIR/home/phoebe/bin/freesurfer_alpha/afni
FSL_DIR /home/phoebe/bin/freesurfer_alpha/fsl
SUBJECTS_DIR/home/phoebe/bin/freesurfer_alpha/subjects
WARNING: /home/phoebe/bin/freesurfer_alpha/mni_tools/Linux/bin does not exist.
WARNING: /home/phoebe/bin/freesurfer_alpha/mni_tools/Linux/lib does not exist.

Any helps will be much appreciated.

Phoebe.

[no subject]

[Collins Assisi]

hello everybody,

i'm trying to extract the following surfaces from mri data using the
mri_strip_skull program
1. outer skin   2. outer skull   3. inner skull

below i've listed the things i tried and the corresponding error messages.

the commands are prefixed, command,  and the corresponding messages,
mssg.

i plotted the surfaces obtained from the output files, and i get a sphere
for the outer skull, a surface with jagged edges for the outer skin and a
relatively smooth surface for the inner skull.

if someone is familiar with the mri_strip_skull program or any other method
to extract the three surfaces please let me know.




after the process volume step in freesurfer i do the following.  the
subject_name is new_s.

command-
mri_strip_skull   subject_name   2

mssg-
nvertices=2562, nfaces=5120
mri_strip_skull: images
/usr/local/FS_DIST.Linux/Subjects/new_s/mri/brain/COR- read
mri_strip_skull: ### File inner_skull.dat not found
xlo=-71.00, xhi=76.00, ylo=-103.00, yhi=74.00,
zlo=-62.00, zhi=94.00
0: sval=90.60,sinval=91.77,soutval=90.60
1: sval=89.44,sinval=91.07,soutval=89.44
 .
 .
 .
7: ad=0.046456, dmax=0.521133, nclip=0
8: ad=0.042548, dmax=0.436750, nclip=0
9: ad=0.039550, dmax=0.378821, nclip=0
mri_strip_skull: triangle file
/usr/local/FS_DIST.Linux/Subjects/new_s/bem/inner_skull.tri written


command:
mri_strip_skull subject_name3

mssg:
nvertices=2562, nfaces=5120
mri_strip_skull: images /usr/local/FS_DIST.Linux/Subjects/new_s/mri/T1/COR-
read
mri_strip_skull: ### File outer_skull.dat not found
mri_strip_skull: move on normal 1.00 mm
mri_strip_skull: triangle file
/usr/local/FS_DIST.Linux/Subjects/new_s/bem/outer_skull.tri written


command:
mri_strip_skull   subject_name   4


mssg:
nvertices=2562, nfaces=5120
mri_strip_skull: images /usr/local/FS_DIST.Linux/Subjects/new_s/mri/T1/COR-
read
mri_strip_skull: ### File outer_skin.dat not found
xlo=-96.00, xhi=97.00, ylo=-103.00, yhi=102.00,
zlo=-102.00, zhi=103.00
0: sval=74.36,sinval=72.63,soutval=74.36
1: sval=72.10,sinval=72.78,soutval=72.10
2: sval=71.50,sinval=73.61,soutval=71.50
 .
 .
 .
7: ad=0.146632, dmax=0.744341, nclip=0
8: ad=0.141502, dmax=0.724049, nclip=0
9: ad=0.137081, dmax=0.706004, nclip=0
mri_strip_skull: triangle file
/usr/local/FS_DIST.Linux/Subjects/new_s/bem/outer_skin.tri written

--







collins assisi
center for complex systems and brain sciences
florida atlantic university
[EMAIL PROTECTED]