Dear Paul,
yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh).
Regards,
Antonin
Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch a...@ikem.cz wrote:
Dear Paul,
the slash problem prevents to properly create symbolic link to fsaverage in your SUBJECTS_DIR.
Then, the mri_label2label could not find the fsaverage label file since symbolic link for fsaverage does not exist, hence produces the error.log you are attaching.
Regards,
Antonin
Thanks Antonin. Also, I got this error.log file in my label folder. Do you think it is due to the slash problem? Best, Paul
On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch a...@ikem.cz wrote:
Dear Paul,
I suppose the clue is following messages from your recon-all.log file:
FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
and
cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
ln: failed to create symbolic link './fsaverage': File exists
The problem is that your FREESURFER_HOME contains slash in the end. Remove it and rerun relevant part of recon-all. It should work then.
Antonin
Hello Freesurfer, I was running recon-all in steps (recon-all -autorecon1, recon-all -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, it exited with error during the BA_exvivo labels part of autorecon3 (please see attached recon-all.log file). Please, how can I fix it? Thanks Best, Paul
Thanks Antonin. I also have different error when running another subject. Recon fails in the smooth stage of recon-all (please see the attached screenshot). How can i fix this? Best, Paul
On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Paul,
yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh).
Regards,
Antonin
Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul.
On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch a...@ikem.cz wrote:
Dear Paul,
the slash problem prevents to properly create symbolic link to fsaverage in your SUBJECTS_DIR.
Then, the mri_label2label could not find the fsaverage label file since symbolic link for fsaverage does not exist, hence produces the error.log you are attaching.
Regards,
Antonin
Thanks Antonin. Also, I got this error.log file in my label folder. Do you think it is due to the slash problem? Best, Paul
On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch a...@ikem.cz wrote:
Dear Paul,
I suppose the clue is following messages from your recon-all.log file:
FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/
and
cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd -
ln: failed to create symbolic link './fsaverage': File exists
The problem is that your FREESURFER_HOME contains slash in the end. Remove it and rerun relevant part of recon-all. It should work then.
Antonin
Hello Freesurfer, I was running recon-all in steps (recon-all -autorecon1, recon-all -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, it exited with error during the BA_exvivo labels part of autorecon3 (please see attached recon-all.log file). Please, how can I fix it? Thanks Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know.
On 03/03/2017 12:10 PM, miracle ozzoude wrote:
Thanks Antonin. I also have different error when running another subject. Recon fails in the smooth stage of recon-all (please see the attached screenshot). How can i fix this? Best, Paul
On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh). Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch <a...@ikem.cz <mailto:a...@ikem.cz>> wrote: > Dear Paul, > > the slash problem prevents to properly create symbolic link to fsaverage in > your SUBJECTS_DIR. > > Then, the mri_label2label could not find the fsaverage label file since > symbolic link for fsaverage does not exist, hence produces the error.log you > are attaching. > > Regards, > > Antonin > > > Thanks Antonin. Also, I got this error.log file in my label folder. Do you > think it is due to the slash problem? > Best, > Paul > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch <a...@ikem.cz <mailto:a...@ikem.cz>> wrote: > > > Dear Paul, > > > > I suppose the clue is following messages from your recon-all.log file: > > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ > > > > and > > > > cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - > > > > ln: failed to create symbolic link './fsaverage': File exists > > > > The problem is that your FREESURFER_HOME contains slash in the end. Remove > > it > > and rerun relevant part of recon-all. It should work then. > > > > Antonin > > > > > > > > > > Hello Freesurfer, > > I was running recon-all in steps (recon-all -autorecon1, recon-all > > -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, > > it exited with error during the BA_exvivo labels part of autorecon3 (please > > see attached recon-all.log file). Please, how can I fix it? Thanks > > Best, > > Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks. Z K Best, Paul
On Fri, Mar 3, 2017 at 12:14 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know.
On 03/03/2017 12:10 PM, miracle ozzoude wrote:
Thanks Antonin. I also have different error when running another subject. Recon fails in the smooth stage of recon-all (please see the attached screenshot). How can i fix this? Best, Paul
On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh). Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch <a...@ikem.cz <mailto:a...@ikem.cz>> wrote:
> Dear Paul, > > the slash problem prevents to properly create symbolic link tofsaverage in
> your SUBJECTS_DIR. > > Then, the mri_label2label could not find the fsaverage label filesince
> symbolic link for fsaverage does not exist, hence produces theerror.log you
> are attaching. > > Regards, > > Antonin > > > Thanks Antonin. Also, I got this error.log file in my labelfolder. Do you
> think it is due to the slash problem? > Best, > Paul > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch <a...@ikem.czmailto:a...@ikem.cz> wrote:
> > > Dear Paul, > > > > I suppose the clue is following messages from your recon-all.logfile:
> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ > > > > and > > > > cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326;ln -s
> > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - > > > > ln: failed to create symbolic link './fsaverage': File exists > > > > The problem is that your FREESURFER_HOME contains slash in theend. Remove
> > it > > and rerun relevant part of recon-all. It should work then. > > > > Antonin > > > > > > > > > > Hello Freesurfer, > > I was running recon-all in steps (recon-all -autorecon1,recon-all
> > -autorecon2, and recon-all - -T2 /T2 volume -T2pialautorecon3). However,
> > it exited with error during the BA_exvivo labels part ofautorecon3 (please
> > see attached recon-all.log file). Please, how can I fix it?Thanks
> > Best, > > Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Z K, Were you able to fix the bug? Best, Paul
On Fri, Mar 3, 2017 at 12:14 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know.
On 03/03/2017 12:10 PM, miracle ozzoude wrote:
Thanks Antonin. I also have different error when running another subject. Recon fails in the smooth stage of recon-all (please see the attached screenshot). How can i fix this? Best, Paul
On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh). Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch <a...@ikem.cz <mailto:a...@ikem.cz>> wrote:
> Dear Paul, > > the slash problem prevents to properly create symbolic link tofsaverage in
> your SUBJECTS_DIR. > > Then, the mri_label2label could not find the fsaverage label filesince
> symbolic link for fsaverage does not exist, hence produces theerror.log you
> are attaching. > > Regards, > > Antonin > > > Thanks Antonin. Also, I got this error.log file in my labelfolder. Do you
> think it is due to the slash problem? > Best, > Paul > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch <a...@ikem.czmailto:a...@ikem.cz> wrote:
> > > Dear Paul, > > > > I suppose the clue is following messages from your recon-all.logfile:
> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ > > > > and > > > > cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326;ln -s
> > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - > > > > ln: failed to create symbolic link './fsaverage': File exists > > > > The problem is that your FREESURFER_HOME contains slash in theend. Remove
> > it > > and rerun relevant part of recon-all. It should work then. > > > > Antonin > > > > > > > > > > Hello Freesurfer, > > I was running recon-all in steps (recon-all -autorecon1,recon-all
> > -autorecon2, and recon-all - -T2 /T2 volume -T2pialautorecon3). However,
> > it exited with error during the BA_exvivo labels part ofautorecon3 (please
> > see attached recon-all.log file). Please, how can I fix it?Thanks
> > Best, > > Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Paul,
I've been trying to replicate it the issue on my Mac without any success. But I do have what might be a potential solution ide like you to try. Could you please source freesurfer, then run the following command.
$> sudo -E fs_update
(This will update a freesurfer file on your machine). Then retry the subject with the parallel flag. Please let me know how it goes. Thanks.
-Zeke
On Mar 6, 2017, at 8:56 AM, miracle ozzoude miracooloz@gmail.com wrote:
Hello Z K, Were you able to fix the bug? Best, Paul
On Fri, Mar 3, 2017 at 12:14 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote: Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know.
On 03/03/2017 12:10 PM, miracle ozzoude wrote:
Thanks Antonin. I also have different error when running another subject. Recon fails in the smooth stage of recon-all (please see the attached screenshot). How can i fix this? Best, Paul
On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh). Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch <a...@ikem.cz <mailto:a...@ikem.cz>> wrote: > Dear Paul, > > the slash problem prevents to properly create symbolic link to fsaverage in > your SUBJECTS_DIR. > > Then, the mri_label2label could not find the fsaverage label file since > symbolic link for fsaverage does not exist, hence produces the error.log you > are attaching. > > Regards, > > Antonin > > > Thanks Antonin. Also, I got this error.log file in my label folder. Do you > think it is due to the slash problem? > Best, > Paul > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch <a...@ikem.cz <mailto:a...@ikem.cz>> wrote: > > > Dear Paul, > > > > I suppose the clue is following messages from your recon-all.log file: > > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ > > > > and > > > > cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s > > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - > > > > ln: failed to create symbolic link './fsaverage': File exists > > > > The problem is that your FREESURFER_HOME contains slash in the end. Remove > > it > > and rerun relevant part of recon-all. It should work then. > > > > Antonin > > > > > > > > > > Hello Freesurfer, > > I was running recon-all in steps (recon-all -autorecon1, recon-all > > -autorecon2, and recon-all - -T2 /T2 volume -T2pial autorecon3). However, > > it exited with error during the BA_exvivo labels part of autorecon3 (please > > see attached recon-all.log file). Please, how can I fix it? Thanks > > Best, > > Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Z K, Thank you. I will do it later and update you. Best, Paul
On Mon, Mar 6, 2017 at 9:07 AM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Hello Paul,
I've been trying to replicate it the issue on my Mac without any success. But I do have what might be a potential solution ide like you to try. Could you please source freesurfer, then run the following command.
$> sudo -E fs_update
(This will update a freesurfer file on your machine). Then retry the subject with the parallel flag. Please let me know how it goes. Thanks.
-Zeke
On Mar 6, 2017, at 8:56 AM, miracle ozzoude miracooloz@gmail.com wrote:
Hello Z K, Were you able to fix the bug? Best, Paul
On Fri, Mar 3, 2017 at 12:14 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Im looking into this now, but I think their might be a bug when using the -parallel flag on Mac platforms. I should have a fix shortly. I will let you know.
On 03/03/2017 12:10 PM, miracle ozzoude wrote:
Thanks Antonin. I also have different error when running another subject. Recon fails in the smooth stage of recon-all (please see the attached screenshot). How can i fix this? Best, Paul
On Thu, Mar 2, 2017 at 7:19 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, yes, this is the modification of FREESURFER_HOME you need to do (using setenv command if you are using tcsh). Regards, Antonin Hey Antonin, Thank you. hence, the right path should be "setenv FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer " Best, Paul. On Thu, Mar 2, 2017 at 5:41 PM, Antonin Skoch <a...@ikem.czmailto:a...@ikem.cz> wrote:
> Dear Paul, > > the slash problem prevents to properly create symbolic link tofsaverage in
> your SUBJECTS_DIR. > > Then, the mri_label2label could not find the fsaverage label filesince
> symbolic link for fsaverage does not exist, hence produces theerror.log you
> are attaching. > > Regards, > > Antonin > > > Thanks Antonin. Also, I got this error.log file in my labelfolder. Do you
> think it is due to the slash problem? > Best, > Paul > > On Thu, Mar 2, 2017 at 4:38 PM, Antonin Skoch <a...@ikem.czmailto:a...@ikem.cz> wrote:
> > > Dear Paul, > > > > I suppose the clue is following messages from yourrecon-all.log file:
> > > > FREESURFER_HOME /opt/freesurfer-6.0.0/freesurfer/ > > > > and > > > > cd /net/synapse/nt/mozzoude/processing/freesurfer/176_003_120326; ln -s
> > /opt/freesurfer-6.0.0/freesurfer//subjects/fsaverage; cd - > > > > ln: failed to create symbolic link './fsaverage': File exists > > > > The problem is that your FREESURFER_HOME contains slash in theend. Remove
> > it > > and rerun relevant part of recon-all. It should work then. > > > > Antonin > > > > > > > > > > Hello Freesurfer, > > I was running recon-all in steps (recon-all -autorecon1,recon-all
> > -autorecon2, and recon-all - -T2 /T2 volume -T2pialautorecon3). However,
> > it exited with error during the BA_exvivo labels part ofautorecon3 (please
> > see attached recon-all.log file). Please, how can I fix it?Thanks
> > Best, > > Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <http://www.partners.org/complianceline> . If the e-mail was sentto
you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
-
Antonin Skoch -
miracle ozzoude -
Z K