Absolutely, sorry about that, the group is now cc'd.
the ls -l says: -rw-rw-r-- 1 vhasfcwui cind 0 Nov 6 15:57 lh.sphere
so it has 0 size to it, and I can't open it in tksurfer
-bash-3.2$ tksurfer PPMI_290_S_3829m12_i395612 lh sphere Using Freesurfer version 5.1.
subject is PPMI_290_S_3829m12_i395612 hemi is lh surface is sphere surfer: current subjects dir: /cind/00/PPMI/Freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /cind/07/PPMI/Freesurfer/subjects checking for nofix files in 'sphere' Reading image info (/cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612) Reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz surfer: Reading header info from /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz ERROR: reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/surf/lh.sphere Read 0 bytes, expected 1
Perhaps I should first try deleting the file and rerun as you recommended?
Thanks, Adam
On Fri, Nov 8, 2013 at 2:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Adam
can you cc the list on your replies so that others can answer? What does ls -l say about the sphere? Can you open it in tksurfer? Maybe the partition filled at some point when it was being written but things opened up later? You might just deleted the lh.sphere file and run
recon-all -make all -s <subject>
cheers
Bruce
On Fri, 8 Nov 2013, Adam Mezher wrote:
Hi Bruce,
Yes I checked and the partition is not full, there should be ample space available. Do you have any other ideas? I've never come across this error before.
Thanks, -Adam
Filesystem Size Used Avail Use% Mounted on cosf:/cind/07 2.3T 2.0T 167G 93% /cind/07
On Fri, Nov 8, 2013 at 2:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Adam
can you check to make sure that the partition isn't full? Bruce On Fri, 8 Nov 2013, Adam Mezher wrote: Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sphere and immediately exits afterward. Thank you, Adam Adam Mezher Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... mris_register: could not read surface file ../surf/lh.sphere ERROR: reading ../surf/lh.sphere Read 0 bytes, expected 1 Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at Wed Nov 6 15:57:07 PST 2013The 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.
just remove it and rerun recon-all with -make all. Something went wrong during write, maybe a full partition, maybe a network glitch, we'll never know
cheers Bruce On Fri, 8 Nov 2013, Adam Mezher wrote:
Absolutely, sorry about that, the group is now cc'd.
the ls -l says: -rw-rw-r-- 1 vhasfcwui cind 0 Nov 6 15:57 lh.sphere
so it has 0 size to it, and I can't open it in tksurfer
-bash-3.2$ tksurfer PPMI_290_S_3829m12_i395612 lh sphere Using Freesurfer version 5.1.
subject is PPMI_290_S_3829m12_i395612 hemi is lh surface is sphere surfer: current subjects dir: /cind/00/PPMI/Freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /cind/07/PPMI/Freesurfer/subjects checking for nofix files in 'sphere' Reading image info (/cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612) Reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz surfer: Reading header info from /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/mri/orig.mgz ERROR: reading /cind/00/PPMI/Freesurfer/subjects/PPMI_290_S_3829m12_i395612/surf/lh.sphere Read 0 bytes, expected 1
Perhaps I should first try deleting the file and rerun as you recommended?
Thanks, Adam
On Fri, Nov 8, 2013 at 2:36 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Adam
can you cc the list on your replies so that others can answer? What does ls -l say about the sphere? Can you open it in tksurfer? Maybe the partition filled at some point when it was being written but things opened up later? You might just deleted the lh.sphere file and run recon-all -make all -s <subject> cheers Bruce On Fri, 8 Nov 2013, Adam Mezher wrote: Hi Bruce, Yes I checked and the partition is not full, there should be ample space available. Do you have any other ideas? I've never come across this error before. Thanks, -Adam Filesystem Size Used Avail Use% Mounted on cosf:/cind/07 2.3T 2.0T 167G 93% /cind/07 On Fri, Nov 8, 2013 at 2:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Adam can you check to make sure that the partition isn't full? Bruce On Fri, 8 Nov 2013, Adam Mezher wrote: Hi FreeSurfer experts, I am repeatedly running into an autorecon3 error (see below). Any ideas how to fix this? It appears that the software is having an issue reading /surf/lh.sphere and immediately exits afterward. Thank you, Adam Adam Mezher Staff Research Associate II Center for Imaging of Neurodegenerative Diseases San Francisco VA Medical Center 4150 Clement St. (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864 using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading surface from ../surf/lh.sphere... mris_register: could not read surface file ../surf/lh.sphere ERROR: reading ../surf/lh.sphere Read 0 bytes, expected 1 Linux aldebaran 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PPMI_290_S_3829m12_i395612 exited with ERRORS at Wed Nov 6 15:57:07 PST 2013 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.
Hello,
I had some questions about setting the dmrirc file for batch processing for DTI.
I set the subject list I put in the 6 subjects I wanted to process. Then in the dcmlist I put in the pathway to the data files for each subject. I put a space in between each subjects pathways. Then I put in the pathway for each subjects bvec and bval file under the set bvec and set bval file respectively. In theory, they are exactly the same for each subject, so if I can only input one that would be fine.
I tried doing this and it processed only one subject. Am I missing something? I am brand new to tracula.
Also, based on what I am understanding, the script will run through 6 subjects simultaneously and not one by one, so should cut down on time since I am working with multiple cores? Do I need to specify the scores on a script so that it will use all cores available?
Thanks so much,
Emily
Hi Emily - Can you please send your configuration file and trac-all.log? It's impossible to tell what's going on without seeing those.
For now the b-values and gradient vectors are assumed to be the same for all subjects, so you enter only one of each.
The code is not set up to run in parallel on multiple cores on a single computer. It's set up to submit each subject as a job if you run it on a cluster. This capability though depends a lot on the specific cluster that you have, and you may need your cluster admin's help to set it up.
Hope this helps, a.y
On Fri, 8 Nov 2013, ebelleau@uwm.edu wrote:
Hello,
I had some questions about setting the dmrirc file for batch processing for DTI.
I set the subject list I put in the 6 subjects I wanted to process. Then in the dcmlist I put in the pathway to the data files for each subject. I put a space in between each subjects pathways. Then I put in the pathway for each subjects bvec and bval file under the set bvec and set bval file respectively. In theory, they are exactly the same for each subject, so if I can only input one that would be fine.
I tried doing this and it processed only one subject. Am I missing something? I am brand new to tracula.
Also, based on what I am understanding, the script will run through 6 subjects simultaneously and not one by one, so should cut down on time since I am working with multiple cores? Do I need to specify the scores on a script so that it will use all cores available?
Thanks so much,
Emily _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Adam Mezher -
Anastasia Yendiki -
Bruce Fischl -
ebelleau＠uwm.edu