Re: [Freesurfer] Fwd: how to use mris_register?

Fatma, it is not sufficient for you to be able to ls that folder, that file must exist, and it must exist in the path that you give it, so try running

ls -l s000_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere

from the folder where you are running mris_register

doug

On 07/10/2013 12:24 PM, fatma zribi wrote:

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

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