expert.opts are being written to the root directory

[chrisgorgo]

Summary

expert.opts file is being written to the root directory which is not writable under singularity.
See https://neurostars.org/t/singularity-fmriprep-export-opts-error/1491 for more details.

[effigies]

At a first glance, this is probably related to previous attempts to properly set the working directory for Nodes.

[oesteban]

nipype/nipype/interfaces/freesurfer/preprocess.py

Line 1317 in 6ca791d

expert_fname = os.path.abspath('expert.opts')

[effigies]

Related: #2368.

[effigies]

Okay, it looks like interface.cmdline is called before the working directory is entered.

Also afterwards, but for some reason the running command is the one generated outside.

Probably the big problem is that it's all a massive hack to turn what should be runtime flags into a file. Maybe we should have gone with the "ExpertOptions" interface (260a275). Anyway, I'll see if there's any plausible way to have cmdline not drop a file in the CWD, whatever that happens to be.

[effigies]

Actually, my mistake. The correct command is being run, the problem is just that cmdline dumps a file wherever it happens to be, and we call node.interface.cmdline before running the node for logging purposes.

[oesteban]

Good catch