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provenance for neuroimaging data

Project description

provenance for neuroimaging data

Pypi Build Docs Coverage DOI

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')

Project details


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Files for niprov, version 0.1.post7
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Filename, size niprov-0.1.post7.tar.gz (29.7 kB) File type Source Python version None Upload date Hashes View

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