Install datalad & others in a virtual environment
virtualenv -p python3.8 env
source env/bin/activate
pip install datalad datalad-neuroimaging datalad-container
Get fmriprep (make sure singualrity is installed)
datalad containers-add fmriprep --url docker://nipreps/fmriprep:20.2.0
Run fmriprep
input_dir=`pwd`/raw
output_dir=`pwd`/fmriprep
participant_label=01
freesurfer_licence=~/Dropbox/Softwares/Freesurfer/License/license_1.txt
datalad containers-run -m "fmriprep 01" \
--container-name fmriprep \
--input ${input_dir} \
--output ${output_dir} \
fmriprep $input_dir ${output_dir} participant \
--participant-label ${participant_label} \
-w /tmp --fs-license-file ${freesurfer_licence} \
--output-spaces T1w:res-native MNI152NLin2009cAsym:res-native