Add ica-aroma to an existing fmriprep output directory

fmriprep

#1

I have run fmriprep using the below udocker command, without the ica-aroma switch, and I am curious if I were to re-execute the command with the “–use-aroma” switch if it would recompute/overwrite everything in the existing output/fmriprep directory, or if there is a simple way to add the ica-aroma to the existing files. Of course, I could run ica-aroma outside of fmriprep, but I suspect this route would be less integrated with the rest of the fmriprep results.

Best,
Scott

udocker run -v /path/to/bids:/input
-v /path/to/bids/derivatives:/output
-v /path/to/freesurfer-6.0.1/freesurfer:/myfsdir
poldracklab/fmriprep:latest
/input /output participant --participant-label 7536262 --fs-license-file /myfsdir/license.txt --fs-no-reconall


#2

The recomputation will be triggered if you use a new working directory. I think by default it is set to current working directory which might not be mounted to a local directory in udocker (if it works the same way as docker). You can, however, specify working directory with -w switch to point to a local directory to avoid such issues in the future.