51 lines
1.7 KiB
Text
51 lines
1.7 KiB
Text
run 'datalad create -c text2git bids-data'
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run 'cd bids-data'
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run 'echo "# A BIDS structured dataset for my input data" > README.md'
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run 'datalad status'
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run 'datalad save -m "Add a short README"'
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run 'datalad clone --dataset . \
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https://github.com/datalad/example-dicom-functional.git \
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inputs/rawdata'
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run 'datalad clone -d . \
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https://github.com/ReproNim/containers.git \
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code/containers'
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run 'datalad containers-list --recursive'
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run 'datalad subdatasets'
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run 'datalad containers-run -m "Convert subject 02 to BIDS" \
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--container-name code/containers/repronim-reproin \
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--input inputs/rawdata/dicoms \
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--output sub-02 \
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"-f reproin -s 02 --bids -l '"'"''"'"' --minmeta -o . --files inputs/rawdata/dicoms"'
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run 'datalad diff -f HEAD~1'
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run 'git log -n 1'
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run 'datalad siblings add -d . \
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--name gin \
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--url git@gin.g-node.org:/adswa/bidsdata.git'
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run 'datalad siblings'
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run 'datalad push --to gin'
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run 'cd ../
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datalad create -c yoda myanalysis'
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run 'cd myanalysis'
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run 'tree'
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run 'datalad clone -d . \
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https://gin.g-node.org/adswa/bids-data \
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input'
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run 'datalad download-url -m "Download code for brain masking from Github" \
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-O code/get_brainmask.py \
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https://raw.githubusercontent.com/datalad-handbook/resources/master/get_brainmask.py'
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run 'datalad containers-add nilearn \
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--url shub://adswa/nilearn-container:latest \
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--call-fmt "singularity exec {img} {cmd}"'
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run 'datalad containers-run -m "Compute brain mask" \
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-n nilearn \
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--input input/sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz \
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--output figures/ \
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--output "sub-02*" \
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"python code/get_brainmask.py"'
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run 'git log sub-02_brain-mask.nii.gz'
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run 'datalad rerun'
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run '# done!'
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run '#'
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run 'Thanks for your attention!'
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