Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 –autorecon3
It ran for about 4.5 hours and then gave this error:
------------------------------------------------------------------------------------------------------- [rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -------------------------------------------------------------------------------------------------------
Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject.
Thanks!
-Robert
********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2
cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
It ran for about 4.5 hours and then gave this error:
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh.label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject.
Thanks!
-Robert
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those.
thanks
-robert
On 6/4/13 8:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2
cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
It ran for about 4.5 hours and then gave this error:
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh. label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject.
Thanks!
-Robert
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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.
********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ok, let us know if it fixes your problem Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote:
ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those.
thanks
-robert
On 6/4/13 8:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2
cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
It ran for about 4.5 hours and then gave this error:
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh. label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject.
Thanks!
-Robert
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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.
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
p.s. you can check to see if those labels exist in your fsaverage/label dir On Tue, 4 Jun 2013, Welsh, Robert wrote:
ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those.
thanks
-robert
On 6/4/13 8:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2
cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
It ran for about 4.5 hours and then gave this error:
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh. label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject.
Thanks!
-Robert
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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.
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
hi bruce,
thanks. from the reading of "recon-all" it looks like this is a failure is occurring in the latter part of autorecon3 so I'm just rerunning that set and skipping autorecon2 on the subjects that failed.
correct?
best,
-robert
On 6/4/13 9:38 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
p.s. you can check to see if those labels exist in your fsaverage/label dir On Tue, 4 Jun 2013, Welsh, Robert wrote:
ah, that probably got there from the 5.2 recon-all. I'll go in and manually change those.
thanks
-robert
On 6/4/13 8:59 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Robert
I think you need to symlink the fsaverage dir to the 5.3 fsaverage instead of 5.2
cheers Bruce On Tue, 4 Jun 2013, Welsh, Robert wrote:
Hi,
We were re-processing a subject to test the fix for 5.2 to 5.3. The initial recon-all and subsequent autrecon2 and autorecon3 were run a few days ago under 5.2. Yesterday I installed 5.3 and we ran the following:
export SUBJECTS_DIR=/net/data4/FreeSurferDaze/FreeSurfer recon-all -s s_ALS51 -white -smooth2 -inflate2 ?autorecon3
It ran for about 4.5 hours and then gave this error:
[rcwelsh@schizo s_ALS51]$ tail scripts/recon-all.log SUBJECTS_DIR /net/data4/ALSSCI/FreeSurferDaze/FreeSurfer FREESURFER_HOME /net/misc/freesurfer_5.3.0_centos4 Loading source label. Invalid argument ERROR reading
/net/data4/ALSSCI/FreeSurferDaze/FreeSurfer/fsaverage/label/lh.BA1.thresh . label Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s s_ALS51 exited with ERRORS at Mon Jun 3 18:32:01 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Some help would be appreciated. There is a file lh.BA1.label but not lh.BA1.thresh.label, indeed there are no files with "thresh" in their name under that subject.
Thanks!
-Robert
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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.
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Welsh, Robert