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.