Open hoptman opened 5 months ago
Hi, can you share the full log file please. It is saved under /logs
Hi, can you share the full log file please. It is saved under
/logs
Please see attached. I had removed the crash, but got the same error in the attached re-run. proc_func_04-02-2024_se_task-rest_acq-AP_bold.txt
Thanks, Matt
Hello Matt,
It appears that the error is occurring due to a memory shortage on your workstation during the pipeline execution. The pipeline is a resource-intensive tool, typically run on robust desktops or SGE clusters. Could you please specify the location where you ran the pipeline? Additionally, consider increasing the allocated virtual memory to address this issue.
Best regards,
Raul
Hello Matt,
It appears that the error is occurring due to a memory shortage on your workstation during the pipeline execution. The pipeline is a resource-intensive tool, typically run on robust desktops or SGE clusters. Could you please specify the location where you ran the pipeline? Additionally, consider increasing the allocated virtual memory to address this issue.
Best regards,
Raul
Hi Raul, Thanks for your response! I was running the command from /mnt/home2/Rockland_sample. How can I allocate more memory to the command? Is it something like --mem-gb? Also, how much memory should I allocate?
Thanks, Matt
Hi again, I just wanted to check in about the issue of insufficient memory allocation: Could you please tell me how I can allocate more memory to the docker micapipe command? Is it something like --mem-gb? Also, how much memory should I allocate?
Thanks, Matt
Hi all, I'm making progress on the data analysis, but I seem to be stuck at the -proc_func stage. I'm running micapipe v.0.2.2 in docker (ubuntu 20.04), and am running the command:
docker run -ti --rm -v
pwd/bids_mica:/bids -v
pwd/micapipe:/out -v
pwd/micapipe_tmp:/tmp -v /mnt/software/freesurfer_7.4.1/license.txt:/opt/licence.txt micalab/micapipe:v0.2.2 -bids /bids -out /out
-fs_licence/opt/licence.txt -threads 10 -sub sub-A00035606 -ses ses-BAS1 -proc_func -acqStr task-rest_acq-AP_bold -dropTR 8 -NSR -noFIX
I get the error: [ INFO ]..... Registering func MRI to nativeproroot @ 42abcf444798 Thu Feb 1 20:07:26 UTC 2024: COMMAND --> mri_synthseg --i /tmp/14903_micapipe_proc-func_sub-A00035606_ses-BAS1/sub-A00035606_ses-BAS1_space-nativepro_desc-T1wbold.nii.gz --o /tmp/14903_micapipe_proc-func_sub-A00035606_ses-BAS1/T1bold_synthseg.nii.gz --robust --threads 10 --cpu terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc /opt/micapipe/functions/utilities.sh: line 1084: 3573 Aborted (core dumped) $l_command
Any thoughts? Thanks, Matt