Adopting Datalad for collaboration

  • Created by Sebastien Tourbier - 2019 Jan 8

Move original BIDS dataset to server

rsync -P -v -avz -e 'ssh' --exclude 'derivatives' --exclude 'code' --exclude '.datalad' --exclude '.git' --exclude '.gitattributes' /media/localadmin/HagmannHDD/Seb/ds-newtest2/* tourbier@<SERVER_IP_ADDRESS>:/home/tourbier/Data/ds-newtest2

Datalad setup and dataset creation on Server (accessible via ssh)

Connect to server

ssh tourbier@<SERVER_IP_ADDRESS>

Install liblzma-dev (datalad pylzma depnendency) and Datalad

sudo apt-get install liblzma-dev
pip install datalad[all]
pip install datalad_containers
pip install datalad_neuroimaging
pip install datalad_revolution

Go to source dataset directory, create a Datalad dataset and save all

cd /home/tourbier/Data/ds-newtest2
datalad rev-create -f -D "Original test dataset on lab server"
datalad rev-save -m 'Source (Origin) BIDS dataset' --version-tag origin

Report on the state of dataset content

datalad rev-status --recursive

Processing using the Connectome Mapper BIDS App on a local workstation

Dataset installation

datalad install -s ssh://tourbier@<SERVER_IP_ADDRESS>:/home/tourbier/Data/ds-newtest2  \
/home/localadmin/Data/ds-newtest2

cd /home/localadmin/Data/ds-newtest2

Get T1w and Diffusion images to be processed, written in a bash script for reproducibility

datalad get -J 4 sub-*/ses-*/anat/sub-*_T1w.nii.gz
datalad get -J 4 sub-*/ses-*/dwi/sub-*_dwi.nii.gz
datalad get -J 4 sub-*/ses-*/dwi/sub-*_dwi.bvec
datalad get -J 4 sub-*/ses-*/dwi/sub-*_dwi.bval

Write datalad get commands to get_required_files_for_analysis.sh

::
mkdir code echo “datalad get -J 4 sub-/ses-/anat/sub-_T1w.nii.gz” > code/get_required_files_for_analysis.sh echo “datalad get -J 4 sub-/ses-/dwi/sub-*_dwi.nii.gz” >> code/get_required_files_for_analysis.sh echo “datalad get -J 4 sub-/ses-/dwi/sub-*_dwi.bvec” >> code/get_required_files_for_analysis.sh echo “datalad get -J 4 sub-/ses-*/dwi/sub-*_dwi.bval” >> code/get_required_files_for_analysis.sh

Add all content in the code/ directory directly to git

datalad add --to-git code

Add the container image of the connectome mapper to the dataset

datalad containers-add connectomemapper-bidsapp-{version-tag} \
--url dhub://sebastientourbier/connectomemapper-bidsapp:{version-tag} \
--update

Save the state of the dataset prior to analysis

datalad rev-save -m "Seb's test dataset on local \
workstation ready for analysis with connectomemapper-bidsapp:{version-tag}" \
--version-tag ready4analysis-<date>-<time>

Run Connectome Mapper on all subjects

datalad containers-run --container-name connectomemapper-bidsapp-{version-tag} \
'/tmp' '/tmp/derivatives' participant \
--anat_pipeline_config '/tmp/code/ref_anatomical_config.ini' \
--dwi_pipeline_config '/tmp/code/ref_diffusion_config.ini' \

Save the state

datalad rev-save -m "Seb's test dataset on local \
workstation processed by connectomemapper-bidsapp:{version-tag}, {Date/Time}" \
--version-tag processed-<date>-<time>

Report on the state of dataset content

datalad rev-status --recursive

With DataLad with don’t have to keep those inputs around – without losing the ability to reproduce an analysis. Let’s uninstall them – checking the size on disk before and after

datalad uninstall sub-*/*

Local collaboration with Bob for Electrical Source Imaging

Processed dataset installation on Bob’s workstation

datalad install -s (ssh://)localadmin@HOS51827:/home/localadmin/Data/ds-newtest2  \
/home/bob/Data/ds-newtest2

cd /home/bob/Data/ds-newtest2

Get connectome mapper output files (Brain Segmentation and Multi-scale Parcellation) used by Bob in his analysis

datalad get -J 4 derivatives/cmp/sub-*/ses-*/anat/sub-*_mask.nii.gz
datalad get -J 4 derivatives/cmp/sub-*/ses-*/anat/sub-*_class-*_dseg.nii.gz
datalad get -J 4 derivatives/cmp/sub-*/ses-*/anat/sub-*_scale*_atlas.nii.gz

Write datalad get commands to get_required_files_for_analysis_by_bob.sh for reproducibility

echo "datalad get -J 4 derivatives/cmp/sub-*/ses-*/anat/sub-*_mask.nii.gz" > code/get_required_files_for_analysis_by_bob.sh
echo "datalad get -J 4 derivatives/cmp/sub-*/ses-*/anat/sub-*_class-*_dseg.nii.gz" >> code/get_required_files_for_analysis_by_bob.sh
echo "datalad get -J 4 derivatives/cmp/sub-*/ses-*/anat/sub-*_scale*_atlas.nii.gz" >> code/get_required_files_for_analysis_by_bob.sh

Add all content in the code/ directory directly to git

datalad add --to-git code

Update derivatives

cd /home/bob/Data/ds-newtest2
mkdir derivatives/cartool ...

Save the state

datalad rev-save -m "Bob's test dataset on local \
workstation processed by cartool:{version-tag}, {Date/Time}" \
--version-tag processed-<date>-<time>

Report on the state of dataset content

datalad rev-status --recursive

With DataLad with don’t have to keep those inputs around – without losing the ability to reproduce an analysis. Let’s uninstall them – checking the size on disk before and after

datalad uninstall sub-*/*
datalad uninstall derivatives/cmp/*
datalad uninstall derivatives/freesurfer/*
datalad uninstall derivatives/nipype/*