neurohackweek/niprov-nhw16

Name: niprov-nhw16

Owner: neurohackweek

Description: Neurohackweek 2016 niprov "slides"

Created: 2016-09-08 21:52:46.0

Updated: 2016-09-08 21:52:46.0

Pushed: 2016-09-08 21:54:06.0

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README

Niprov

Neurohackweek 2016

Jasper J.F. van den Bosch

Slides at neurohackweek.github.com/niprov-nhw16

Setup python environment

ualenv env
ce env/bin/activate
install -U pip

Download sample data

 https://github.com/ilogue/niprov/archive/master.zip
p master.zip
iprov-master

Install Niprov

install niprov

Optional packages

install -r optional.txt # pydicom nibabel mne matplotlib

Why niprov?

• reproducibility
• need story, metadata of brain images
• provenance: history, origin of a file
• NeuroImaging Provenance

Commandline API

enance -h
enance discover ./testdata
enance export
enance export --file testdata/parrec/T1.PAR
enance record "parrec2nii testdata/parrec/T1.PAR" --parent testdata/parrec/T1.PAR --new T1.nii
enance record "mcflirt -in T1.nii -out T1_reg.nii.gz"
enance export --file T1_reg.nii.gz

Web browser

enance serve

Python API

 niprov import ProvenanceContext
enance = ProvenanceContext()

image in provenance.get().bySubject('05aug14test'):
image.viewSnapshot() 

ke sure two files were acquired with the same parameters:
.compare(img2).assertEqual()

Configuration

iprov.cfg ~/niprov.cfg
t ~/niprov.cfg