Julien Cohen-Adad, PhD Assistant Professor Institute of

Spine Hack
2014-05-16 Milan, Italy
Spinal Cord Toolbox
Julien Cohen-Adad, PhD
Assistant Professor
Institute of Biomedical Engineering, Polytechnique Montreal
Functional Neuroimaging Unit, CRIUGM, Université de Montréal
Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s inside the toolbox?
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s inside the toolbox?
MNI-Poly-AMU template and atlas of the spinal cord
T2-weighted template
Probabilistic structure
Montreal
Neurological
Institute
Polytechnique
Montreal
White matter atlas
white matter
C1
0
1
C3
gray matter
Aix-Marseille
University
C5
0
1
cerebrospinal fluid
T1
spinothalamic
spinocerebellar
corticospinal
cuneatus
gracilis
Fonov, IRMSM’13 #1119 ; Fonov ISMRM’14 #1713 ; Taso ISMRM’14 #1710 ; Benhamou ISMRM’14 #13 ;
Cohen-Adad ISMRM’14 #1727 ; Cohen-Adad OHBM’14
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s inside the toolbox?
Advanced registration tools
• Registration of multi-
modal data to template
• Non-rigid diffeomorphic
deformation (SyN) [1]
• Label-based (e.g., C2, T3)
• Robust registration
using pre-segmentation
1 Avants, Med
Image Anal 2008
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s inside the toolbox?
Robust, Fast & Automatic Segmentation
Automatically
detects a point in
the spinal cord
Initialization of mesh and
iterative progagation
.
De Leener, Neuroimage (in press)
De Leener, SPIE 2014 (in press)
De Leener, OHBM 2014 (accepted)
Benjamin De
Leener
T2-weighted
T1-weighted
30s later
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s inside the toolbox?
Automatic vertebrae detection
•
•
Uses centerline and detection of intervertebral disks
High robustness (100%) and accuracy (2mm) thanks to
probabilistic constraints
C1
C2
C3
C4
C5
C6
C7
T1
T2
T3
T4
T5
T6
spinal level?
T7
T8
T9
T10
T11
T12
Ullmann, Int J Biomed Imaging (accepted)
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s inside the toolbox?
Predicting nerve root location
Manual identification of
nerve rootlets in 0.6mm
T2w images (N=22)
Establish predictive
model based on
morphological features
spinal
levels
C3
C3
C4
C4
C5
C5
C6
C6
C7
C7
C8
T1
T1
neck height
C2
probability (x10-3)
vertebral
levels
Map spinal and vertebral
locations relative to
pontomedullary junction (PMJ)
distance from PMJ (mm)
nerve rootlet location
relative to PMJ
Accuracy = 3 mm (versus 20 mm
for current method)
Cadotte, ISMRM’14 #1719
D. Cadotte, M. Fehlings (Univ. Toronto) 7
Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
What’s really inside the toolbox?
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Content of SpinalCordToolbox
Organization
compiled binaries
template, atlas
python, bash scripts
testing scripts for each function
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Content of SpinalCordToolbox
Functions
non-rigid deformation
register to template
segment spinal cord (PropSeg)
quantify metric
in pathways
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Applications
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Applications
Mapping axon diameter in humans
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•
5 subjects
•
•
•
•
•
64ch head/spine coil
Tanguy Duval
left
rubrospinal right
rubrospinal left
3T MRI with 300 mT/m
gradients (connectom scanner)
AxCaliber protocol
Eddy + motion correction
Registration to template
Quantification of axon diameter
and density within specific tracts
Duval, ISMRM’14 #99
C1
C2
C3
C4
Larry Wald (MGH Martinos Center)
6 µm
2 µm
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Applications
Multi-center DTI study
•
•
•
3 sites
5 subjects per site
Two MRI brands (Philips, Siemens)
London
Vanderbilt
Montreal
Left
Right
Template
R
FA
b=0
A
L
P
FA
Atlas
0.1
Cohen-Adad, ISMRM’14 #1727
0.9
Claudia Wheeler-Kingshott (UCL Institute of Neurology)
Seth Smith (Vanderbilt University)
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Cohen-Adad et al.
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Where to get the toolbox?
•
Freely available at:
http://sourceforge.net/projects/spinalcordtoolbox
•
•
•
•
Release date (v1.0): 2014-06-15
Documentation, Support (Wiki, Forum)
Open source (git)
Dependent software
•
•
•
Python
FSL
ANTs (install from github!)
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OS used by spinal cord community
N=39
21%
56%
23%
OSX
Windows
Linux
Number of Matlab users: 28
Number of Python users: 5
Number of FSL users: 22
Number of SPM users: 18
Number of AFNI users: 4
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References
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•
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•
•
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Fonov, IRMSM 2013:1119
Fonov, ISMRM 2014:1713
Taso, ISMRM 2014:1710
Benhamou, ISMRM 2014:13
Cadotte, ISMRM 2014:1719
Cohen-Adad, ISMRM 2014:1727
Cohen-Adad, OHBM 2014
De Leener, Neuroimage 2014 DOI: 10.1016/j.neuroimage.2014.04.051
Duval, ISMRM 2014:0099
Ullmann, Int J Biomed Imaging (in press)
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Main contributors
Collaborators
Julien Cohen-Adad
Louis Collins
Habib Benali
Wheeler-Kingshott
Benjamin De Leener
Marc Benhamou
Vladimir Fonov
PF Pradat
Torben Schneider
Tanguy Duval
Geoffrey Lévêque
Simon Lévy
Eugénie Ullmann
JF Pelletier Paquette
William Thong
Julien Touati
Raju Karun
Michael Fehlings
David Cadotte
Seth Smith
Virginie Callot
Manuel Taso
Arnaud Le Troter
M. Sdika (CREATIS)
Larry Wald
Julien Doyon
Kawin Setsompop
Pierre Rainville
Funding sources:
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Cohen-Adad et al.
http://sourceforge.net/projects/spinalcordtoolbox
Check out the book!
Quantitative
MRI of the
Spinal Cord
Edited by
Julien Cohen-Adad
Cl audia A. M. Wheeler-Kingshot t
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