---------- 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/**compliancelinehttp://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.
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 FatmaThe 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.
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 ifyou 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 atemplate., I have this message of error:
mris_register -1 s000/surf/lh.sphereavg_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 FatmaThe 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/**compliancelinehttp://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.
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 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.
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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.
freesurfer@nmr.mgh.harvard.edu
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fatma zribi