2013/7/10 fatma zribi <zribi.fatma@gmail.com>

SURFACE INFO ========================================
type        : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE
num vertices: 143704
num faces   : 287404
num strips : 0
surface area: 125661
AvgVtxArea       0.874440
AvgVtxDist       1.078393
StdVtxDist       0.419625
ctr         : (0.000782013, 0.000278473, -0.000354767)
vertex locs : surfaceRAS
talairch.xfm:
1.055   0.061   0.112 -14.422;
-0.160   1.180   0.231 -36.683;
-0.122 -0.333   1.316 -37.246;
0.000   0.000   0.000   1.000;
surfaceRAS to talaraiched surfaceRAS:
1.055   0.061   0.112 -0.656;
-0.160   1.180   0.231 -13.306;
-0.122 -0.333   1.316 -39.910;
0.000   0.000   0.000   1.000;
talairached surfaceRAS to surfaceRAS:
0.930 -0.067 -0.068 -2.975;
0.104   0.800 -0.149   4.763;
0.113   0.196   0.716   31.244;
0.000   0.000   0.000   1.000;
volume geometry:
extent : (256, 256, 256)
voxel   : ( 1.0000, 1.0000, 1.0000)
x_(ras) : (-1.0000, 0.0000, 0.0000)
y_(ras) : (-0.0000, -0.0000, -1.0000)
z_(ras) : ( 0.0000, 1.0000, 0.0000)
c_(ras) : (11.4210, 20.5397, 4.2289)
file    : ../mri/filled-pretess255.mgz
cmd[0]: mris_remove_intersection ../surf/lh.orig ../surf/lh.orig ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:20:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_remove_intersection.c,v 1.6 2011/03/02 00:04:32 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400
cmd[1]: mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs s000_open_brain_sanlm_+TIR_normlalized lh ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:21:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400
cmd[2]: mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:26:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400
cmd[3]: mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:26:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400
cmd[4]: mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/03-20:28:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: meyer.l Machine: jarron Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400
mris_info
creationtime 2013/07/10-16:39:42-GMT
sysname Linux
hostname frioul03
machine x86_64
surfacefile s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
hemicode    0
talairach_flag 0
rescale     0.000000
nvertices   143704
nfaces      287404
total_area 125660.585938
group_avg_vtxarea_loaded 0
avgvtxarea 0.874440
avgvtxdist 1.078393
stdvtxdist 0.419625
vtx0xyz   30.075546 -90.141014 -31.145763

2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu>

and how about:

mris_info s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere

On Wed, 10 Jul 2013, fatma zribi wrote:

Dear Bruce,
this is the result:

-rwxrwxr-x 1 zribi.f scalp 5175759 Jun 21 14:57 s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere

2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Fatma

this not what we meant. From here please run:
cd ..
ls -l s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere

cheers
Bruce

On Wed, 10 Jul 2013, fatma zribi wrote:

---------- Forwarded message ----------
From: fatma zribi <zribi.fatma@gmail.com>
Date: 2013/7/10
Subject: Re: [Freesurfer] Fwd: how to use mris_register?
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Copie1/s000_open_brain_sanlm_+TIR_normlalized$ ls -l
total 704
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 bem
drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 label
drwxrwxr-x 4 zribi.f scalp 4096 Jul 5 17:12 mri
drwxrwxr-x 2 zribi.f scalp 4096 Jul 9 10:44 scripts
drwxrwxr-x 2 zribi.f scalp 4096 Jul 2 10:49 SD
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 src
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 stats
drwxrwxr-x 6 zribi.f scalp 4096 Jul 9 10:44 surf
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 tmp
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 touch
drwxrwxr-x 2 zribi.f scalp 4096 Jul 5 17:12 trash

2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
I meant can you run it and send us the results? If we can't open the file it is not an FS issue,
but something with
the file system. Run ls -l with the same path that you are giving mris_register

Bruce

On Wed, 10 Jul 2013, fatma zribi wrote:

Hi Bruce,
Yes i can run ls -l in the directory

2013/7/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Fatma

are you sure you don't have a typo in the path? Can you run ls -l on that file?
Bruce
On Wed, 10 Jul 2013, fatma zribi wrote:

---------- Forwarded message ----------
From: fatma zribi <zribi.fatma@gmail.com>
Date: 2013/7/10
Subject: Re: [Freesurfer] how to use mris_register?
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu>

Hi Bruce,

Thank you very much for your help but it still don't work.

mris_register s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
avg_all_subjects_SD/lh.reg.template.tif lh.sphere_reg

$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere...
MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere): could not open
file
No such file or directory
mris_register: could not read surface file
s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere
No such file or directory

note that the file exist in the folder and i have changed the SUBJECT_DIR to the
appropriate
folder

Thank you very much for your help

with best regards,

Fatma

2013/7/9 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Hi Fatma

don't use the -1 flag if you are regtering to a template, only if you are
registering
individual
surfaces to each
other. You probably want the output to be named lh.sphere_reg and go in
the s000/surf
dir.

cheers
Bruce

On Tue, 9 Jul 2013, fatma zribi wrote:

Dear Mr,

When I execute mris_register to register one subject to a template.,
I have this
message of
error:

mris_register -1 s000/surf/lh.sphere
avg_all_subjects_SD/lh.reg.template.tif
sphere_reg
treating target as a single subject's surface...
$Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading surface from
s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere...
MRISread(s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere):
could not open
file
No such file or directory
mris_register: could not read surface file s000/surf/lh.sphere
No such file or directory

note that the file exist in the specifeid SUBJECT_DIR

Thank you for your help

Fatma

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