provenance for neuroimaging data
Project description
provenance for neuroimaging data
See the full online documentation (or pdf) and PyPi package.
To inspect image files, install nibabel,mne and/or pydicom.
A list with all provenance attributes collected can be found here.
Commandline Usage
Look for image files below the current directory, inspect them and store the obtained provenance metadata:
provenance discover .
Run a transformation command and log it as provenance for the new file:
provenance record mcflirt -in t1flip_all_orig -out t1all_reg -refvol 0
Alternatively, log the provenance after running the command:
provenance log 'motion correction' --new fmri-3dmc.nii --parent fmri.nii
Publish provenance of known files for subject ‘John Doe’ as an html file:
provenance report --subject "John Doe" --html
Python API
import niprov
niprov.discover('.')
analysispackage.correctmotion(input='JD-fmri.nii', output='JD-fmri-3dmc.nii')
niprov.log('JD-fmri.nii', 'motion correction', ['JD-fmri-3dmc.nii'])
niprov.record('mcflirt -in t1flip_all_orig -out t1all_reg -refvol 0')
files = niprov.report(forSubject='John Doe')
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