Computational Environment for
Radiotherapy Research
CERR 3.0 beta 1
- Getting Started -
Outline
• To give an overview of various features in
CERR 3.0 beta 1
• Intended Audience
– New CERR users
– CERR 2.6 users
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Features that are discussed here
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F1: Conversion from RTOG/DICOM to .mat file format
F2: Review Imported Plan
F3: View CT scans, doses and contours
F4: Colorwash / isodose dose display
F5: Dose-volume and Dose-surface histogram analysis
F6: Contouring/re-contouring tools
F7: Simultaneous Contouring / Zooming tool
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Features that are discussed here
(Contd.)
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F8: 3-D viewing of contours and dose
F9: Thumbnail CT navigation tool
F10: IMRT Dose Calculation
F11: Dose / CT profile plots
F12: Dose metric comparison and subtraction tools
F13: Merge Plans
F14: Make doses/scans remote
F15: Easy programmable access to all data
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F1 - Conversion of RTOG format treatment
planning archives or DICOM-RT into the
Matlab-readable CERR format.
RTOG or DICOM
Formats can be
imported here
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F2 - Review the imported plans
Review RTOG or
DICOM imported
plans here
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F3 - A transverse/sagittal/coronal slice
viewing program for reviewing contours, CT
scans, and dose distributions.
Use View to
toggle between
Scan, Structures
and Dose or all.
The main CERR viewer window
can display transverse, sagittal
and coronal images
simultaneously with or without
transparency. Plane locators
show where each view is located
with respect to the others. The
dynamic color bar allows for easy
cutoff and rescaling of the colors
used for dose display.
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F4 - Colorwash, transparent colorwash or
isodose line dose display
Toggle between
Isodose and
Colorwash dose
display
Dose distributions can
be displayed using
isodose lines, a
transparent colorwash,
or an opaque colorwash
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F4 - Colorwash, transparent colorwash or
isodose line dose display (Contd.)
Set Dose
Transparency
Dose distributions can
be displayed using
isodose lines, a
transparent colorwash,
or an opaque colorwash
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F5 - Dose-volume and Dose-surface
histogram analysis
DVH analysis
DVHs and DSHs can
be calculated and
displayed with both
absolute and relative
vol/surf area. Dx and
Vx values can be read
easily from the
extended information
panel on the right.
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F6 - Contouring/re-contouring tools
Drawing and
Editing Contours
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F7 – Simultaneous Contouring /
Zooming tool
New Contours can
be drawn by hitting
the create button.
Use mouse leftclick to draw the
contour and use
mouse double-click
to close the contour
Contouring and
Zooming can be done
simultaneously.
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F7 – Simultaneous Contouring /
Zooming tool (Contd.)
Hitting Zoom Mode
button enters the
zoom-in, zoom-out
mode.
When this feature is
used while drawing a
contour, use shift+left
mouse click to zoomin and right mouseclick to zoom-out.
When this feature is
used alone, use left
mouse click or shift+
left mouse click to
zoom-in and right
mouse-click to zoomout.
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F7 – Simultaneous Contouring /
Zooming tool (Contd.)
Hitting Zoom Mode
button enters the
zoom-in, zoom-out
mode.
Right-clicking within
the Zoom Mode gives
zoom-out options
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F8 - 3-D viewing of contours and dose
Type 3d on the
CERR command
line and hit ‘return’
key
The 3D viewer can
display structure
volumes and isodose
surfaces with
transparency
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F8 - 3-D viewing of contours and dose
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F9 - Thumbnail CT navigation tool
Navigation montage pops –
up when a plan is reviewed. It
can be turned on/off in the
CERROptions. For multiple
CT scans, the required
montage can be chosen from
‘scan’ drop-down menu.
The navigation montage is
clickable and responds to arrow
keys. It can also mark every slice
where user specified structures
exist, and can bookmark slices
for easy access.
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F10: IMRT Dose Calculation
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F11 - Dose / CT profile plots
Right click on
any view and
choose
Dose/CT
Profile to go
into this mode
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F11 - Dose / CT profile plots (Contd.)
• Click and drag
into a view to
create a line along
which dose/CT
profile is to be
generated.
• Also, the
difference between
various doses can
be plotted by
selecting a base
dose (displayed in
bold letters).
•The range to be
displayed can be
selected by sliding
these triangles.
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F12 - Dose metric comparison and
subtraction tools
Use this for Dose
metric comparison
The graphical
comparison tool is an
easy way to visually
compare multiple dose
distributions. Different
metrics are applied over
each dose distribution
and the results are
shown in bar graph
format. A composite
score is calculated for
each dose based on
user-selected weights
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F12 - Dose metric comparison and
subtraction tools (Contd.)
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F13 - Merge Plans
After 1st plan has
been loaded,
select ‘Merge
Plans’ from the
‘File’ drop-down
menu.
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F13 - Merge Plans (Contd.)
-The ‘Merge Plan’
GUI will pop-up.
- Hit the Browse
button to locate the
plan to merge.
- After selecting
the plan to merge,
wait for all the
fields in GUI to
populate. This may
take a few
seconds.
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F13 - Merge Plans (Contd.)
- Figure shows
how the ‘Merge
Plan’ GUI will look
after selecting the
plan to be merged.
- Now select the
scan, doses and
structures you
want to merge and
hit ‘Merge’.
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F13 - Merge Plans (Contd.)
- How to look at two different plans ?
- Before we learn
how to look at two
different plans, we
need to know how
to switch between
various layouts.
- Select ‘Panel
Layout’ from ‘View’
drop-down menu
and select the
layout you want.
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F13 - Merge Plans (Contd.)
- How to look at two different plans ?
- You can rightclick on the view
(axis) you want to
display / change
your view.
-As shown in
figure, you can
switch between
transverse,
sagittal, coronal
views.
-These plans use
the same colorbar.
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F13 - Merge Plans (Contd.)
- How to look at two different plans ?
- You can rightclick on the view
(axis) you want to
display/change
your view.
- As shown in
figure, you can
switch between
various scans.
- Similarly, you can
switch between
various doses and
structures.
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F13 - Merge Plans (Contd.)
- How to look at two different plans ?
-You can also
switch between
various plans
using the scan
drop-down menu.
- Note that a new
navigation
Montage pops-up
every time you
switch between
plans using this
feature.
- Similarly you can
switch between
various doses
using the dose
drop-down menu
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F14 - Make doses / scans remote
Dose Management
can be accessed
from Dose dropdown menu
- In order to keep
RAM usage in check,
you can store the
doses / scans on
hard disk instead of
RAM.
- If a remote
dose/scan is chosen,
it is automatically
made available to
RAM and then
displayed
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F14 - Make doses / scans remote (Contd.)
• Choose “Use Disk” to
make the selected dose
remote. The dose is
now stored in the same
directory as the plan in
tarball zipped format
within the subdirectory
PlanName_store.tgz.
To increase efficiency,
save this plan and the
*_store.tgz files so that
these doses/scans are
remote even the next
time when the plan is
loaded.
• As is obvious, the
other features are to
compress a dose, save
a dose in .mat format to
a selected location and
delete a dose.
Dose Management
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F14 - Make doses / scans remote (Contd.)
Scan Management
• Scan Management can be
accessed from “Scan” pulldown menu.
• Choose “Use Disk” to
make the selected scan
remote. The scan is now
stored in the same
directory as the plan in
tarball zipped format within
the subdirectory
PlanName_store.tgz. To
increase efficiency, save
this plan and the
*_store.tgz files so that
these doses/scans are
remote even the next time
when the plan is loaded.
• As is obvious, the other
features are to compress a
scan and save a scan in
.mat format to a selected
location
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F15 - Easy programmable access
to all data
• The data in a CERR
plan is easily
accessible from the
Matlab prompt
through the planC
object.
• The indices of
various fileds of the
structure planC are
stored as the values
of the end field of
planC
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