applied neurodebian: python in...

http://www.pymvpa.org

http://neuro.debian.net

Applied NeuroDebian: Python in Neuroimaging

Yaroslav O. Halchenko

Dartmouth College, USA

Munich, Germany 2012

YOH (Dartmouth) Python & NeuroDebian Munich, Germany 2012 1 / 20

YOH (Dartmouth) NeuroDebian Munich, Germany 2012 2 / 20

The Vision

We (society) have the software platform. . .

that works on all devices, operating systems, . . .that is guaranteed to be available for as long as we want,wherever we wantthat we can freely share with anyonethat makes manual maintenance trivial, or superfluousso all software is available in a single environmentso we can share our experience with colleaguesso we can share data processing workflows easilyso developers can focus their scarce resources


How do we get there?

Role modelOrigin of most active software distributionsVast archive of maintained software(≈30000 binary packages) – provenproceduresSelf-governed, “do-ocracy”, no need toearn money, going strong for 20 years

We . . .Adopt standards and proceduresParticipate in the Debian project andintegrate all research softwareBenefit from the work of thousandsof additional developersCall it , add fancy logo


NeuroDebian from a researcher’s perspective

Install simple editor

apt-get install gedit

Install complex MRI analysis package

apt-get install fsl

Install software collection for psycho-physics

apt-get install science-psychophysics

Keep the whole system up-to-date

apt-get upgrade


NeuroDebian (http://neuro.debian.net)after X years and the contributions of many people:



Python in Neuroimaging (http://www.nipy.org)


http://www.nipy.org

Python in NeuroImaging

Find the community @ http://www.nipy.org

Stimuli Delivery

PsychoPyhttp://www.psychopy.org

PsychoPy is an easy, precise, platform-independent pack-age for stimulus presentation. Suitable for psychophysics,neuroimaging, and all areas of psychology.∙ Huge variety of stimuli generated in real-time∙ Cross-platform – run the same script on Linux, Win or

OS X∙ Flexible stimulus units (degrees, cm, or pixels)∙ Coder interface for those that like to program∙ Builder interface for those that don’t∙ Input from keyboard, mouse, joystick or button boxes∙ Multi-monitor support∙ Automated monitor calibration (supported photometers)

OpenSesamehttp://www.cogsci.nl/software/opensesame

OpenSesame is a graphical experiment builder for the socialsciences.∙ A comprehensive and intuitive graphical user interface∙ WYSIWYG drawing tools for creating visual stimuli∙ Cross-platform∙ Python scripting for complex tasks∙ A plug-in framework∙ Compatibility (through plug-ins) with commonly used

devices: (e.g. Eyelink eye trackers, serial responseboxes, Mantra object tracker)

∙ Compatibility with popular Python libraries: PsychoPy,PyGame, PyOpenGL, etc.

Data I/O

NiBabelhttp://nipy.org/nibabel

Nibabel provides read and write access to some commonmedical and neuroimaging file formats, including: ANA-LYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, aswell as PAR/REC. NiBabel is the successor of PyNIfTI.The various image format classes give full or selective ac-cess to header (meta) information and access to the imagedata is made available via NumPy arrays.

Analysis

BrainVISAhttp://brainvisa.info

BrainVISA is an open-source, modular and customizablesoftware platform built to host heterogeneous tools ded-

icated to neuroimaging research. It aims at helping re-searchers in developing new neuroimaging tools, sharingdata and distributing their software.∙ Databasing capabilities∙ Massive computation facilities using Soma-workflow∙ Open environment, with many toolboxes∙ Specialized toolboxes for T1 MRI processing, sulci ang

gyri morphometry, diffusion imaging and fibers tracking,surfacic and structural analysis, 3D histology. . .

∙ Links with other software like SPM, FSL, FreeSurfer, orCIVET

D. Geffroy, D. Rivière, I. Denghien, N. Souedet, S. Laguitton,and Y. Cointepas. BrainVISA: a complete software platform forneuroimaging. In Python in Neuroscience workshop, Paris, Aug.2011.

DiPyhttp://nipy.org/dipy

Dipy is an international FOSS project for diffusion mag-netic resonance imaging analysis. Dipy is multiplatformand will run under any standard operating system such asWindows, Linux, Mac OS X. Some of our state-of-the-artapplications are:∙ Reconstruction algorithms e.g. GQI, DTI∙ Tractography generation algorithms e.g. EuDX∙ Intelligent downsampling of tracks∙ Ultra fast tractography clustering∙ Resampling datasets with anisotropic voxels to isotropic∙ Visualizing multiple brains simultaneously∙ Finding track correspondence between different brains∙ Warping tractographies into another (e.g. MNI) space∙ Support of various file formats e.g. Trackvis or NIfTI




Stimuli Delivery








Data I/O



Analysis










http://goo.gl/DXZXB http://github.com/nipy/nipy-artwork

http://goo.gl/DXZXB

http://github.com/nipy/nipy-artwork


PsychoPy is an easy, precise, platform-independentpackage for stimulus presentation. Suitable forpsychophysics, neuroimaging, and all areas of psychology.

Huge variety of stimuli generated in real-timeCross-platform – run the same script on Linux, Win or OS XFlexible stimulus units (degrees, cm, or pixels)Coder interface for those that like to programBuilder interface for those that don’tInput from keyboard, mouse, joystick or button boxesMulti-monitor supportAutomated monitor calibration (supported photometers)


http://www.psychopy.org

PsychoPy: Builderhttp://www.psychopy.org


http://www.psychopy.org


NiBabel (successor of PyNIfTI) provides read and writeaccess to some common medical and neuroimaging formats:

ANALYZE (plain, SPM99, SPM2)GIFTINIfTI1MINCPAR/RECFreesurfer volume/surface/spec

The various image format classes give full or selective access toheader (meta) information and access to the image data is madeavailable via NumPy arrays.Handy tools...


http://nipy.org/nibabel

http://niftilib.sourceforge.net/pynifti/

http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm

http://www.nitrc.org/projects/gifti

http://nifti.nimh.nih.gov/nifti-1/

http://wiki.bic.mni.mcgill.ca/index.php/MINC

http://surfer.nmr.mgh.harvard.edu

NiBabel: Handy toolshttp://nipy.org/nibabel

nib-dicomfs :FUSE filesystem on top of a directory with DICOMs

nib-ls :ls for neuroimaging data files


http://nipy.org/nibabel

NiPyhttp://nipy.org/nipy

NIPY provides a rich suite of algorithms for pre-processing andanalysis of neuroimaging data

General linear model (GLM) statistical analysisCombined slice time correction and motion correctionGeneral image registration routines with flexible cost functions,optimizers and resampling schemesImage segmentationBasic visualization of results in 2D and 3DBasic time series diagnosticsClustering and activation pattern analysis across subjectsReproducibility analysis for group studies


http://nipy.org/nipy

Nipypehttp://nipy.org/nipype

Nipype allows you tointeract with tools from different software packages (SPM, FSL,FreeSurfer,Camino, AFNI, Slicer)combine processing steps from different packagesdevelop new workflows faster by reusing common steps from oldonesprocess data faster by running in parallelmake your research easily reproducibleshare your processing workflows with the community


http://nipy.org/nipype

Nipypehttp://nipy.org/nipype


http://nipy.org/nipype

PyMVPAhttp://www.pymvpa.org

PyMVPA eases statistical learning analyses(or otherwise called Multivariate pattern analysis, MVPA) of largedatasets, with an accent on neuroimaging.

Easy I/O to Neuroimaging data (via NiBabel)Variety of machine learning methods (e.g. SVM, SMLR, kNN)Uniform interfaces to other toolkits (e.g. MDP, Shogun,Scikit-learn)Flexible Searchlight-ingUber-Fast GNB/M1NN Searchlight-ingHyperalignment (Haxby et al 2011, Neuron)




PyMVPAhttp://www.pymvpa.org

Σ

S1S2S3S4S5S6S7S8S9

S0

Time (ms)

Unit #42 sensitivities 4-4

31

21

ANOVAI-RELIEFSMLRlinGPRlinCSVM

time (s)

.2 .4

-0.1

0.1

0.2 NormalizedSensitivityPz

21

EEG

fMRI

ECR

Classifier

FeatureSensitivity

FeatureSelection

FeatureNormalization

LOC, in

f.

TOFC

LOC, s

up.

Lingu

al G.

Front

al Po

le

Occ. P

ole

Angula

r G.

Hesch

l's G

.

.04

.08

.12 L1-normed sensitivities

SMLR-weightsANOVA




PySurferhttp://pysurfer.github.com

PySurfer is a module for visualization and interaction with corticalsurface representations of neuroimaging data from Freesurfer.


http://pysurfer.github.com



Stimuli Delivery








Data I/O



Analysis










http://goo.gl/DXZXB http://github.com/nipy/nipy-artwork

http://goo.gl/DXZXB

http://github.com/nipy/nipy-artwork

Acknowledgements

Michael Hanke

FOSS developers ofPython, NumPy, SciPy,Matplotlib, H5Py, Rpy,

Nipy, nibabel, ...Inkscape, ...

Debian Community

James V. HaxbyStephen J. Hanson

INCF

Dr. Yaroslav O. HalchenkoDartmouth College, NH, [email protected]

about the slides:should become available at http://neuro.debian.netc© 2012 Yaroslav O. Halchenko & artwork authors,

snake-brain c© 2010 Arno Kleinslide style inspired by Stefano Zacchiroli

CC BY-SA 3.0 — Creative Commons Attribution-ShareAlike 3.0


[email protected]


http://creativecommons.org/licenses/by-sa/3.0/

OS market share

Windows (W)

Mac OS X (M)

Debian basedRed Hat based

GNU/Linux (L)

Other OS

< 50%> 50%

Operating systems

Usage time

Always

Never

VirtualHost

VirtualGuest

Personal

Managed

A) B)

0#

Rep

ort

ed

com

bin

ati

on

s1

05

Proportion of participants

0 20 40 60 80 100%

MWL

Pers

on

al O

S

Managed OS

LW

MV

irtu

al h

ost

OS

Virtual guest OS

LW

M

L W M

L W M

Hanke & Halchenko, 2011, Front. Neuroinf.YOH (Dartmouth) NeuroDebian Munich, Germany 2012 19 / 20

NeuroDebian Paper

Halchenko & Hanke, 2012, Front. Neuroinf.YOH (Dartmouth) NeuroDebian Munich, Germany 2012 20 / 20

applied neurodebian: python in...

Documents