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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