fMRIPrep with gadolinium enhanced T1w images


I have a clinical imaging dataset that I am trying to run through the fMRIprep workflow but the process is not completing. The input data contains 3 subjects.

In the clinical imaging workflow, gadolinium is delivered prior to the MRI scan session to save time. This means the T1w sequences are gadolinium-enhanced. It seems the extra contrast in the T1w sequences is causing fMRIprep to hang.

I am running fMRIprep v1.5.4 as a singularity container on a remote HPC with the following parameters:

--nthreads 8 --n_cpus 8 --mem_mb 32000 -anat-only

I have tried adjusting the job resources but it still hangs after 72hrs. It appears to be stuck on recon-all.

I’m wondering what else I could try? Has anyone tried fMRIprep on gadolinium-enhanced T1w images?