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invernizzi_tutorial_..
Tutorial: matplotlib
Intr
odu
ctio
n
•
Fare clic per modificare stili del testo dello schema
Secondo
livello
Dynamic
phase-contrast
(PC) MRI is being used for quantitation of
Terzo
livelloand flow in many clinical applications.
pulsatile
motion
Quarto livello
In order to achieve accurate and consistent flow measurements, a
Quinto livello
reliable automated method for segmentation of the lumen region is
needed.
The difference in temporal information from pixels located in the
lumen and in the surrounding tissue is used as a segmentation
Criterion. (Alperin and Lee 2004)
Alg
orit
hm
des
crip
tion
The
•
automated
Fare clic per
procedure
modificare
includes
stili del
four
testo
steps:
dello schema
Secondo
livello
1) selecting
a reference
velocity waveform
Terzo livello
2) generating
CC map
Quarto livello
3) computing optimal CC threshold
Quinto livello
4) tracking the edge of the segmented region
Alg
orit
hm
des
crip
tion
•
1)
Fare
selecting
clic per
a modificare
reference velocity
stili del testo dello schema
Secondo
waveform
livello
livello
PhaseTerzo
contrast
image with location of the
Quarto
livello
reference
waveform
Quinto livello
2) generating CC map
The CC coefficient is used to quantify
similarity between the reference
waveform and waveforms obtained
from other pixels in the image
Alg
orit
hm
des
crip
tion
3)
• computing
Fare clic optimal
per modificare
CC threshold
stili del testo dello schema
Secondo
A histogram
oflivello
number of pixels with
Terzo livello
CC value
livello for different
aboveQuarto
the threshold
Quinto
livello
threshold
values
is
generated.
The optimal threshold CC value is
selected at the point
of transition from region C to region B
Alg
orit
hm
des
crip
tion
4) tracking
Fare
clic per
the
modificare
edge of the
stili del testo dello schema
Secondo livello
segmented
region
Terzo livello
Region-growing
algorithm is applied
Quarto
in orderlivello
to obtain a
Quinto
livello image based on
segmentated
similarity threshold value
criterion.
•
if C(xy)>threshold OK
Imp
lem
ent
atio
n
Use IPython for interactive processing analysis
Fare
stili
del (loadtxt
testo dellofunction)
schema
Load clic
dataper
filemodificare
into numpy
array
Secondo livello
Visualize temporal data (imshow function) and choose time
Terzo livello
reference image.
Quarto livello
•
Apply
rectangular selection to select a sub-region of interest.
Quintoalivello
(RectangleSelector)
•
Choose a pixel inside the lumen area (picker event)
•
Plot the waveform of selected pixel and of the surrounding
ones (using subplot)
•
Compute CC matrix and plot CC histogram (bar)
•
Track the edge of the segmented region and show it (imshow)
•
Plot the 3d-surface and animate it through time
(plot_surface and animation)
•
••
•
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