NA-MIC - Contrasting Tractography Method

Conference

Utah/UNC results

Sylvain GouttardGuido Gerig

Casey Goodlett

Santa Fe,October 1st & 2nd 2007

Overview

Processing description: DWI to tensors

ROIs

Tracking

Bundling / cleaning

Results: Fiber tracked

FA/MD analysis

Conclusion

Original Data

High resolution DWI with 59 images (8 B0's and 51 directions)

size 256*256*81 resolution 0.9,0.9,1.7

Tensor field

Tensor estimation using dtiestim:- Linear least square- B0 threshold = 500

ROIs

5 ROIs: Arcuate

Cingulum

Fornix

Internal Capsule

Uncinate Original ROIs not appropriate for our tractography tool

(need volumetric ROIs) Had to specify target and source labels Split right and left

ROIs - Arcuate

No editing

ROIs - Cingulum

Original ROIs Edited ROIs

ROIs – Fornix

Original ROIs Edited ROIs

ROIs – Internal Capsule

Original ROIs

Edited ROIs

ROIs - UncinateOriginal ROIs Edited ROIs

Fiber tracking

Fiber tracking done with the FiberTracking

tool, based on Susumu Mori's tool.

Input: tensor field & ROI

Output: Streamlines

Parameters:

min FA threshold 0.15

angle of max dev 0.35

Post processing – FiberViewer Clustering and cleaning

bundle cleaning via clustering: Metrics for clustering:

fiber length

center of mass

Hausdorff

Fiber cutting

Post processing - FiberViewerDiffusion statistics

Diffusion statistics for each bundle: Definition of coordinate origin FA

MD

λ 1,2,3diffusion val.

geodesic distance

0 +L-L

Specifications

Computational resources:

2 Intel Xeon processors 2GHz

2G of RAM

linux

Average execution time per case:

DWI -> tensors: <1min

Tractography: 2 < t < 10 min

Cleaning: 2 < t < 5 min (manual interaction)

Results – High resolution cases 10 cases (dim:256*256*81 res:0.9,0.9,1.7) 5 ROIs (Arcuate, Cingulate, Fornix, Int. Capsule, Uncinate)

Arcuate

0

20

40

60

80

100

120

140

# of Fiber - Arcuate

ROI

# fi

be

rs

Cingulate

0

50

100

150

200

250

300

350

# of Fiber - Cingulum

ROI

# fi

be

rs

Fornix

0

10

20

30

40

50

60

70

80

90

# of Fiber - Fornix

ROI

# fi

be

rsInternalCapsule

0

200

400

600

800

1000

1200

1400

1600

1800

2000

# of Fiber - Internal Capsule

ROI

# fi

be

rs

Uncinate

0

100

200

300

400

500

600

700

# of Fiber - Uncinate

ROI

# fi

be

rs

D00917D00920D00924D00925D00928D00935D00936D00938D00939

D00940

We use the number of streamlines for comparison but know that it is limited

Fiber tracking example

D00925 ; Internal capsule 19 fibers

D00935 ; Internal capsule 740 fibers

D00935 cleaned ; Internal capsule ; 545 fibers

Fiber tracking example

D00920 ; Arcuate ; 29 fibers D00928 ; Arcuate ; 99 fibers

Fiber tracking example

D00925

Cingulum

2 fibers

D00917 ; Cingulum ; 175 fibers D00917 cleaned ; Cingulum ; 170 fibers

Fiber tracking example

D00925 ; Fornix ; 3 fibers D00928 ; Fornix ; 77 fibers

Fiber tracking example

D00936

Uncinate

1 fibers

D00935 ; Uncinate ; 140 fibers D00935 cleaned ; Uncinate ; 100 fibers

Resulting data structure

Origin plane manually placedArc-length parameterization Diffusion values along fibers (FA, MD, λ's,GA) in excel format

FA-MD plots - Cingulum

FAMD

0.0

0.8615

0

FA-MD plots - Fornix

FAMD

0.0

0.7540

0

Analysis:

- 1 branch at a time?

- 2 at the same time?

FA-MD plots – Internal capsule

FAMD

0.0

0.7515

0

FA-MD plots - Uncinate

FAMD

0.0

0.8015

0

Evaluation of preprocessing

2 cases with: Orignal data (dim:256*256*81 res:0.9,0.9,1.7) Eddy current correction (dim:256*256*81 res:0.9,0.9,1.7) Eddy current correction and sub sampled (dim:144*144*81

res:1.6,1.6,1.7)

Original Dataset Corrected Dataset Corrected-subsampled dataset

ROIs D00925 D00935 D00925 D00935 D00925 D00935Arcuate L 20 11 0 0 13 4

Arcuate R 16 10 0 0 4 3

Cingulum L 5 144 0 0 38 166

Cingulum R 2 165 0 0 105 92

Fornix 3 8 0 4 3 46

InternalCapsule L 19 740 22 842 54 691

InternalCapsule R 143 679 305 963 210 740

Uncinate L 435 140 564 190 25 76

Uncinate R 190 216 283 275 53 52

# of fibers

Evaluation of preprocessing

Tensors filtered using MedINRIA tensor smoothing

=> Inconsistent results

Internal Capsule: - Not filtered => 59 fib - Filtered => 179 fib

Cingulum: - Not filtered => ~140 fib - Filtered => 0 fib

Examples:

Summary / Problems

ROIs: need redrawing to do tractography with our

tools

Noise level seems high w.r.t. to streamline tracking

High variability across cases =>

subject specific?

scanning artefacts?

motion? distortion?

...

ROIs D00928 D00936Arcuate 129 12

Cingulum 209 58Fornix 77 11

InternalCapsule 1855 376Uncinate 382 110

Summary / Problems (2)

Coordinate system inconsistency: ROIs are individually placed FiberViewer: origin plane manually set for

statistics

Metric for comparison: number of fibers: does not describe quality

High resolution casesPercentage of fibers (with Left and Right)

0

5

10

15

20

25

30

35

40

45

50

Percentage of fibers over all the fibers per ROI

D00917D00920D00924D00925D00928D00935D00936D00938D00939D00949

High resolution casesFiber tracked numbers

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate L 6 29 18 20 99 11 2 0 16 16

Arcuate R 24 11 74 16 30 10 10 0 27 7

Cingulum L 175 35 108 5 32 144 21 7 10 8

Cingulum R 55 2 96 2 177 165 37 2 7 77

Fornix 29 7 9 3 77 8 11 5 15 42

InternalCapsule L 600 64 385 19 663 740 116 199 727 334

InternalCapsule R 678 250 1094 143 1192 679 260 1021 381 459

Uncinate L 315 172 109 435 102 140 1 332 171 190

Uncinate R 298 303 112 190 280 216 109 265 302 278

Percentage

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate L 2.76 13.36 8.29 9.22 45.62 5.07 0.92 0 7.37 7.37

Arcuate R 11.48 5.26 35.41 7.66 14.35 4.78 4.78 0 12.92 3.35

Cingulum L 32.11 6.42 19.82 0.92 5.87 26.42 3.85 1.28 1.83 1.47

Cingulum R 8.87 0.32 15.48 0.32 28.55 26.61 5.97 0.32 1.13 12.42

Fornix 14.08 3.4 4.37 1.46 37.38 3.88 5.34 2.43 7.28 20.39

InternalCapsule L 15.6 1.66 10.01 0.49 17.23 19.24 3.02 5.17 18.9 8.68

InternalCapsule R 11.01 4.06 17.77 2.32 19.36 11.03 4.22 16.58 6.19 7.45

Uncinate L 16.01 8.74 5.54 22.11 5.19 7.12 0.05 16.88 8.69 9.66

Uncinate R 12.66 12.88 4.76 8.07 11.9 9.18 4.63 11.26 12.83 11.81

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate 30 40 92 36 129 21 12 0 43 23

Cingulum 230 37 204 7 209 309 58 9 17 85

Fornix 29 7 9 3 77 8 11 5 15 42

InternalCapsule 1278 314 1479 162 1855 1419 376 1220 1108 793

Uncinate 613 475 221 625 382 356 110 597 473 468

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate 7.04% 9.39% 21.60% 8.45% 30.28% 4.93% 2.82% 0.00% 10.09% 5.40%

Cingulum 19.74% 3.18% 17.51% 0.60% 17.94% 26.52% 4.98% 0.77% 1.46% 7.30%

Fornix 14.08% 3.40% 4.37% 1.46% 37.38% 3.88% 5.34% 2.43% 7.28% 20.39%

InternalCapsule 12.77% 3.14% 14.78% 1.62% 18.54% 14.18% 3.76% 12.20% 11.08% 7.93%

Uncinate 14.19% 11.00% 5.12% 14.47% 8.84% 8.24% 2.55% 13.82% 10.95% 10.83%

High resolution casesFiber cleaned numbers

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate L 6 29 18 20 99 11 2 0 16 16

Arcuate R 24 11 74 16 30 10 10 0 27 7

Cingulum L 176 35 106 0 32 144 21 0 0 0

Cingulum R 50 0 79 0 177 165 37 0 0 77

Fornix 29 0 9 0 77 0 0 0 15 0

InternalCapsule L 346 61 292 19 362 549 101 108 463 158

InternalCapsule R 394 169 780 104 648 428 167 625 357 368

Uncinate L 133 89 75 269 63 114 0 93 92 75

Uncinate R 202 108 46 79 159 72 5 105 180 149

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate L 2.76% 13.36% 8.29% 9.22% 45.62% 5.07% 0.92% 0.00% 7.37% 7.37%

Arcuate R 11.48% 5.26% 35.41% 7.66% 14.35% 4.78% 4.78% 0.00% 12.92% 3.35%

Cingulum L 34.24% 6.81% 20.62% 0.00% 6.23% 28.02% 4.09% 0.00% 0.00% 0.00%

Cingulum R 8.55% 0.00% 13.50% 0.00% 30.26% 28.21% 6.32% 0.00% 0.00% 13.16%

Fornix 22.31% 0.00% 6.92% 0.00% 59.23% 0.00% 0.00% 0.00% 11.54% 0.00%

InternalCapsule L 14.07% 2.48% 11.87% 0.77% 14.72% 22.33% 4.11% 4.39% 18.83% 6.43%

InternalCapsule R 9.75% 4.18% 19.31% 2.57% 16.04% 10.59% 4.13% 15.47% 8.84% 9.11%

Uncinate L 13.26% 8.87% 7.48% 26.82% 6.28% 11.37% 0.00% 9.27% 9.17% 7.48%

Uncinate R 18.28% 9.77% 4.16% 7.15% 14.39% 6.52% 0.45% 9.50% 16.29% 13.48%

Left and Right together

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate 30 40 92 36 129 21 12 0 43 23

Cingulum 226 35 185 0 209 309 58 0 0 77

Fornix 29 0 9 0 77 0 0 0 15 0

InternalCapsule 740 230 1072 123 1010 977 268 733 820 526

Uncinate 335 197 121 348 222 186 5 198 272 224

ROIs D00917 D00920 D00924 D00925 D00928 D00935 D00936 D00938 D00939 D00940Arcuate 7.04% 9.39% 21.60% 8.45% 30.28% 4.93% 2.82% 0.00% 10.09% 5.40%

Cingulum 20.56% 3.18% 16.83% 0.00% 19.02% 28.12% 5.28% 0.00% 0.00% 7.01%

Fornix 22.31% 0.00% 6.92% 0.00% 59.23% 0.00% 0.00% 0.00% 11.54% 0.00%

InternalCapsule 11.39% 3.54% 16.49% 1.89% 15.54% 15.03% 4.12% 11.28% 12.62% 8.09%

Uncinate 15.89% 9.35% 5.74% 16.51% 10.53% 8.82% 0.24% 9.39% 12.90% 10.63%

ResultsHigh resolution cases after cleaning

Arcuate

0

20

40

60

80

100

120

140

# of Fiber - Arcuate

ROI

# fi

be

rs

Cingulate

0

50

100

150

200

250

300

350

# of Fiber - Cingulum

ROI

# fi

be

rs

Fornix

0

10

20

30

40

50

60

70

80

90

# of Fiber - Fornix

ROI

# fi

be

rsInternalCapsule

0

200

400

600

800

1000

1200

# of Fiber - Internal Capsule

ROI

# fi

be

rs

Uncinate

0

50

100

150

200

250

300

350

400

# of Fiber - Uncinate

ROI

# fi

be

rs

D00917D00920D00924D00925D00928D00935D00936D00938D00939

D00940

Results – High resolution cases 10 cases (dim:256*256*81 res:0.9,0.9,1.7) 5 ROIs (Arcuate, Cingulate, Fornix, Int. Capsule, Uncinate)

Arcuate Cingulum Fornix InternalCapsule Uncinate

0

200

400

600

800

1000

1200

1400

1600

1800

2000

Number of fiber tracked

D00917

D00920

D00924

D00925

D00928

D00935

D00936

D00938

D00939

D00949

Case ID

# of

fib

ers

Arcuate Cingulum Fornix InternalCapsule Uncinate0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

Percentage of fiber tracked for each ROI

D00917

D00920

D00924

D00925

D00928

D00935

D00936

D00938

D00939

D00949

ROI

% o

f fib o

f th

e s

am

e R

OI

ResultsHigh resolution cases after cleaning

Arcuate Cingulum Fornix InternalCapsule Uncinate

0

200

400

600

800

1000

1200

Number of fibers after cleaning

D00917

D00920

D00924

D00925

D00928

D00935

D00936

D00938

D00939

D00949

ROI

# o

f fibers

Arcuate Cingulum Fornix InternalCapsule Uncinate

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

Percentage of each fiber bundle cleaned

D00917

D00920

D00924

D00925

D00928

D00935

D00936

D00938

D00939

D00949

ROI

% o

f fi

b o

f th

e s

am

e R

OI