fMRIPrep "No storage left on device"

Hi there,

I need some help with regard to where fMRIprep is writing interim files.

My source directory and output directory are on a hard drive with 2TB free. However, after 2 days of running fMRIprep, the process quit complaining about no storage left on device.

I think what is happening is that fMRIprep is writing its interim files somewhere in the root directory (which indeed has very little space left). I didn’t realize this is the default working directory. I would have thought the default would have been in the same drive.

From now on I will always specify the -w working directory.

Is there anyway to salvage what has already been created by fMRIprep so when I rerun the command I don’t start from scratch (i.e., saving 2 days of running)? I understand that I can copy over the freesurfer dir, but I would like to reuse the analysis in fMRIprep if at all possible since it was almost done, and many of the output files were written! Is this possible even though I didn’t specify the working directory initially? What is the default working directory for fmriprep? And can I just copy that over to a new working directory and use the -w flag?

Thanks so much.

By default FMRIPREP uses timestamps and file sizes to check if a particular step needs to be rerun. This is faster than using hashes of file content, but at the same time makes moving working directories impossible (without some timestamp trickery). Good news is that the bulk of the processing should be freesurfer which will be reused if present in the output directory.