fmriprep_vincent_2020

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The fmriprep tutorial for COSN @2020 by Qing Wang (Vincent).

Commands for building fMRIPrep containers

sudo docker pull poldracklab/fmriprep:latest

sudo singularity build fmriprep_latest.simg docker://poldracklab/fmriprep:latest

Running fMRIPrep on local machine

Docker

sudo docker run -it -v host_bids_dir:/data:ro -v host_derivates_dir:/out poldracklab/fmriprep:latest /data /out --participant_label sub-0001

• You need to change "host_bids_dir" for your BIDS path on your machine, and \data is the BIDS path inside the container;
• You need to change "host_derivates_dir" for your output directory.

Singularity

singularity run --cleanenv -B host_bids_dir:/data:ro -B host_derivates_dir:/out fmriprep_latest.simg (singularity container) /data /out --participant_label sub-0001

• You need to change "host_bids_dir" for your BIDS path on your machine, and \data is the BIDS path inside the container;
• You need to change "host_derivates_dir" for your output directory.

Running fMRIPrep on slurm HPC (codes in /scripts)

fmriprep.sh

Prepare running env and submit job.

fmriprep.slurm

Scripts for running fMRIPrep in parallel.

fmriprep.format

Collect the results.

select_ses-2.json

Select specific input data (session 2 here for both T1 and bold images).