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

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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