Fmriprep: shared libraries error in v1.3.2

[manishsaggar1]

Hi all,

I am getting the shared libraries error when I run fmriprep (v1.3.2) on the cluster (Sherlock). Not sure how to fix it. Please help.

I built the singularity image using:

singularity build /my_images/fmriprep-v1.3.2.simg docker://poldracklab/fmriprep:latest

Interestingly, the same image ran perfectly last week on another dataset. However, it keeps crashing with the following error with the current dataset.

Standard error: fslmaths: error while loading shared libraries: libnewimage.so: cannot open shared object file: No such file or directory Return code: 127

[ds7711]

One simple thing to check is whether you have the "/my_images/" directory/folder. "/my_images/fmriprep-v1.3.2.simg" should be where you want to store your image and differ between computers/users.

[manishsaggar1]

Thanks, yes I do. "/my_images" is only a placeholder in the command I pasted above.

[ds7711]

Sorry, I misread what your issue is. What command do you use to run fMRIprep? I encountered similar problems and the cause is that I was not using srun before the singularity command.
Did you try something like
srun singularity run --cleanenv /my_images/fmriprep-1.3.2.simg \ path/to/data/dir path/to/output/dir \ participant \ --participant-label lab -w path/to/temprory_working_dir

[manishsaggar1]

Thanks. Not sure about srun. But using --cleanenv flag helped.

[oesteban]

Yes, this is likely some LD_* environment variable leaking into the container.