Transcript Positron Emission Tomography - training IBRO CEERC Summer School 2005 Miklós Emri , Iván Valastyán, Gábor Opposits PET Center University of Debrecen.

Positron Emission Tomography
- training IBRO CEERC Summer School 2005
Miklós Emri , Iván Valastyán, Gábor Opposits
PET Center
University of Debrecen
2005
PET-method
1. Isotope preparation
F18, O15, C11, N13
2. Radiopharmacon evaluation
FDG, Metionine, F-dopa, Butanol. H2O
3. Imaging
Static-, dynamic, ECG gated scans
4. Image processing
…
GE PETtrace cyclotron
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6 target slots
1 h irradiation 2,5 Ci F18
F18, O15, C11, N13
… to radiochemistry …
Radiochemistry
Radipharmacons used in human studies
• 18FDG
: oncology, cardiology
• 11C-Metionine
: oncology
• 15O-butanol, 15O-water
: brain research
Under development
• 18F-DOPA
• 11C-choline
• 18F-fallypride
• 11C-raclopride
• 11C-flumazenyl
• 18F OLIGO
Quality Control
radiopharmacons
GMP
… to PET lab …
ECAT Exact PET scanner
• whole body scanner
• 16.5 cm axial FOV
• spatial resolution 6 mm
Reconstructed PET images
… to image processing …
A PET-scan
Evaluate a 3D distribution of
the radioactivity concentration
Limited axial field of view (FOV), wrong temporal resolution and signal/noise ratio
Structure of 3D tomographic images
MRI
SPECT
CT
PET
+ gammacamera, US, .....
• 3D array of voxels
• coordinate system
• voxel-value
• nCi/mm3,
• intensity vs. integrated
• other information
• patient, scanner, protokoll
Volume = set of slices
2 mm
voxel
256 mm
128 pixel
2 mm
2 mm
128 pixel
15 slices
2 mm
slice
Image Processing
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Single modality medical image processing
Multimodality medical image processing
Statistical parametric mapping
Small animal PET imaging
Preferred places for medical imaging
technique and software
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www.bic.mni.mcgill.ca/software
www.loni.ucla.edu/ICBM
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Image registration, visualization, basic and
advanced manipulation software, brain atlas
technique, …
www.fil.ion.ucl.ac.uk/SPM
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Statistical parametric mapping
Own medical imaging software for
basic and advanced image processing
www.pet.dote.hu/braincad
BrainCAD
BrainCAD
• Analyze, MINC, Interfile, Dicom,
file input and output
• fast and smooth visualization
• basic image processing tools
Computer
Aided
flip, clamp, normalize, smooth, resample, reshape, ...
Diagnostic
and research ...
• advanced slice series dumping for diagnostic purpose
• ROI drawing
• ROI export from HBA (Karolinska brain atlas)
• single & dual volume imaging and manipulation
image fusion display and documentation features,
landmark based registration
• SPM color palette
• extensible menu for external binaries
• ...
BrainCAD
fast and smooth visualization
menu, toolbar, color palette, etc ..
3D navigation windows
real-time interpolation
3D cursor
real-time zoom & shift
BrainCAD
slice dumper window for diagnostic
and presentation purposes
interactive ‘3D bounding box’ for
real-time slicing
toolboxes & menus:
axial, sagittal, coronal selection,
number of sections, zoom, shift
etc ..
BrainCAD
dual volume visualization
dual color palette
different layouts
3D cursor modes:
synchronous & asynchronous
BrainCAD
dual volume visualization:
image fusion mode
dual color palette
fusion layout
fusion slicing
BrainCAD
dual volume visualization:
MNI register mode
reference volume
reslice volume
register function
& different layout mode
landmarks
BrainCAD
dual volume visualization:
SPM palette, and documentation
deactivation & activation
palette
simple, fusion layout
SPM palette & fused slicing
Exercise 0:
Start BrainCAD and get
acquainted with the GUI
The GUI of the BrainCAD
BrainCAD’s
main
window is divided into
four regions:
menu
list and toolbar
volume
selector(s)
and colour palette(s)
toolbox
container
visualization
area
The toolbar and the color palette
Single modality image
processing
Exercise 1:
Load and investigate a PET
data file
Volume loading
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Select single visualization mode on the toolbar.
Press File/Open volume or ‘CTRL+O’ and select a data file (e.g.
fdg.mnc or but.mnc) from practice/p1 subdirectory
Press OK or use double click
Navigation, zoom, change colors
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Navigation, zoom and image shift
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Move the cursor by left mouse button over any slice: the other slices will
change.
Roll the mouse roller (on the middle mouse button) over any slice: this slice
will change.
Press and hold down the middle mouse button and move the mouse forward
(zoom in) or backward (zoom out).
Press shift key + left mouse button and move the mouse in an arbitrary
direction.
Press Reset zoom button on the toolbar.
Changing the Colours
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Move over the colour palette and drag the low border of the palette by the
left mouse button. Shift the low border with mouse into a proper value.
Check this value in the Low input filed of the Colour Palette Dialog.
Enter any number in the High input filed of the Colour Palette Dialog.
Select the hotmetal palette from the Palette type combo box.
Try the Reset and Expand buttons of the Colour Palette Dialog.
Try any other palette
Check the extent and voxel size of the
loaded volume
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Choose the Edit/Edit file header menu
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the matrix
: 128x128x15
the voxel size : 2x2x6.5 mm
128
2x2x6.5 mm
15
128
Creating Slice Dump
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Choose the Slice dump
Toolbox on the toolbox
container.
Set the source to Reference
Set the direction to Axial
Set slice distance to 6.5 mm
Set the number of columns
and rows, e.g.: 4 x 4: the
generated slices will be seen
in the slice dump window.
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Now you can see
original slices of
reconstructed image
the
the
Try the zoom and shift
features on any axial slice:
the action will be seen on
other slices, as well.
Try the sagittal and coronal
slices
… print it …
Printing images - documentation
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Set white background, click on the
icon on the
toolbar
Click on the image area, what you want to print
Press the SHIFT+P keys and find the hardcopy
dialog on the screen
Turn off the Save to file checkbox
Press the Preview button to check your result
Close the preview window and press the Ok button
to print your pictures.
Exercise 2:
Interpolate the volume into
2x2x2mm voxel size
Resample (volume interpolation)
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Choose the Resample toolbox and check the original voxel size
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Set all voxel sizes to 2mm. Try the iso-voxelsize button right from
the input fields.
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Press the Apply button: a new volume will be generated. The name
of the generated volume is r_filename (where the ’r_’ means:
resampled). The old volume will not be overwritten, you can get it
back by the undo button on the toolbar or you can select it from the
volume selector. (Try the undo/redo buttons.)
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Press File / Save As…, type the new filename and press save.
Exercise 3:
Selection a 3D part of a volume
Reshape
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Choose the Resample toolbox. The sections of the bounding box
are delineated by white rectangle on the slices in the Volume
Viewer. You can resize it using the mouse: drag with the left mouse
button on the edge or on the corner and move it.
Press the apply button: a new volume will be generated. The name
of the generated volume is r_filename (where the ’r_’ means:
reshaped). The old volume will not be overwritten, you can get it
back by the undo button or by the volume selector above the toolbox
container:
Try the undo/redo buttons on the toolbar
Press File / Save As… and type the new filename and press save
Exercise 4:
Region Of Interest (ROI)
analysis
polygon
ROI: region-of-interest
set of polygons, 2D
VOI: volume-of-interest
is defined as a stack of
planar, closed polygons
set of ROIs, 3D
Creating VOI from a polygon ROIs
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Select a volume from the volume selector list box, or load a
volume.
Switch to the VOI toolbox.
Press the New VOI button.
Push the Polygon ROI button and mark out the vertices of the
polygon with the left mouse button. To finish close the polygon
by the right mouse button.
Try the open/close numerical values button on the VOI list box
Try the Real-time calculation checkbox
Try the copy ROI to the next/prev slice button
Try the VOI result table button
Press the Save VOI button and save the VOI into a file.
Creating VOI from a freehand ROI
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Press the New VOI button .
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Push the Freehand ROI button
onto an axial slice. Draw around
the area of ROI by the smoothly moved mouse with pressed left
mouse button and release it at the end of drawing.
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Choose another axial slice and create a new freehand ROI again.
Important note: the Freehand ROI mode is already selected, so there
is no need to select it again.
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Save the VOI by the Save VOI button on the VOI Toolbox.
Dual modality image
processing
Exercise 5:
Image registration based on the
manually adjusted affine transformation
Adjustable transformations
Translation
Rotation
Scaling
Shearing
Load two unregistered volumes
Clear all volumes and VOIs
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Select VOI toolbox and choose the Delete all VOIs button
Select File/Close all volumes menu
Select Dual Visualization mode on the toolbar.
Click on the reference (left) volume viewer: the border of this
viewer will turn red.
Load practice/p5/t1.mnc data file (T1-weighted MRI), select gray
scale and adjust the low and high level of the colour palette.
Click on the reslice (right) volume viewer: the border of this viewer
will turn red.
Load practice/p5/fdg.mnc data file (FDG study) and adjust the
colour palette.
Select the Fusion visualization mode.
Try the Blending-value ruler near the volume selector boxes.
Manually adjusted affine transformation based
registration
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Choose the Register visualisation mode from the toolbar.
Switch on the Sync cursor button
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The cursor will be positioned to the same point in all the three volume
viewers.
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Choose the Transform toolbox
Click on the reslice (middle) volume and it becomes the source
volume of the transformation.
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Translate or rotate the source volume using the mouse or the sliders.
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Try the fused visualisation mode
and
the
transformation
manipulation buttons
Watch on the fused volume
viewer and stop when the
transformation is OK press the
Apply button.
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Exercise 6:
Landmark Based Registration
Landmark Based Registration
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Choose the register visualisation mode from the taskbar.
Click on the first (reference) volume viewer and load the reference
volume of the registration (practice/p5/t1.mnc).
Click on the middle (reslice) volume viewer and load a volume from
the same patient. (practice/p5/fdg.mnc). This volume will be
transformed into the coordinate system of the reference volume.
Select the 6-parameter transformation type (3 translations and 3
rotations) from the XFM-type list box.
Switch on the edit mode button:
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Switch off the sync cursor mode button on the toolbar.
Move the cursors of the reference and reslice volume viewer into the
anatomical equivalent anatomical position and put down landmarks:
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by the right mouse button, or
by the spacebar on the keypad.
If a point is not in the proper place drag it with the left mouse button
and move it into the best place.
Landmark Based Registration
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Put additional 4 landmarks. In the case of the first 4 landmarks only
the translation parameters will be calculated while if there are more
than 4 landmarks the parameters of the rotation will be estimated
too.
When you have exactly as many landmarks as you need, select the
target ‘lattice’ of the transformed volume.
Select the interpolation method. (Possible values: ‘nearest
neighbour’, ‘linear’ )
If you want to save the landmarks or the transformation matrix into a
file save them before using the apply button, because after the
transformation of the reslice volume all landmarks will be deleted and
the transformation matrix will be set as identical matrix.
Click on the Apply button to transform the reslice volume into the
coordinate space of reference volume. Important note: This
procedure erases all landmarks and sets the current transformation
matrix to identity.
Landmark Based Registration
Check your result
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Select the dual visualization mode (clear all landmarks!)
Load into the left volume visualisation area the practice/p5/t1fdg.mnc
Choose the bottom volume selector box your registered fdg volume
(t_fdg.mnc)
Choose the fusion visulization mode and check the difference of the
volumes.
Repeat the registration if it is necessary!
Try to solve the butanol-T1 and metionine-T1 registration. Use the
practice/p5/but.mnc and practice/p5/met.mnc files!
Task 1: Create VOIs on fused images
Exercise 7:
Investigating SPM results
Brain Activation Studies
Elektromágneses módszerek (EEG, MEG)
Haemodinamic, metabolic methods (PET, SPECT, fMRI)
Haemodinamic effect
Neuron activation
perfusion changing
delay: ~ 500 ms
time
FWMH: ~ 1000 ms
time
A PET-scan
15O-butanol
or
15O-water used for
dynamic scans
These scans used for evaluation
quantitave rCBF value or
40-110 sec accumulation distributions
Limited axial field of view (FOV), wrong temporal resolution and signal/noise ratio
Arrangement of a brain activation study
A
S1
2 conditions
A: reference
B: investigated
cognitive task,
vestibular signaling
word shadowing)
S2
S3
8 subjects
3 repetition
/6 PET + 1 MR scan per subject/
S8
B
A
B
A
B
MR
PET-PET registration
A
B
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B
A
See for more details www.bic.mni.mcgill.ca/software
B
MRI-PET registration
See for more details www.bic.mni.mcgill.ca/software
Spatial normalization of T1-wighted MRI scans
MNI template
Average of 305 healthy ,
T1-weighted MRI scans transformed into
the Talairach space
Finding linear or non-linear transformations which transform the MRI dataset into
the Talairach or the MNI coordinate system
See for more details www.bic.mni.mcgill.ca/software
Transformation of the perfusion scans into the
Talairach (or MNI) coordinate system
S1
S2
S3
. . .. .
A
B
Getting the values of same voxel from each scans
gives a perfusion distribution of the an anatomical location
represented by the selected voxel.
See for more details www.fil.ion.ucl.ac.uk/SPM
S8
Creating Student-T maps
A
B
SPM{t} map
H0 : CBFA = CBFB
H1 : CBFA < CBFB
H2 : CBFA > CBFB
H2
See for more details
www.fil.ion.ucl.ac.uk/SPM
H0
H1
Load MRI and SPM datasets
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Clear all volumes, landmarks and transformations
Select the dual visualization mode
Load
into
the
left
volume
visualization
area
the
parctice/p7/t1_individual_brain.mnc (scalp-edited, spatial standardized
individual
T1-weighted
data
set)
or
t1_population_brain.mnc
practice/p7/t1-fdg.mnc (average of 8 scalp-edited, spatial standardized
individual T1-weighted data sets)
Load 3 SPM generated 3D Student-T maps from the practice/p7
subdirectory into the right visualization area. Use the Control key and the left
mouse button to select 3 files on the Load file dialog box. The available SPM
files:
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spmT_speach.mnc
spmT_cognitive.mnc
spmT_vestibular.mnc
: result of a word shadowing single subject study
: result of a 8 12 subject odd-ball paradigm based cognitive study
: result of a 8 subjects caloric vestibular provocation study.
Choice the fusion visualization mode
Choice a dual colored palette for the SPM files.
Select the slice dump toolbox and select the fusion visualization mode on it.
Try the coronal, sagittal selection and the bounding box manipulation on the
Slice dump tool box.
SPM visualization by Student-T color palette
Exercise 8:
Generating a 3D Surface
Generating a 3D surface - 1
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Clear all volumes, landmarks, transformation matrices and VOIs.
Switch to the VOI toolbox
Choose the single visualisation mode and load a volume:
parctice/p7/t1_individual_brain.mnc
(scalp-edited,
spatial
standardized individual T1-weighted data set)
Press the New VOI button.
Switch on the Contour ROI with 1 base point button. Click on a
voxel of the axial slice: the isocontour ROI is based on the voxel
value of the point you have selected, i.e. this value is the contour
level value of the isocontour ROI. (It is also called the isodensity
value.) The contour circumscribes all regions in which all the voxel
values are higher than this isodensity value. Use the zoom
functions of the visualization layer!
If the result is improper move the pivot point of this ROI into a
better place using the left mouse button.
Generating a 3D Surface - 2
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Set the colour for your VOI to gray.
Press the Convert VOI to Polyhedron button: the contours of
the isosurface will be seen on every slice.
Press the 3D button: the 3D volume viewer will appear.
Press the Refresh button.
Use the mouse to rotate (left button) and zoom in and out
(middle button).
Try the Set view, Blending, Rotating, Shading and Wireframe
buttons.
Arrange the BrainCAD main- and the 3D windows on your
desktop.
Select the Polyhedron panel on the VOI toolbox.
Switch on the Clip options for the selected VOI.
Select Clip a corner function on the 3D window and check on
the Slice check-box on the visualisation section, as well.
Move the cursor on the braincad’s visualization area…
Exercise 8:
Visualization of SPM results by colorized
brain surfaces
(parametric surfaces)
Visualization of a parametric surface
(This practice is based on the Practice 7.)
 Close the 3D window.
 Choose the dual visualization mode.
 Select the left window the loaded T1-weighted volume and load into
the right window a 3D Student-T map from a brain activation study:
practice/p7/speech.hdr. Select the Analyze file-type in the Load
dialog box!
 Choose the Polyhedron page on the VOI toolbox.
 Enable the color function of the polyhedra (CFunc→ON)
 Choose one of the color functions (1-3) in the 3D viewer window.
 Change the blending value of the palette.
 Investigate the colored surface.
 Try the color functions, palettes and clipping functions.
Task 2: Create a presentation for the results of the
vestibular brain activation study
Controls
Patients
Vestibular signaling
Emri M, Kisely M, Lengyel Zs, Balkay L, Márián T, Mikó L, Berényi E, Sziklai I, Trón L, Tóth. Á. (2003)
Cortical projection of peripheral vestibular signaling. J. Neurophysol, 80:2639-2646.
Task 3: Create a 3D parametric surface presentation
for cognitive study
pcorr < 0.05
Controls
pcorr < 0.12
Patients
Example: Visualization standard VOI
libraries by BrainCAD
ICBM labels
HBA structures
Example: Interactive Maximal Intensity
Projection and volume rendering
MIP
volume rendering