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ukbb_scripts

This repository holds all scripts to preprocess ukbb using ctb-pbellec tape server and rrg-jacquese (or def-jacquese) allocation.

First time setup

Pre-requirements

Before moving on, you need to make sure of few things.

First you will need to connect to the server (for example beluga) and then go into your home.

ssh $USER@beluga.computecanada.ca

Check that git is correctly configured, and deactivate the environment

git config --global user.name "GITHUB_USER"
git config --global user.email "GITHUB_MAIL@example.com"
deactivate

You should also be able to connect to github passwordless:

ssh -T git@github.com

Finally double check that you have the following line in your ~/.bashrc file:

source /project/def-pbellec/share/data_admin/etc/bashrc

If that is not the case, you can add it, and log-out, log-in so it takes effect:

echo "source /project/def-pbellec/share/data_admin/etc/bashrc" >> ~/.bashrc
exit
ssh $USER@beluga.computecanada.ca

Environment

  1. Clone this repo in your HPC HOME
git clone https://github.com/ccna-biomarkers/ukbb_scripts.git ~/ukbb_scripts
  1. Create a virtual environment that will be used to initialize ukbb-bids with datalad
module load python/3.8
mkdir ~/.virtualenvs
python3 -m venv ~/.virtualenvs/datalad-ukbb
source ~/.virtualenvs/datalad-ukbb/bin/activate
python3 -m pip install -r $HOME/ukbb_scripts/requirements.txt
deactivate
  1. To use ukbfetch with pre-downloaded data, install the surrogate file
ln -s $HOME/ukbb_scripts/ukbfetch_surrogate.sh $HOME/.virtualenvs/datalad-ukbb/bin/ukbfetch
  1. Install the ukbb dataset layout
mkdir -p $SCRATCH/datasets
git clone https://github.com/ccna-biomarkers/ukbb-preprocess-template.git $SCRATCH/datasets/ukbb
  1. Install the timeserie extraction tool in your home.
module load python/3.8
python3 -m venv ~/.virtualenvs/ts_extraction
source ~/.virtualenvs/ts_extraction/bin/activate
git clone https://github.com/ccna-biomarkers/ccna_ts_extraction.git ~/ccna_ts_extraction
python3 -m pip install -r ccna_ts_extraction/requirements.txt
deactivate

Data

  1. (if needed) Download ukbb zip files using ukbbfetch utility

Note

If you have access to the rrg-jacquese allocation on beluga, the data was already downloaded on beluga with ukbbfetch. The anatomical data is at ~/projects/rrg-jacquese/All_user_common_folder/RAW_DATA/UKBIOBANK-DATA/UKBIOBANK_IMAGING/UKB_MRI_download/UKB_T1w and the functionnal data at ~/projects/rrg-jacquese/All_user_common_folder/RAW_DATA/UKBIOBANK-DATA/UKBIOBANK_IMAGING/UKB_MRI_download/UKB_rfMRI.

  1. Create a directory $SCRATCH/ukbb_zip_files and move all the zip archives in it.

  2. Download all templates needed by fmriprep:

python3 -c "from templateflow.api import get; get(['MNI152NLin2009cAsym', 'MNI152NLin6Asym', 'OASIS30ANTs', 'MNIPediatricAsym', 'MNIInfant'])"
  1. Get the segmented difumo atlas in your $SCRATCH avalaible on beluga.
mkdir -p ${SCRATCH}/atlases
scp beluga.computecanada.ca:/nearline/ctb-pbellec/atlases/segmented_difumo_atlases_2022-02-03.tar.gz $SCRATCH/atlases/
tar -zxvf $SCRATCH/atlases/segmented_difumo_atlases_2022-02-03.tar.gz -C ${SCRATCH}/atlases
scp -r ${SCRATCH}/atlases/segmented_difumo_atlases/* ${SCRATCH}/atlases && rm -r ${SCRATCH}/atlases/segmented_difumo_atlases && rm $SCRATCH/atlases/segmented_difumo_atlases_2022-02-03.tar.gz
  1. Make sure you have the freesurfer license by following those instructions.

Usage

Launching preprocessing job

Submit a preprocessing job for one participant PARTICIPANT_ID with:

mkdir -p ${SCRATCH}/.slurm
PARTICIPANT_ID=xxx
sbatch --account=rrg-abc --job-name=fmriprep_ukbb_${PARTICIPANT_ID}_%j.job --mail-user="xxx@xxx.com" --output=/scratch/%u/.slurm/fmriprep_ukbb_${PARTICIPANT_ID}_%j.out --error=/scratch/%u/.slurm/fmriprep_ukbb_${PARTICIPANT_ID}_%j.err ${HOME}/ukbb_scripts/fmriprep-slurm_ukbb.bash ${PARTICIPANT_ID}

Using your jobid, the preprocessing logs will be available at /scratch/$USER/.slurm/fmriprep_ukbb_${PARTICIPANT_ID}_${jobid}.err and /scratch/$USER/.slurm/fmriprep_ukbb_${PARTICIPANT_ID}_${jobid}.out.

Sharing

After preprocessing, all the data will be availble at $SCRATCH/datasets/ukbb. The preprocessing outputs is archived at /nearline/ctb-pbellec/preprocessed_data/ukbb* and raw data is at /nearline/ctb-pbellec/datasets/ukbb.

To download the data, you will manually copy into the desired system. For example if you need to QC the data you can:

scp -r /nearline/ctb-pbellec/preprocessed_data/ukbb.qc /PATH/TO/MY/DIR
cd /PATH/TO/MY/DIR/ukbb.qc
find . -name "*.tar.gz" -exec bash -c 'tar -xzvf "$0" -C "${0%/*}"; rm "$0"' {} \;