accelerated dsi with compressed sensing using adaptive...
TRANSCRIPT
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Accelerated DSI with Compressed Sensing
using Adaptive Dictionaries
Berkin Bilgic1, Kawin Setsompop2,3, Julien Cohen-Adad4,
Van Wedeen2,3, Lawrence L. Wald2,3,5, Elfar Adalsteinsson1,5
1 MIT
2 Martinos Center for Biomedical Imaging
3 Harvard Medical School
4 Ecole Polytechnique de Montreal
5 Harvard-MIT Division of Health Sciences and Technology
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Diffusion Spectrum Imaging (DSI)
DSI offers detailed information on complex distributions of
intravoxel fiber orientations
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Diffusion Spectrum Imaging (DSI)
DSI offers detailed information on complex distributions of
intravoxel fiber orientations
And results in magnitude representation of the full q-space
![Page 4: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/4.jpg)
Diffusion Spectrum Imaging (DSI)
DSI offers detailed information on complex distributions of
intravoxel fiber orientations
And results in magnitude representation of the full q-space
Q-space of a single voxel
515 directions
Probability Density Function (pdf)
of a single voxel
DFT
Sampling full q-space takes ~1 hour x
y
z
![Page 5: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/5.jpg)
Undersampled DSI
To reduce scan time, undersample q-space
Use sparsity prior to reconstruct the pdfs [1]
Undersampled q-space
of a single voxel
CS
1. Menzel MI et al MRM 2011
undersampled
DFT pdf q-samples wavelet total variation
𝑚𝑖𝑛𝒑 𝐅Ω𝒑 − 𝒒 22+ 𝛼 ∙ 𝚿𝒑 1 + 𝛽 ∙ TV(𝒑)
x
y
z
Probability Density Function (pdf)
of a single voxel
![Page 6: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/6.jpg)
i. fix D and solve for sparse X using OMP
ii. update D and X using SVD based technique
Step2: Use dictionary to impose sparsity constraint
K-SVD algorithm for DSI
Is pdf sparse in TV and wavelet?
Use a transform tailored for sparse representation of pdfs
Step1: Create dictionary from a training pdf dataset [P]
𝑚𝑖𝑛𝐏,𝐃 𝒙𝑖 0 subject to 𝐏 − 𝐃𝐗 𝐹2≤ 𝜖
𝑖
1. Aharon M, et al IEEE Trans Signal Processing 2006
𝑚𝑖𝑛 𝒙 1 such that 𝐅Ω𝐃𝒙 = 𝒒
2. Gorodnitsky IF, et al IEEE Trans Signal processing 1997
K-SVD[1] iterative algorithm was used to obtain [D]
FOCUSS[2] was used to provide parameter free recon
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Methods
3 healthy volunteers, 3T Siemens Skyra
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Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients†, 64-chan head coil [1]
1. Keil B, et al MRM 2012
† MAGNETOM Skyra CONNECTOM
system (Siemens Healthcare)
Gmax = 300 mT / m
Conventional = 45 mT / m
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Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients, 64-chan head coil [1]
2.3 mm isotropic, bmax = 8000 s/mm2
1. Keil B, et al MRM 2012
![Page 10: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/10.jpg)
Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients, 64-chan head coil [1]
2.3 mm isotropic, bmax = 8000 s/mm2
515 q-space points, 50 min scan time
1. Keil B, et al MRM 2012
![Page 11: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/11.jpg)
Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients, 64-chan head coil [1]
2.3 mm isotropic, bmax = 8000 s/mm2
515 q-space points, 50 min scan time
One dictionary trained with data from each subject
Recon experiments at accelerations R = 3, 5 and 9
1. Keil B, et al MRM 2012
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Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients, 64-chan head coil [1]
2.3 mm isotropic, bmax = 8000 s/mm2
515 q-space points, 50 min scan time
One dictionary trained with data from each subject
Recon experiments at accelerations R = 3, 5 and 9
Comparison of methods:
i. Wavelet + TV (Menzel et al [2])
ii. L1-FOCUSS (apply L1 penalty on pdfs)
iii. Dictionary-FOCUSS (proposed)
2. Menzel MI et al MRM 2011
1. Keil B, et al MRM 2012
![Page 13: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/13.jpg)
Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients, 64-chan head coil [1]
2.3 mm isotropic, bmax = 8000 s/mm2
515 q-space points, 50 min scan time
10 average collected at 5 q-space points
Low-noise data, serve as ground truth
2. Menzel MI et al MRM 2011
1. Keil B, et al MRM 2012
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Methods
3 healthy volunteers, 3T Siemens Skyra
Connectom gradients, 64-chan head coil [1]
2.3 mm isotropic, bmax = 8000 s/mm2
515 q-space points, 50 min scan time
10 average collected at 5 q-space points
Low-noise data, serve as ground truth
Tractography comparison:
Fully-sampled vs. R = 3 Dictionary-FOCUSS
Fractional Anisotropy compared for 18 major fiber bundles
2. Menzel MI et al MRM 2011
1. Keil B, et al MRM 2012
![Page 15: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/15.jpg)
Subject A, pdf reconstruction error Slice 40
15.8% RMSE
Wavelet+TV
15.0% RMSE
𝓵𝟏-FOCUSS
Acceleration
R = 3
20%
0%
Wav+TV @ R=3 15.8% error
𝓵𝟏-FOCUSS @ R=3 15.0% error
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Subject A, pdf reconstruction error Slice 40
15.8% RMSE
Wavelet+TV
15.0% RMSE
𝓵𝟏-FOCUSS
Acceleration
R = 3
20%
0%
20%
0%
Trained on
subject A
7.8% RMSE
Trained on
subject B
7.8% RMSE 8.2% RMSE
Trained on
subject C
Dictionary-FOCUSS
Wav+TV @ R=3 15.8% error
𝓵𝟏-FOCUSS @ R=3 15.0% error
Dictionary @ R=3 7.8% error
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Subject A, pdf reconstruction error Slice 40
15.8% RMSE
Wavelet+TV
15.0% RMSE
𝓵𝟏-FOCUSS
Acceleration
R = 3
20%
0%
20%
0%
Trained on
subject A
7.8% RMSE
Trained on
subject B
7.8% RMSE 8.2% RMSE
Trained on
subject C
Dictionary-FOCUSS
Acceleration
R = 5
20%
0% 8.9% RMSE 8.9% RMSE 9.3% RMSE
Wav+TV @ R=3 15.8% error
𝓵𝟏-FOCUSS @ R=3 15.0% error
Dictionary @ R=3 7.8% error
Dictionary @ R=5 8.9% error
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Subject A, pdf reconstruction error Slice 40
15.8% RMSE
Wavelet+TV
15.0% RMSE
𝓵𝟏-FOCUSS
Acceleration
R = 3
20%
0%
20%
0%
Trained on
subject A
7.8% RMSE
Trained on
subject B
7.8% RMSE 8.2% RMSE
Trained on
subject C
Dictionary-FOCUSS
8.9% RMSE 8.9% RMSE 9.3% RMSE
Acceleration
R = 5
20%
0%
10.0% RMSE 10.0% RMSE 10.4% RMSE
20%
0%
Acceleration
R = 9
Wav+TV @ R=3 15.8% error
𝓵𝟏-FOCUSS @ R=3 15.0% error
Dictionary @ R=3 7.8% error
Dictionary @ R=5 8.9% error
Dictionary @ R=9 10.0% error
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Subject A, pdf reconstruction error Slice 40
15.8% RMSE
Wavelet+TV
15.0% RMSE
𝓵𝟏-FOCUSS
Acceleration
R = 3
20%
0%
10%
0%
Trained on
subject A
7.8% RMSE
Trained on
subject B
7.8% RMSE 8.2% RMSE
Trained on
subject C
Dictionary-FOCUSS
8.9% RMSE 8.9% RMSE 9.3% RMSE
Acceleration
R = 5
12%
0%
10.0% RMSE 10.0% RMSE 10.4% RMSE
13%
0%
Acceleration
R = 9
Wav+TV @ R=3 15.8% error
𝓵𝟏-FOCUSS @ R=3 15.0% error
Dictionary @ R=3 7.8% error
Dictionary @ R=5 8.9% error
Dictionary @ R=9 10.0% error
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q=[5,0,0]
Missing q-space directions
` %
RM
SE
in q
-space
q-space reconstructions at q=[5,0,0]
Fully-sampled
1 average
Dict-FOCUSS 𝓁1-FOCUSS Wavelet+TV
increasing |q|
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q-space reconstructions at q=[5,0,0]
Fully-sampled
10 average
Dict-FOCUSS 𝓁1-FOCUSS Wavelet+TV
q=[5,0,0]
Missing q-space directions
` %
RM
SE
in q
-space
increasing |q|
![Page 22: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/22.jpg)
q-space reconstructions at q=[5,0,0]
Fully-sampled
10 average
Dict-FOCUSS 𝓁1-FOCUSS Wavelet+TV
same 𝓁2 norm as 10 average
poor performance good
performance
q=[5,0,0]
Missing q-space directions
` %
RM
SE
in q
-space
increasing |q|
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SNR drops substantially at the outer q-space
RMSE computed relative to 1 average fully-sampled data
includes noise and recon error
To isolate recon error, collected 10 avg on 5 q-space points
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SNR drops substantially at the outer q-space
RMSE computed relative to 1 average fully-sampled data
includes noise and recon error
q = [5,0,0]
1 avg fully-sampled 10 avg fully-sampled
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SNR drops substantially at the outer q-space
RMSE computed relative to 1 average fully-sampled data
includes noise and recon error
Lower RMSE than
acquired data
Denoising effect [1]
1. Patel V, et al ISBI 2011, p1805
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Tractography solutions for subject A
SLFP
FMAJ
FMIN
CST
CCG
ATR
Fully-sampled data Dictionary-FOCUSS recon
with 3-fold acceleration
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Tractography solutions for subject A
Avera
ge F
A
R=1 R=3
1. Yendiki A et al
Front Neuroinform 2011
SLFP FMAJ
FMIN
CST
CCG
ATR
Fully-sampled data Dictionary-FOCUSS recon with 3-fold acceleration
Average Fractional Anisotropy
for 18 labeled white-matter pathways [1]
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Avera
ge F
A
R=1 R=3
Tractography solutions for subject A
SLFP FMAJ
FMIN
CST
CCG
ATR
Fully-sampled data Dictionary-FOCUSS recon with 3-fold acceleration
Mean FA error = 3%
1. Yendiki A et al
Front Neuroinform 2011
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Concluding Remarks
Up to 2-times RMSE reduction in pdf domain
Dictionary-FOCUSS (proposed) vs. Wavelet+TV [1]
1. Menzel MI et al MRM 2011
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Concluding Remarks
Up to 2-times RMSE reduction in pdf domain
Dictionary-FOCUSS (proposed) vs. Wavelet+TV [1]
3-fold accelerated Dict-FOCUSS ≈ Fully-sampled data
Low-noise 10 average data validation
Tractography comparison
1. Menzel MI et al MRM 2011
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Concluding Remarks
Up to 2-times RMSE reduction in pdf domain
Dictionary-FOCUSS (proposed) vs. Wavelet+TV [1]
3-fold accelerated Dict-FOCUSS ≈ Fully-sampled data
Parallel imaging with Simultaneous Multi-Slice (SMS) [2]
3-fold acceleration with minor loss in SNR
Orthogonal to CS, 3×3 = 9-fold acceleration combined
1. Menzel MI et al MRM 2011
2. Setsompop K et al MRM 2012
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Concluding Remarks
Up to 2-times RMSE reduction in pdf domain
Dictionary-FOCUSS (proposed) vs. Wavelet+TV [1]
3-fold accelerated Dict-FOCUSS ≈ Fully-sampled data
Dictionary from single slice seems to generalizes to other slices
and to other subjects
1. Menzel MI et al MRM 2011
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Concluding Remarks
Voxel-by-voxel recon
Dictionary-FOCUSS: 12 sec / voxel
Wavelet+TV: 27 sec / voxel in Matlab
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Concluding Remarks
Voxel-by-voxel recon
Dictionary-FOCUSS: 12 sec / voxel
Wavelet+TV: 27 sec / voxel in Matlab
Full-brain processing: DAYS of computation time
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Concluding Remarks
Voxel-by-voxel recon
Dictionary-FOCUSS: 12 sec / voxel
Wavelet+TV: 27 sec / voxel in Matlab
Full-brain processing: DAYS of computation time
Do dictionaries generalize across healthy–patient populations?
across different age groups?
![Page 36: Accelerated DSI with Compressed Sensing using Adaptive ...martinos.org/~berkin/Bilgic_MICCAI_DSI_talk_2012.pdfAccelerated DSI with Compressed Sensing using Adaptive Dictionaries Berkin](https://reader035.vdocument.in/reader035/viewer/2022081613/5fb39d417ab04453ea09f812/html5/thumbnails/36.jpg)
Concluding Remarks
Voxel-by-voxel recon
Dictionary-FOCUSS: 12 sec / voxel
Wavelet+TV: 27 sec / voxel in Matlab
Full-brain processing: DAYS of computation time
Do dictionaries generalize across healthy–patient populations?
Matlab code online at:
http://web.mit.edu/berkin/www/software.html
across different age groups?
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Acknowledgments
Thanks to:
Itthi Chatnuntawech
Kawin Setsompop
Stephen Cauley
Julien Cohen-Adad
Anastasia Yendiki
Lawrence Wald
Elfar Adalsteinsson
Sponsors:
MIT-CIMIT Medical Engineering
Fellowship
Siemens Healthcare
Siemens-MIT Alliance
Grants:
K99EB012107, U01MH093765,
R01EB006847, R01EB007942,
R01EB000790, P41RR14075