I’m having some trouble processing data on openneuro with fmriprep. The data is multiband data with a TR of 460 ms (wasn’t my choice) and 894 volumes. I have 6 runs and my analysis for a single-subject takes over 48 hrs so the jobs are being killed. Looking at the logs, it appears that melodic took 19 hours for one run:
1527000915333 180522-14:55:15,333 workflow INFO: 1527000915333 [Node] Setting-up "fmriprep_wf.single_subject_M80398983_wf.func_preproc_task_ritl_acq_MB_run_05_wf.ica_aroma_wf.melodic" in "/root/src/fmriprep/work/fmriprep_wf/single_subject_M80398983_wf/func_preproc_task_ritl_acq_MB_run_05_wf/ica_aroma_wf/melodic". 1527000915337 180522-14:55:15,337 workflow INFO: 1527000915337 [Node] Running "melodic" ("niworkflows.nipype.interfaces.fsl.model.MELODIC"), a CommandLine Interface with command: 1527000915337 melodic -i /root/src/fmriprep/work/fmriprep_wf/single_subject_M80398983_wf/func_preproc_task_ritl_acq_MB_run_05_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_smooth.nii.gz -m /root/src/fmriprep/work/fmriprep_wf/single_subject_M80398983_wf/func_preproc_task_ritl_acq_MB_run_05_wf/ica_aroma_wf/bold_mni_trans_wf/mask_mni_tfm/ref_image_corrected_brain_mask_maths_trans.nii.gz --mmthresh=0.500000 --nobet -o /root/src/fmriprep/work/fmriprep_wf/single_subject_M80398983_wf/func_preproc_task_ritl_acq_MB_run_05_wf/ica_aroma_wf/melodic --Ostats --tr=0.460000 1527068015039 180523-09:33:35,38 workflow INFO: 1527068015039 [Node] Finished "fmriprep_wf.single_subject_M80398983_wf.func_preproc_task_ritl_acq_MB_run_05_wf.ica_aroma_wf.melodic". 1527068017774 180523-09:33:37,773 workflow INFO:
I’ve run MELODIC on these data before through ICA_AROMA.py and I’m pretty sure they only took a few hours. Is there anything I can do to reduce the duration?
I’ve tried re-running the analysis hoping it would pick up where it left off like fmriprep will do with docker, but it doesn’t appear that this is the case.