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.