Below is the output from mris_euler_number:
zion:/nfs/home/Subjects/ttt/surf> mris_euler_number rh.sphere.reg euler # = v-e+f = 2g-2: 134807 - 404415 + 269610 = 2 --> 0 holes F =2V-4: 269610 = 269614-4 (0) 2E=3F: 808830 = 808830 (0) total defect index = 0
zion:/nfs/home/Subjects/ttt/surf> mris_euler_number rh.smoothwm euler # = v-e+f = 2g-2: 134807 - 404415 + 269610 = 2 --> 0 holes F =2V-4: 269610 = 269614-4 (0) 2E=3F: 808830 = 808830 (0)
total defect index = 0
zion:/nfs/home/Subjects/ttt/surf> mris_euler_number rh.orig euler # = v-e+f = 2g-2: 134807 - 404415 + 269610 = 2 --> 0 holes F =2V-4: 269610 = 269614-4 (0) 2E=3F: 808830 = 808830 (0) total defect index = 0
Besides, there is no version # for mris_register (mris_register --version), but we are using the newest release (February 18th 2004). Thanks again for your help on this issue.
Jia
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 8:16 PM To: Jia Liu Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] questions on check_subject
can you run mris_euler_number on them and send me the results? It may be that you have a somewhat newer version of mris_register that embeds geometry info into the surface file.
On Tue, 31 May 2005, Jia Liu wrote:
No, I am using Linux (Fedora 1) but not Mac OS X, and yes, the problem exists in all my subjects (I happened to notice it when I ran check_subject). Best, jia
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 7:43 PM To: Jia Liu Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] questions on check_subject
is this only on Tiger? And does it happen with all your subjects now
that
you have upgraded? On Tue, 31 May 2005, Jia Liu wrote:
Hi, Bruce-
Thanks for your reply. I re-did morph for the right hemisphere, and
the
problem persists.
CHECKING SUBJECT ttt WARN: time for rh.orig is older than rh.qsphere WARN: file rh.sphere.reg is not equal in size to rh.smoothwm
-rw-rw-r-- 1 jliu jliu 4853285 May 31 12:45 rh.sphere.reg -rwxrwxr-x 1 jliu jliu 4853068 May 31 09:43 rh.smoothwm -rwxrwxr-x 1 jliu jliu 4853068 May 31 09:43 rh.orig
The log file is attached. What should I do to correct this problem?
Thanks
again for your help!
Best,
jia
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sunday, May 29, 2005 9:42 PM To: Jia Liu Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] questions on check_subject
you will need to rerun the morph. On Sun, 29 May 2005, Jia Liu wrote:
Hi, Bruce-
No, the ?h.sphere.reg files are slightly larger than the orig files.
Below
is the list of files in the surf directory.
-rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.inflated -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.orig -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.pial -rw-rw-r-- 1 app app 4858721 Mar 16 23:46
lh.rh.sphere.reg
-rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.smoothwm -rw-rw-r-- 1 app app 4858504 Mar 16 20:35 lh.sphere -rw-rw-r-- 1 app app 4858721 Mar 16 22:14
lh.sphere.reg
-rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.white -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.inflated -rw-rw-r-- 1 app app 4853285 Mar 16 18:54
rh.lh.sphere.reg
-rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.orig -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.pial -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.smoothwm -rw-rw-r-- 1 app app 4853068 Mar 16 15:17 rh.sphere -rw-rw-r-- 1 app app 4853285 Mar 16 16:59
rh.sphere.reg
-rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.white
Will this affect the surface-based group analysis?
Thanks again for your help!
Best,
jia
> -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Friday, May 27, 2005 8:10 PM > To: Jia Liu > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] questions on check_subject > > not sure why the smoothwm would be different size. Is it the same
size
as
> the orig? How about the rest of the surfaces for each hemis
(sphere,
white, > pial) > > On Fri, 27 May 2005, Jia > Liu wrote: > >> Hi, >> >> I used check_subject and found following error message on all my subjects: >> >> Zion:/nfs/home/Subjects> check_subject subKL >> CHECKING SUBJECT subKL >> WARN: file rh.sphere.reg is not equal in size to rh.smoothwm >> WARN: file lh.sphere.reg is not equal in size to lh.smoothwm >> WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm >> Exit 3 >> >> However, I looked through recon-all log files and found no error messages. >> So what does the error message above mean? How to correct this
problem?
Is >> there any document on check_subject? Thanks a lot for your help! >> >> Best, >> >> Jia >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>
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