Hi, silly question here. My fMRIprep run on a large number of subjects did fine, except for one participant’s surface reconstruction which is taking too many days (due to a «XL defect» spotted by mris_fix_topology).
What would be a good/preferred way to stop that participant’s preprocessing and have the reports produced? I could not find it out by reading the documentation.
This is an interesting challenge. If you just press Ctrl-C you will probably close FMRIPREP without generating the report at all. What you need to do is to terminate (kill) the process that is taking too long. This should lead FMRIPREP to generate a partial report. If you are using singularity or native installation you can use ps or top to find the process for mris_fix_topology and terminate it using kill. Alternatively you can try to kill all such processses with killall -9 mris_fix_topology. If you are usin Docker you will have to attach to a running container to run those commands.
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