External Email - Use Caution
Hi,
My trac-all -path exited with error after trying to load BEDPOST parameter samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong with my bedpostX from trac-all -bedp? Should I run bedpostX separately again without trac-all. Though my last step '-bedp' didn't prompt 'finished without error' log message as preproc did, expected files were created. BTW, which log script should I look into? the one follows SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the trac-all -path log.
Thank you so much! Best, Qi
You exceeded the memory limit: TERM_MEMLIMIT: job killed after reaching LSF memory usage limit. Exited with exit code 1.
How big is are your diffusion data sets (matrix size and number of directions)? Your cluster probably has a way for you to request more memory when you submit jobs - you'd have to look at the documentation for your cluster. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Friday, May 1, 2020 3:07 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] longitudinal trac-all -path exited with error
External Email - Use Caution
Hi,
My trac-all -path exited with error after trying to load BEDPOST parameter samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong with my bedpostX from trac-all -bedp? Should I run bedpostX separately again without trac-all. Though my last step '-bedp' didn't prompt 'finished without error' log message as preproc did, expected files were created. BTW, which log script should I look into? the one follows SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the trac-all -path log.
Thank you so much! Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
External Email - Use Caution
Hi Anastasia,
I increased the memory limit and ran again with trac-all -path. However, this time "Could not read SUBJ1_base/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz" since I have no files created in the folder SUBJ1_base/dlabel/mni/~. Was it supposed to be generated in the step of "trac-all -bedp"? To recap what I did in '-bedp': 1) log file: "queuing post processing" However, 2) I have all needed outputs generated in SUBJ1_ses1.long.SUBJ1_base/bedpostX and SUBJ1_ses2.long.SUBJ1_base/bedpostX I have attached the trac-all -path log file below.
Thank you so much! Best, Qi
On Fri, May 1, 2020 at 10:01 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:
You exceeded the memory limit: TERM_MEMLIMIT: job killed after reaching LSF memory usage limit. Exited with exit code 1.
How big is are your diffusion data sets (matrix size and number of directions)? Your cluster probably has a way for you to request more memory when you submit jobs - you'd have to look at the documentation for your cluster.
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi < qi.zeng@icahn.mssm.edu> *Sent:* Friday, May 1, 2020 3:07 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] longitudinal trac-all -path exited with error
External Email - Use CautionHi,
My trac-all -path exited with error after trying to load BEDPOST parameter samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong with my bedpostX from trac-all -bedp? Should I run bedpostX separately again without trac-all. Though my last step '-bedp' didn't prompt 'finished without error' log message as preproc did, expected files were created. BTW, which log script should I look into? the one follows SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the trac-all -path log.
Thank you so much! Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
They are created during the -prior step (last step within -prep), which looks like it didn't complete. You probably also ran out memory in that step and didn't notice. Rerun -prior with increased memory and then try -path again. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zeng, Qi qi.zeng@icahn.mssm.edu Sent: Monday, May 4, 2020 1:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal trac-all -path exited with error
External Email - Use Caution
Hi Anastasia,
I increased the memory limit and ran again with trac-all -path. However, this time "Could not read SUBJ1_base/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz" since I have no files created in the folder SUBJ1_base/dlabel/mni/~. Was it supposed to be generated in the step of "trac-all -bedp"? To recap what I did in '-bedp': 1) log file: "queuing post processing" However, 2) I have all needed outputs generated in SUBJ1_ses1.long.SUBJ1_base/bedpostX and SUBJ1_ses2.long.SUBJ1_base/bedpostX I have attached the trac-all -path log file below.
Thank you so much! Best, Qi
On Fri, May 1, 2020 at 10:01 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote: You exceeded the memory limit: TERM_MEMLIMIT: job killed after reaching LSF memory usage limit. Exited with exit code 1.
How big is are your diffusion data sets (matrix size and number of directions)? Your cluster probably has a way for you to request more memory when you submit jobs - you'd have to look at the documentation for your cluster. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Sent: Friday, May 1, 2020 3:07 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] longitudinal trac-all -path exited with error
External Email - Use Caution
Hi,
My trac-all -path exited with error after trying to load BEDPOST parameter samples from SUBJ.long.SUBJ_base/dmri.bedpostX. So is there something wrong with my bedpostX from trac-all -bedp? Should I run bedpostX separately again without trac-all. Though my last step '-bedp' didn't prompt 'finished without error' log message as preproc did, expected files were created. BTW, which log script should I look into? the one follows SUBJ_base/script or SUBJ_ses-1.long.SUBJ_base/script? Here attached the trac-all -path log.
Thank you so much! Best, Qi
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Ph.D. candidate Icahn School of Medicine at Mount Sinai
freesurfer@nmr.mgh.harvard.edu
-
Yendiki, Anastasia -
Zeng, Qi