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4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1, 2013 ICC Chiba Color Experts’ Day 2013

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Page 1: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

4D-MRI Reconstruction of Thoracoabdominal Organs

Windra Swastika

Graduate School of Engineering, Chiba University, Japan

Feb 1, 2013

ICC Chiba Color Experts’ Day 2013

Page 2: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Outline

• Background

• Methodology

• Results

• Conclusion

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Page 3: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Background

• Understanding respiratory organ motion can be useful in many clinical applications: locating the tumors position in

radiotherapy planning, examining pulmonary diseases, analyzing some irregularities in

respiratory.

respiratory organ motion

However, to capture “real-time” 4D MRI using current MR Scanner is not possible. • Long acquisition time. • Image resolution problems. • Respiratory motion can cause noise/artifacts.

Time series 2D MRI

4D MRI

construct

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Page 4: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Background

• 4D MRI Reconstruction

Z

X

Y

n

1

4D MRI

2D MRI

*) Masuda, Y. Haneishi, H. “4D MR Imaging of Respiratory Organ Motion using Intersection Profile Method”. Proc of SPIE Vol. 7625, 2010.

4D MRI Reconstruction

• Done semi-automatically. • Total acquisition time per

person is about 30 minutes.

Some issues in 4D MRI reconstruction are:

What is needed are: Simplify 4D MRI using

statistical modeling. Automatic process and

reduce time acquisition. Faster acquisition time of

2D MRI using compressed sensing.

Reconstruction

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Page 5: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Methodology

Coordinate system

Navigator Slice (NS) Data Slice (DS)

Y

X x

Z

fnavi

fdata(yi)

fdata(y1)

fdata(y2)

fnavi fdata(yi)

Navigator Slice (NS ) (fnavi )

NS is time sequential 2D-MR images in sagittal plane which consists of several hundred frames that forms several respiratory patterns.

Data Slice (DS) (fdata (yi ))

DS is time sequential 2D-MR images in coronal plane. One set data slice consists of several slices along the y axis to cover 3D images volume.

DS are set along the Y axis and intersect with a single NS.

• fdata(yi) intersect with fnavi at location (x, yi). • One set of DS consists of several slices along the Y axis to

cover 3D images volume.

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2D Image acquisition

• NS is obtained first at certain X axis location, followed by DS acquisition at location yi1, 2, 3, …, n sequentially.

• The number of frame in NS, varies between 400, 800 and 1200 frames.

Page 6: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

STEP 1

Methodology

Determine the intersection location of NS and DS.

1. Extract Respiratory Patterns at NS

Generate n spatio-temporal patterns from fnavi(tns) at intersection location (yi1, 2, 3,

…, n), denoted as Snavi(yi)

STEP 2

y1 yn

y1

yn

STEP 3 Find respiratory patterns and set region of interest (ROI) based on the diaphragm boundary of all respiratory patterns found in Snavi(yi).

y1

yn

… … time

time

Z

Z

Z

Y 6

Spatio temporal patterns

time

Page 7: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Methodology 2. Find the best intersection

STEP 4 Generate a spatio-temporal patterns from each DS at intersection location.

Spatio-temporal generated from DS at certain y position

STEP 5 Find best normalized cross correlation (NCC) value between each respiratory patterns found in Snavi(yi) and Sdata(yi).

Find the best NCC value from all Y position. Calculate the geomean of all respiratory patterns found. The geomean for p-th pattern is expressed as:

STEP 6

7

NCC value

Page 8: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Methodology 3. Time reduction using threshold

Total time required to obtain DS

1 min

y1

y6

1 min

y24

1 min

24 min

Total time Calculate NCC

In many yi positions, the best NCC value can be found in the first one or two hundreds frame, as illustrated below.

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NCC value

Page 9: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Methodology 3. Time reduction using threshold

Fixed Threshold (FT) method

NCC

Skipped frames

* Threshold value

0.9 * * *

Threshold = average(first-three-peaks) *

Adaptive Threshold method

frame frame

NCC

1

0.5

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Page 10: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Results

• 4D MRI Reconstruction and volume rendering

The reconstructed 4D-MR images were visualized by a volume rendering technique implemented in Osirix

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Fixed Threshold Adaptive Threshold

Page 11: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Results

0.0 10.0 20.0 30.0 40.0 50.0 60.0 70.0 80.0

1 2 3 4 5 6

(

%)

Subject

FT(0.9) AT (a=1.02)

Percentage of time reduction

0.8

0.85

0.9

0.95

1

1 2 3 4 5 6

Ge

om

ean

Subject

w/o T

FT -0.9

AT (a=1.02)

Geomean (quality) of 4D-MRI reconstruction

By applying FT and AT approach, the total time acquisition can be reduced by 45% on average for FT approach and 47% on average for AT approach compared with w/o T approach. However, the trade-off of time reduction is the quality of 4D-MRI reconstruction – as seen in the graph above.

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Page 12: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Results

Displacement error in Z axis of 4D-MRI reconstruction

2

2.5

3

3.5

4

1 2 3 4 5 6

Ave

rage

err

or

(mm

)

Subject

w/o T FT AT (1.02)

The displacement error range of 6 subjects are 2.9-3.5mm, 3.0-3.6mm and 2.3-3.6mm for w/o T, FT and AT approach respectively. This error is thought to be a clinically acceptable error, because the typical size of tumors requiring treatment is on the order of tens of millimeters

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Page 13: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Conclusion

• 4D-MRI reconstruction using intersection profile method.

• Reduce time acquisition by applying fixed threshold (FT) and adaptive threshold (AT).

• Data acquisition can be reduced on average 45% (FT) and 47% (AT).

• The displacement error of Z position was 3.0-3.6mm (FT) and 2.3-3.6mm (AT), which is implementable for clinical application.

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Page 14: 4D-MRI Reconstruction of Thoracoabdominal Organs · 4D-MRI Reconstruction of Thoracoabdominal Organs Windra Swastika Graduate School of Engineering, Chiba University, Japan Feb 1,

Thank you for your attention

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