75 lines
2.7 KiB
Text
75 lines
2.7 KiB
Text
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run 'datalad --version'
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run 'git config --global --add user.name "Adina Wagner"
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git config --global --add user.email "adina.wagner@t-online.de"'
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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 'echo "Contains functional data of one subject who underwent a localizer task" >> README.md'
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run 'datalad status'
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run 'datalad save -m "Add information on the dataset contents to the README"'
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run 'git log'
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run 'cd ../
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datalad clone https://github.com/psychoinformatics-de/studyforrest-data-phase2.git'
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run 'cd studyforrest-data-phase2
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ls'
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run '# print the size of the directory in human readable sizes
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du -sh'
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run 'datalad get sub-01/ses-localizer/func/sub-01_ses-localizer_task-objectcategories_run-*.nii.gz'
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run 'datalad drop sub-01/ses-localizer/func/sub-01_ses-localizer_task-objectcategories_run-4_bold.nii.gz'
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run 'datalad get sub-01/ses-localizer/func/sub-01_ses-localizer_task-objectcategories_run-4_bold.nii.gz'
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run 'cd ../bids-data'
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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/bids-data2.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 '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 '# in preparations of the next section, please run the following command!'
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run 'datalad clone ///adhd200/RawDataBIDS/Brown
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cd Brown
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datalad get .'
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run '#'
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