neurodatascience / tutorial_fMRIPrep_2020_vincent

The fMRIPrep tutorial for the ORIGAMI lab.

tutorial_fMRIPrep_2020_vincent

The fMRIPrep tutorial for the ORIGAMI lab. fMRIPrep link.

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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).

Resources

Official websites:

1. fMRIPrep and its github;
2. BIDS, BIDS App github and BIDS derivatives;
3. NeuroStars for more questions;
4. Compute Canada documentation.

Tutorials.

1. The Standford fMRIPrep tutorial;
2. Andrew's Brain Book with youtube videos;
3. DartBrains course chapter by Sasha Brietzke & Luke Chang;
4. Tutorials: BIDS, fMRIPrep, MRIQC by Saren Seeley;
5. Brainlife tutorials;
6. Neuroimaging Core Documentation by Dianne Patterson.