slice timing correction failed

[sarahfan128]

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]

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

[sarahfan128]

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

[effigies]

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]

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]

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