niprov 0.1.post5

provenance for neuroimaging data

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')