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





                                    The information in this e-mail is intended only for the person to whom it is
                                    addressed. If you believe this e-mail was sent to you in error and the e-mail
                                    contains patient information, please contact the Partners Compliance HelpLine at
                                    http://www.partners.org/complianceline . If the e-mail was sent to you in error
                                    but does not contain patient information, please contact the sender and properly
                                    dispose of the e-mail.