Nipype

What is Nipype?

What Nipype is not?

How do you typically use it?

Realign

realign = pe.Node(interface = spm.Realign(), name = "realign")

realign.inputs.register_to_mean = True

coregister = pe.Node(interface=spm.Coregister(), name = "coregister")

workflow = pe.Workflow(name="first_level_analysis")

workflow.connect(realign, "mean_image", coregister, "source")

smooth = pe.Node(interface=fs.Smooth(), name = "smooth")

smooth.inputs.surface_fwhm = 4

Node: gen_fa.bet.BET.fsl

========================

Hierarchy : gen_fa.bet

Exec ID : bet.a1

Original Inputs

---------------

* args : <undefined>

* center : <undefined>

* environ : {'FSLOUTPUTTYPE': 'NIFTI', 'DISPLAY': ':1'}

* frac : 0.34

* functional : <undefined>

* ignore_exception : False

* in_file : /mnt/data/nipype_examples/tbss_example/l1/gen_fa/eddy_correct/_subject_id_3313349/split/vol0000.nii

* mask : True

* mesh : <undefined>

* no_output : <undefined>

* out_file : <undefined>

* outline : <undefined>

* output_type : NIFTI

* padding : <undefined>

* radius : <undefined>

* reduce_bias : <undefined>

* remove_eyes : <undefined>

* robust : <undefined>

* skull : <undefined>

* surfaces : <undefined>

* t2_guided : <undefined>

* threshold : <undefined>

* vertical_gradient : <undefined>

Execution Inputs

----------------

* args : <undefined>

* center : <undefined>

* environ : {'FSLOUTPUTTYPE': 'NIFTI', 'DISPLAY': ':1'}

* frac : 0.34

* functional : <undefined>

* ignore_exception : False

* in_file : /mnt/data/nipype_examples/tbss_example/l1/gen_fa/eddy_correct/_subject_id_3313349/split/vol0000.nii

* mask : True

* mesh : <undefined>

* no_output : <undefined>

* out_file : <undefined>

* outline : <undefined>

* output_type : NIFTI

* padding : <undefined>

* radius : <undefined>

* reduce_bias : <undefined>

* remove_eyes : <undefined>

* robust : <undefined>

* skull : <undefined>

* surfaces : <undefined>

* t2_guided : <undefined>

* threshold : <undefined>

* vertical_gradient : <undefined>

Execution Outputs

-----------------

* mask_file : /mnt/data/nipype_examples/tbss_example/l1/gen_fa/_subject_id_3313349/bet/vol0000_brain_mask.nii

* meshfile : <undefined>

* out_file : /mnt/data/nipype_examples/tbss_example/l1/gen_fa/_subject_id_3313349/bet/vol0000_brain.nii

* outline_file : <undefined>

Runtime info

------------

* command : bet /mnt/data/nipype_examples/tbss_example/l1/gen_fa/eddy_correct/_subject_id_3313349/split/vol0000.nii /mnt/data/nipype_examples/tbss_example/l1/gen_fa/_subject_id_3313349/bet/vol0000_brain.nii -f 0.34 -m

* duration : 2.97426009178

* hostname : filolaptop

Terminal output

~~~~~~~~~~~~~~~

Environment

~~~~~~~~~~~

* COMPIZ_CONFIG_PROFILE : ubuntu

* DBUS_SESSION_BUS_ADDRESS : unix:abstract=/tmp/dbus-oGR4OCXmrw,guid=5c168e734effcc0d0ebb936000000036

* DEFAULTS_PATH : /usr/share/gconf/ubuntu.default.path

* DESKTOP_SESSION : ubuntu

* DISPLAY : :1

* DJANGO_SETTINGS_MODULE : nipype.settings

* ECLIPSE_HOME : /home/filo/opt/eclipse

* FREESURFER_HOME : ~/opt/freesurfer/

* FSLBROWSER : /etc/alternatives/x-www-browser

* FSLDIR : /usr/share/fsl/4.1

* FSLLOCKDIR :

* FSLMACHINELIST :

* FSLMULTIFILEQUIT : TRUE

* FSLOUTPUTTYPE : NIFTI

* FSLREMOTECALL :

* FSLTCLSH : /usr/bin/tclsh

* FSLWISH : /usr/bin/wish

* GDMSESSION : ubuntu

* GIO_LAUNCHED_DESKTOP_FILE : /usr/share/applications/eclipse.desktop

* GIO_LAUNCHED_DESKTOP_FILE_PID : 2010

* GNOME_DESKTOP_SESSION_ID : this-is-deprecated

* GNOME_KEYRING_CONTROL : /tmp/keyring-HeXpxG

* GNOME_KEYRING_PID : 1775

* GPG_AGENT_INFO : /tmp/keyring-HeXpxG/gpg:0:1

* GTK_MODULES : canberra-gtk-module:canberra-gtk-module

* HOME : /home/filo

* IBUS_ENABLE_SYNC_MODE : 1

* LANG : en_GB.UTF-8

* LANGUAGE : en_GB:en

* LC_COLLATE : en_GB.UTF-8

* LC_CTYPE : en_GB.UTF-8

* LC_MESSAGES : en_GB.UTF-8

* LD_LIBRARY_PATH : /usr/lib/fsl/4.1

* LIBGL_DRIVERS_PATH : /usr/lib/fglrx/dri:/usr/lib32/fglrx/dri

* LOGNAME : filo

* MANDATORY_PATH : /usr/share/gconf/ubuntu.mandatory.path

* PATH : /home/filo/bin/:/home/filo/opt/freesurfer/bin:/usr/lib/mrtrix/bin:/home/filo/opt/camino/bin:/usr/lib/lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/lib/fsl/4.1

* POSSUMDIR : /usr/share/fsl/4.1

* PWD : /home/filo

* PYDEV_COMPLETER_PYTHONPATH : /home/filo/opt/eclipse/plugins/org.python.pydev_2.4.0.2012020116/PySrc

* PYDEV_CONSOLE_ENCODING : UTF-8

* PYTHONIOENCODING : UTF-8

* PYTHONPATH : /home/filo/opt/eclipse/plugins/org.python.pydev_2.4.0.2012020116/PySrc/pydev_sitecustomize:/home/filo/workspace/nipype:/home/filo/workspace/nipy:/home/filo/workspace/nibabel:/home/filo/workspace/nipype:/home/filo/workspace/neuroutils/src:/usr/lib/python2.7:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/PIL:/usr/lib/python2.7/dist-packages/gst-0.10:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/ubuntu-sso-client:/usr/lib/python2.7/dist-packages/ubuntuone-client:/usr/lib/python2.7/dist-packages/ubuntuone-control-panel:/usr/lib/python2.7/dist-packages/ubuntuone-couch:/usr/lib/python2.7/dist-packages/ubuntuone-installer:/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol:/usr/lib/python2.7/dist-packages/wx-2.8-gtk2-unicode

* SESSION_MANAGER : local/filolaptop:@/tmp/.ICE-unix/1787,unix/filolaptop:/tmp/.ICE-unix/1787

* SHELL : /bin/bash

* SSH_AGENT_PID : 1825

* SSH_AUTH_SOCK : /tmp/keyring-HeXpxG/ssh

* SUBJECTS_DIR : .

* UBUNTU_MENUPROXY : 0

* USER : filo

* USERNAME : filo

* XAUTHORITY : /home/filo/.Xauthority

* XDG_CONFIG_DIRS : /etc/xdg/xdg-ubuntu:/etc/xdg

* XDG_CURRENT_DESKTOP : Unity

* XDG_DATA_DIRS : /usr/share/ubuntu:/usr/share/gnome:/usr/local/share/:/usr/share/

* XDG_SEAT_PATH : /org/freedesktop/DisplayManager/Seat0

* XDG_SESSION_COOKIE : 2a3add18f6300a18a2280d8a00000016-1329312824.439272-802333621

* XDG_SESSION_PATH : /org/freedesktop/DisplayManager/Session0

nipy.org/nipype

Portability and flexibility

Funding

Transparency

Acknowledgements

Automation and reuse

other

code

Neuroimaging data processing using Nipype

Part I: I had the same problems as you

Chris Gorgolewski

Matthew Brett

Michael Castelle

Philippe Ciuciu

Yann Cointepas

Mark D'Esposito

Susan Gabrieli

Brian Hawthorne

Tim Leslie

Fernando Perez

Tyler Perrachione

Jean-Baptiste Poline

Alexis Roche

Denis Riviere

Gretchen Reynolds

Jonathan Taylor

Bertrand Thirion

Bernjamin Thyreau

Mike Trumpis

Karl Young

Tom Waite

John Salvatore

Joerg Stadlerg

Julia Huntenburg

Karlo Hamalainen

Lijie Huan

Michael Hallquist

Michael Hanke

Michael Waskom

Oscar Esteban

Oliver Hinds

Rosalia Tungaraza

Satrajit Ghosh

Sami Andberg

Sharad Sikka

Stephan Gerhard

Thomas Nickson

Valentin Haenel

Xiangzhen Kong

Xu Wang

Yannick Schwartz

Yaroslav Halchenko

Alexandre Gramfort

Anisha Keshavan

Ariel Rokem

Arman Eshaghi

Basile Pinsard

Blake Davey

Charl Linssen

Chris Filo Gorgolewski

Christian Haselgrove

Christopher Burns

Cindee Madison

Colin Buchanan

Demian Wassermann

Daniel Ginsburg

Drew Erickson

Erik Ziegler

Fred Loney

Gael Varoquaux

Hans Johnson

Jarrod Millman

Jeff Lai

Max Planck Institute for Human Cognitive and Brain Sciences

Performance

Provenance

BIG Data

Part II: We came up with a solution

you might like

Human Connectome Project

ADHD200

Nathan Kline Institute Enhanced

ABIDE

FCON1000

An fMRI example - iterables

An fMRI example

An fMRI example - caching

Encapsulation and Reuse

An fMRI example - FreeSurfer

Efficient Execution

AFNI

• topological search on the dependency tree
• seamless multicore support
• SGE/Condor support == cluster execution ready

Seed

extract_timeseries = pe.Node(afni.Maskave(), name="extract_timeseries")

correlation_map = pe.Node(afni.Fim(), name="correlation_map")

wf.connect(extract_timeseries, "out_file", correlation_map, "ideal_file")

Smooth

smooth = pe.Node(interface=fs.Smooth(), name = "smooth")

smooth.inputs.surface_fwhm = 8

smooth = pe.Node(interface=spm.Smooth(), name = "smooth")

smooth.inputs.fwhm = 4

smooth = pe.Node(interface=fs.Smooth(), name = "smooth")

smooth.iterables = ('surface_fwhm', [4,6,8])

Realign

workflow = pe.Workflow(name="first_level_analysis")

workflow.connect(realign, "mean_image", coregister, "source")

Coregister

Normalize

realign = pe.Node(interface = spm.Realign(), name = "realign")

realign.inputs.register_to_mean = True

coregister = pe.Node(interface=spm.Coregister(), name = "coregister")

normalize = pe.Node(interface = spm.Normalize(), name = "normalize")

Reporting

Training new staff

Reproducible science

Sharing and discussing methods

Software build on top of Nipype

Brain Imaging Pipelines

THE END

C-PAC

to learn more see

Part III: The Bigger Picture

Testing

Open Science needs Open Source

Good coding practice

Part IV: Behind the scenes