Dear all,
I've been running recon-all on my dataset, but all of them are exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3
The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012
What should I do? Thanks!
Cheers, Linda
Hi Linda
it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers Bruce
On Fri, 2 Nov 2012, Linda Zhang wrote:
Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3
The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012
What should I do? Thanks!
Cheers, Linda
Dear all,
After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012
Another set is exiting simply with:
#@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing?
Thanks!
Cheers, Linda
On 2 November 2012 21:40, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Linda
it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers Bruce
On Fri, 2 Nov 2012, Linda Zhang wrote:
Dear all,
I've been running recon-all on my dataset, but all of them are exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3
The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/subjects/lh.EC_** average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/**subjects/lh.EC_average/surf/** lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012
What should I do? Thanks!
Cheers, Linda
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.
sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote:
Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012
Another set is exiting simply with:
#@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing?
Thanks!
Cheers, Linda
On 2 November 2012 21:40, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Linda
it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012 What should I do? Thanks! Cheers, LindaThe 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.
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again.
On 14 Nov 2012 22:14, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote:
Dear all,
After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-----------------------------**--------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012
Another set is exiting simply with:
#@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/**average/RB_all_2008-03-26.gca transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012
To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing?
Thanks!
Cheers, Linda
On 2 November 2012 21:40, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Linda
it sounds like you put your own subjects into the directory$FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of themare exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -oncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/subjects/lh.EC_**average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/**subjects/lh.EC_average/surf/** lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 2511:54:37 HKT 2012
What should I do? Thanks! Cheers, LindaThe 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.
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers, Linda
On 14 November 2012 22:29, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again.
On 14 Nov 2012 22:14, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote:
Dear all,
After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-----------------------------**--------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-save transforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012
Another set is exiting simply with:
#@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/**average/RB_all_2008-03-26.gca transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012
To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing?
Thanks!
Cheers, Linda
On 2 November 2012 21:40, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Linda
it sounds like you put your own subjects into the directory$FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of themare exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -oncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/subjects/lh.EC_**average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/**subjects/lh.EC_average/surf/* *lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Sat Aug 2511:54:37 HKT 2012
What should I do? Thanks! Cheers, LindaThe 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.
ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/
not sure why it thinks it doesn't exist. What are the permissions on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
can you do an ls on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf
and post the results? Also do:
ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
On Wed, 19 Dec 2012, Linda Zhang wrote:
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers, Linda
On 14 November 2012 22:29, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again. On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote: Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows: 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012 Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting What's the problem I should be addressing? Thanks! Cheers, Linda On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Linda it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012 What should I do? Thanks! Cheers, Linda 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.
Hi Bruce,
This is what I get:
FreeSurfer:~/freesurfer/lindadata> ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> /home/virtualuser/freesurfer/subjects/lh.EC_average FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/ cvs_avg35 fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 README V1_average
On 19 December 2012 21:43, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/
not sure why it thinks it doesn't exist. What are the permissions on
/home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
can you do an ls on
/home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average/surf
and post the results? Also do:
ls -l /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
On Wed, 19 Dec 2012, Linda Zhang wrote:
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**lindadata/subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/lindadata/subjects/** lh.EC_average/surf/lh.sphere.**reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_** average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/** lindadata/subjects/ncpoCCW/**scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers, Linda
On 14 November 2012 22:29, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm runninganother process alongside it. I'll stop the other one and try again.
On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote:
Dear all, After moving my data to a different folder, I've comeacross a different error when running recon-all (autorecon2 and 3). The last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0,invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-----------------------------**--------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/** lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-savetransforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP FriMar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 1415:47:38 HKT 2012
Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/**average/RB_all_2008-03-26.gca transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP FriMar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 1217:43:06 HKT 2012
To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing? Thanks! Cheers, Linda On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Linda
it sounds like you put your own subjects into thedirectory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset,but all of them are exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2-autorecon3
The error reads: #@# Ex-vivo Entorhinal Cortex Label lh SatAug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**subjects;ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
mris_spherical_average -erode 1 -origwhite -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/subjects/lh.EC_**average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/** subjects/lh.EC_average/surf/**lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS atSat Aug 25 11:54:37 HKT 2012
What should I do? Thanks! Cheers, Linda The information in this e-mail is intended only for theperson 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.
Looks like you don't have
/home/virtualuser/freesurfer/subjects/lh.EC_average
You will need to download it Cheers Bruce
On Dec 20, 2012, at 12:32 AM, Linda Zhang lzhang87@gmail.com wrote:
Hi Bruce,
This is what I get:
FreeSurfer:~/freesurfer/lindadata> ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> /home/virtualuser/freesurfer/subjects/lh.EC_average FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/ cvs_avg35 fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 README V1_average
On 19 December 2012 21:43, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/
not sure why it thinks it doesn't exist. What are the permissions on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
can you do an ls on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf
and post the results? Also do:
ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
On Wed, 19 Dec 2012, Linda Zhang wrote:
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers, Linda
On 14 November 2012 22:29, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again. On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote: Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows: 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012 Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting What's the problem I should be addressing? Thanks! Cheers, Linda On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Linda it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012 What should I do? Thanks! Cheers, Linda 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.
Thanks Bruce, from where? Should I download the other directories I seem to be missing as well? On 20 Dec 2012 21:26, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Looks like you don't have
/home/virtualuser/freesurfer/subjects/lh.EC_average
You will need to download it Cheers Bruce
On Dec 20, 2012, at 12:32 AM, Linda Zhang lzhang87@gmail.com wrote:
Hi Bruce,
This is what I get:
FreeSurfer:~/freesurfer/lindadata> ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> /home/virtualuser/freesurfer/subjects/lh.EC_average FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/ cvs_avg35 fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 README V1_average
On 19 December 2012 21:43, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/
not sure why it thinks it doesn't exist. What are the permissions on
/home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
can you do an ls on
/home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average/surf
and post the results? Also do:
ls -l /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_**average
On Wed, 19 Dec 2012, Linda Zhang wrote:
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**lindadata/subjects; ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/lindadata/subjects/** lh.EC_average/surf/lh.sphere.**reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/**lindadata/subjects/lh.EC_** average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/** lindadata/subjects/ncpoCCW/**scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.** edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers, Linda
On 14 November 2012 22:29, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm runninganother process alongside it. I'll stop the other one and try again.
On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote:
Dear all, After moving my data to a different folder, I've comeacross a different error when running recon-all (autorecon2 and 3). The last few lines are as follows:
0117: dt=32.368000, rms=0.713 (0.122%), neg=0,invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-----------------------------**--------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/** lindadata/subjects/ncvoCYJ/mri
mri_ca_register -invert-and-savetransforms/talairach.m3z
Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP FriMar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 1415:47:38 HKT 2012
Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/**lindadata/subjects/ncvoLML/mri
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/**average/RB_all_2008-03-26.gca transforms/talairach.lta
Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP FriMar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncvoLML exited with ERRORS at Mon Nov 1217:43:06 HKT 2012
To report a problem, seehttp://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
What's the problem I should be addressing? Thanks! Cheers, Linda On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Linda
it sounds like you put your own subjects intothe directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else
cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset,but all of them are exiting with the same error.
The command line is: recon-all -subjid ncpoCCW -autorecon2-autorecon3
The error reads: #@# Ex-vivo Entorhinal Cortex Label lh SatAug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/**subjects;ln -s /home/virtualuser/freesurfer/**subjects/lh.EC_average; cd -
mris_spherical_average -erode 1 -origwhite -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/**freesurfer/subjects/lh.EC_**average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/** subjects/lh.EC_average/surf/**lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS atSat Aug 25 11:54:37 HKT 2012
What should I do? Thanks! Cheers, Linda The information in this e-mail is intended only forthe 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.
Which other ones? Grab a whole new distribution, unpack it somewhere and either use it or move the dirs you need where you want them. Or wait a few weeks for 5.2 Bruce
On Dec 20, 2012, at 8:29 AM, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce, from where? Should I download the other directories I seem to be missing as well?
On 20 Dec 2012 21:26, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Looks like you don't have
/home/virtualuser/freesurfer/subjects/lh.EC_average
You will need to download it Cheers Bruce
On Dec 20, 2012, at 12:32 AM, Linda Zhang lzhang87@gmail.com wrote:
Hi Bruce,
This is what I get:
FreeSurfer:~/freesurfer/lindadata> ls -l drwxr-sr-x 42 virtualuser virtualuser 4096 2012-11-17 07:38 subjects FreeSurfer:~/freesurfer/lindadata> ls /subjects/lh.EC_average/surf ls: cannot access /subjects/lh.EC_average/surf: No such file or directory FreeSurfer:~/freesurfer/lindadata> ls -l /subjects/lh.EC_average lrwxrwxrwx 1 virtualuser virtualuser 51 2012-11-17 07:38 /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average -> /home/virtualuser/freesurfer/subjects/lh.EC_average FreeSurfer:~/freesurfer/lindadata> ls /home/virtualuser/freesurfer/subjects/ cvs_avg35 fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 README V1_average
On 19 December 2012 21:43, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: ls -1 $FREESURFER_HOME/subjects cvs_avg35/ cvs_avg35_inMNI152/ fsaverage/ fsaverage3/ fsaverage4/ fsaverage5/ fsaverage6/ fsaverage_sym/ lh.EC_average/ README rh.EC_average/ sample-001.mgz sample-002.mgz surfer.log V1_average/
not sure why it thinks it doesn't exist. What are the permissions on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
can you do an ls on
/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf
and post the results? Also do:
ls -l /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average
On Wed, 19 Dec 2012, Linda Zhang wrote:
Dear all,
I've run into the same error with recon-all -autorecon3. It could be that when I moved my data into the new SUBJECTS_DIR, I missed something out. What files should be in the $FREESURFER_HOME/subjects directory?
The error reads as follows:
#@# Ex-vivo Entorhinal Cortex Label lh Fri Dec 14 19:07:03 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject...
cd /home/virtualuser/freesurfer/lindadata/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd -
ln: creating symbolic link `./lh.EC_average': File exists
mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing No such file or directory mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/lindadata/subjects/lh.EC_average/surf/lh.sphere.reg No such file or directory Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux
recon-all -s ncpoCCW exited with ERRORS at Fri Dec 14 19:07:07 HKT 2012
For more details, see the log file /home/virtualuser/freesurfer/lindadata/subjects/ncpoCCW/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Cheers, Linda
On 14 November 2012 22:29, Linda Zhang lzhang87@gmail.com wrote:
Thanks Bruce. It has 6gb assigned to the virtualbox, I'm running another process alongside it. I'll stop the other one and try again. On 14 Nov 2012 22:14, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: sounds like you are running out of memory. How much ram is in that machine? Are other processes running at the same time? On Wed, 14 Nov 2012, Linda Zhang wrote: Dear all, After moving my data to a different folder, I've come across a different error when running recon-all (autorecon2 and 3). The last few lines are as follows: 0117: dt=32.368000, rms=0.713 (0.122%), neg=0, invalid=766 0118: dt=32.368000, rms=0.713 (0.033%), neg=0, invalid=766 0119: dt=32.368000, rms=0.712 (0.059%), neg=0, invalid=766 0120: dt=32.368000, rms=0.712 (0.081%), neg=0, invalid=766 0121: dt=16.184000, rms=0.712 (0.009%), neg=0, invalid=766 Killed ERROR: mri_ca_register with non-zero status 137 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Nov 14 15:47:37 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoCYJ/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoCYJ exited with ERRORS at Wed Nov 14 15:47:38 HKT 2012 Another set is exiting simply with: #@# EM Registration Mon Nov 12 17:43:05 HKT 2012 /home/virtualuser/freesurfer/lindadata/subjects/ncvoLML/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /home/virtualuser/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncvoLML exited with ERRORS at Mon Nov 12 17:43:06 HKT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting What's the problem I should be addressing? Thanks! Cheers, Linda On 2 November 2012 21:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Linda it sounds like you put your own subjects into the directory $FREESURFER_HOME/subjects, which is where we store our average data and symlink within your SUBJECTS_DIR. Try putting them somewhere else cheers Bruce On Fri, 2 Nov 2012, Linda Zhang wrote: Dear all, I've been running recon-all on my dataset, but all of them are exiting with the same error. The command line is: recon-all -subjid ncpoCCW -autorecon2 -autorecon3 The error reads: #@# Ex-vivo Entorhinal Cortex Label lh Sat Aug 25 11:54:33 HKT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /home/virtualuser/freesurfer/subjects; ln -s /home/virtualuser/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o ncpoCCW label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject ncpoCCW. processing subject lh.EC_average... MRISread(/home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere .reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /home/virtualuser/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg Too many levels of symbolic links Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s ncpoCCW exited with ERRORS at Sat Aug 25 11:54:37 HKT 2012 What should I do? Thanks! Cheers, Linda 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
-
Bruce Fischl -
Linda Zhang