See my original post at the end of this message and some more information included below.
What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points.
On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith cnsmith@ucsd.edu wrote:
Here it is:
New invocation of recon-all
Thu Oct 4 03:52:22 PDT 2012 /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 /usr/local/freesurfer/bin/recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel #-------------------------------------- #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012
On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what were the last 20 lines or so of the recon-all.log?
On Tue, 30 Oct 2012, Christine Smith wrote:
Hello,
After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step.
What should I be looking for to track down the reason that errors were generated?
I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too.
Thanks, Christine
so your recon-all command line was:
recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
usually -s just takes the subject name/identifier, not the whole path, and why are you only rerunning calabel? I don't see what the error is, but this is an unusual usage
On Tue, 30 Oct 2012, Christine Smith wrote:
See my original post at the end of this message and some more information included below.
What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points.
On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith cnsmith@ucsd.edu wrote:
Here it is:
New invocation of recon-all
Thu Oct 4 03:52:22 PDT 2012 /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 /usr/local/freesurfer/bin/recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel #-------------------------------------- #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012
On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what were the last 20 lines or so of the recon-all.log?
On Tue, 30 Oct 2012, Christine Smith wrote:
Hello,
After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step.
What should I be looking for to track down the reason that errors were generated?
I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too.
Thanks, Christine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The command line was: recon-all -make -s CON1
I am not sure why the log said it was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
I am running it again right now and it said the command line was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -careg -careginv
It seems to be running through the processing stream. I will let you know what it says after it finishes sometime tomorrow.
Christine
On Tue, Oct 30, 2012 at 6:13 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
so your recon-all command line was:
recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
usually -s just takes the subject name/identifier, not the whole path, and why are you only rerunning calabel? I don't see what the error is, but this is an unusual usage
On Tue, 30 Oct 2012, Christine Smith wrote:
See my original post at the end of this message and some more information included below.
What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points.
On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith cnsmith@ucsd.edu wrote:
Here it is:
New invocation of recon-all
Thu Oct 4 03:52:22 PDT 2012 /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 /usr/local/freesurfer/bin/recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel #-------------------------------------- #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012
On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what were the last 20 lines or so of the recon-all.log?
On Tue, 30 Oct 2012, Christine Smith wrote:
Hello,
After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step.
What should I be looking for to track down the reason that errors were generated?
I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too.
Thanks, Christine
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.
Well, that is funny. Now it has finished without errors. I am not quite sure what happened. The command line was the same both times: recon-all -make all -subjid CON1
Is it possible that some other process that was going on on our server caused the processing for this subject to end abnormally? We sometimes run 3 subjects at a time, but this does not exhaust our RAM or the number of processors.
Christine
On Wed, Oct 31, 2012 at 9:31 AM, Christine Smith cnsmith@ucsd.edu wrote:
The command line was: recon-all -make -s CON1
I am not sure why the log said it was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel
I am running it again right now and it said the command line was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -careg -careginv
It seems to be running through the processing stream. I will let you know what it says after it finishes sometime tomorrow.
Christine
On Tue, Oct 30, 2012 at 6:13 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
so your recon-all command line was:
recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1
-calabel
usually -s just takes the subject name/identifier, not the whole path,
and
why are you only rerunning calabel? I don't see what the error is, but
this
is an unusual usage
On Tue, 30 Oct 2012, Christine Smith wrote:
See my original post at the end of this message and some more information included below.
What would have been edited between the previous run without errors and the current run with errors is the brainmask, the wm.mgz file, and control points.
On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith cnsmith@ucsd.edu
wrote:
Here it is:
New invocation of recon-all
Thu Oct 4 03:52:22 PDT 2012 /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 /usr/local/freesurfer/bin/recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel #-------------------------------------- #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012
mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff aseg.manedit.mgz
Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012
On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what were the last 20 lines or so of the recon-all.log?
On Tue, 30 Oct 2012, Christine Smith wrote:
Hello,
After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step.
What should I be looking for to track down the reason that errors
were
generated?
I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too.
Thanks, Christine
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.
-- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego
how much ram do you have? On Thu, 1 Nov 2012, Christine Smith wrote:
Well, that is funny. Now it has finished without errors. I am not quite sure what happened. The command line was the same both times: recon-all -make all -subjid CON1
Is it possible that some other process that was going on on our server caused the processing for this subject to end abnormally? We sometimes run 3 subjects at a time, but this does not exhaust our RAM or the number of processors.
Christine
On Wed, Oct 31, 2012 at 9:31 AM, Christine Smith cnsmith@ucsd.edu wrote: The command line was: recon-all -make -s CON1
I am not sure why the log said it was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel I am running it again right now and it said the command line was: recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -careg -careginv It seems to be running through the processing stream. I will let you know what it says after it finishes sometime tomorrow. Christine On Tue, Oct 30, 2012 at 6:13 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > so your recon-all command line was: > > recon-all -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel > > usually -s just takes the subject name/identifier, not the whole path, and > why are you only rerunning calabel? I don't see what the error is, but this > is an unusual usage > > > > > On Tue, 30 Oct 2012, Christine Smith wrote: > >> See my original post at the end of this message and some more >> information included below. >> >> What would have been edited between the previous run without errors >> and the current run with errors is the brainmask, the wm.mgz file, and >> control points. >> >> On Tue, Oct 30, 2012 at 1:21 PM, Christine Smith <cnsmith@ucsd.edu> wrote: >>> >>> Here it is: >>> >>> New invocation of recon-all >>> >>> Thu Oct 4 03:52:22 PDT 2012 >>> /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 >>> /usr/local/freesurfer/bin/recon-all >>> -s /usr/local/mridata/D_New_Patient/Lobe_Analysis/CON1 -calabel >>> #-------------------------------------- >>> #@# SubCort Seg Thu Oct 4 03:52:22 PDT 2012 >>> >>> mri_seg_diff --seg1 aseg.auto.mgz --seg2 aseg.mgz --diff >>> aseg.manedit.mgz >>> >>> Linux squirelab.ucsd.edu 2.6.18-308.13.1.el5 #1 SMP Tue Aug 21 >>> 18:44:22 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux >>> >>> recon-all -s CON1 exited with ERRORS at Thu Oct 4 03:52:22 PDT 2012 >>> >>> On Tue, Oct 30, 2012 at 12:45 PM, Bruce Fischl >>> <fischl@nmr.mgh.harvard.edu> wrote: >>>> >>>> what were the last 20 lines or so of the recon-all.log? >>>> >>>> On Tue, 30 Oct 2012, Christine Smith wrote: >>>> >>>>> Hello, >>>>> >>>>> After successfully running a subject through freesurfer (recon-all >>>>> -make all) several times as I fixed some pial and white matter edits, >>>>> I now get the message that recon-all finished with errors. Inspection >>>>> of the recon-all.log doesn't reveal any error messages to me in any >>>>> particular step. >>>>> >>>>> What should I be looking for to track down the reason that errors were >>>>> generated? >>>>> >>>>> I already examined the talairach transform and that looks great. >>>>> I loaded the pial and white matter surfaces and they look fine. The >>>>> segmentation aparc+aseg looks great too. >>>>> >>>>> Thanks, >>>>> Christine >>>>> >>>>> >>>> >> _______________________________________________ >> 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. >-- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego
-- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Christine Smith