search

nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
628 stars 290 forks source link

slice timing correction failed #3192

Open sarahfan128 opened 8 months ago

sarahfan128 commented 8 months ago

Hi, I have been running a bunch of subjects using fmriprep (fmriprep/23.1.4) While most of my subjects run fine, slice timing error keeps occuring in some subject even I tried to rerun it in a fresh work directory. I've also checked my slice timings and they all seemed to be correct to me. Acquisition times are kind of the same across all individuals. No specific bad motions and artifacts have been spotted. So I am running out of ideas of what it could cause this. I've attached my slice timing crash report here.

Many thanks, Sarah crash-20231222-145204-sf674-slice_timing_correction-f867cc0a-b263-4618-934f-44a83dd8a5f6.txt

effigies commented 8 months ago

It says the job is getting killed. Likely this is an out of memory error.

sarahfan128 commented 8 months ago

Thanks for the fast reply. I just double check on our server, we have enough memories...

effigies commented 8 months ago

Okay. Then I would try changing directory to the working directory of the failing command, then run it manually to see if you get more information.

sarahfan128 commented 8 months ago

Sorry I am fairly new to fmriprep. Do I understand correctly that I re run this subject by going into the slice_timing_correction working directory (see below)? And what exactly do you mean by running it mannually to see? Like running the usual fmriprep preprocessing command? Many thanks. /home/sf674/palmer_scratch/predcode/mprc/20/work/fmriprep_23_1_wf/single_subject_M085678_wf/func_preproc_ses_A5512_task_kamin_acq_AP_wf/bold_stc_wf/slice_timing_correction

amirhusseinab commented 8 months ago

Hi Sarah, Can you try binding the tmpdir/scratch to your singularity or docker run like: -B $TMPDIR:$TMPDIR