Quanta2 Pipeline: A Training Tutorial
Imaging of Dementia and Aging (IDeA) Laboratory,
UC Davis School of Medicine: Neurology
Amy Liu
Launch Quanta2
Once Quanta2 is launched in a terminal, select and confirm initials.
From the main window, click the “Pipelines” button.
Select the “Quanta Classic Pipeline” button.
On the next window, select an image to start the pipeline.
After Preprocessing, the dialog box shown above will appear.
Note: You can save the pipeline at any stage by using the “Save ‘n’ Exit” button.
Resume by reloading the pipeline when prompted.
Click on the “Continue” button to launch The Cranial Vault (TCV) Tracer. Click “OK” on
the next window.
On the right hand side, the Pipeline Progress window is shown. This will update as the
pipeline wizard progresses
TCV TRACER
• This section of the tutorial will detail functionality
of The Cranial Vault (TCV) Tracer and progress
through several exemplary brain slices.
 Examples are traced on a Fluid Attenuated Inversion Recovery
(FLAIR) image, a modality for depicting hyperintense regions.
 Moving dorsally to ventrally, traces will increase in complexity.
 Note the various anatomical structures that should be excluded.
• TCV Tracer creates an .ima file.
TCV Tracer
Graphical User Interface
Functions include:
• “View Original” button can be
used to toggle between traced and
original view of the image.
• “Revert Slice” button reverts the
completed trace image to original.
This must be done each time
BEFORE retracing a slice.
•
“Flip Y” button changes the image
view vertically. Here, Flip Y may be
used to display the anterior of the
head at the top of the window.
•
“Full View TCV” button displays
traced slices in a new window,
which can be used after
completing tracing on the file and
acts as a check for continuity.
TCV Tracer
Graphical User Interface
Functions include:
• “Save TCV” button will write the
traced image as an .ima file to disk.
• This .ima file is a binary file that
will be used in all stages of the
pipeline henceforth to save postprocess data of each step.
•
“Brightness” and “Contrast”
adjustment bars allow for userpreferred display settings.
•
“Reset” buttons will restore
default settings.
TCV Tracer: Example
Locating starting slice
Depending on preference, it may be
easiest to begin TCV Tracing on a slice
displaying representative brain matter.
Thus, scroll to a slice halfway through
the brain that appears similar to this
image:
TCV Tracer: Example
Tracing Mode
To start TCV tracing, click “Begin
Tracing” button.
This will activate tracing mode:
• Left mouse button is used to plot
individual trace points, which will
be sequentially connected.
• Middle mouse button, or “Undo
Last Point”, erases plotted trace
points.
• Right mouse button, or “Complete
Tracing”, will complete and close
the first and last points of the
traced region curve.
• “Cancel Tracing” button erases all
uncompleted trace points and
deactivates tracing mode.
Note: scrolling between slices is NOT
possible in tracing mode.
TCV Tracer: Example Tracing Mode
Using the left mouse button, trace along the interior edge of the dura mater by plotting individual points
that will sequentially connect.
• Exclude the dura mater and superior sagittal sinus.
• Exclude any noise or bright signal that may appear along the interior edge of the dura mater.
Clicking the right mouse button will connect the first and last plotted points, completing the trace.
• Note the absence of the skull, dura mater, and superior sagittal sinus in the traced image.
Original Image
Traced Image
Dura
1st and last
points will
connect
Superior
Sagittal Sinus
TCV Tracer: Example
Excluding Structures
Continue tracing successive slices,
staying along the interior edge of the
dura mater and removing the
structures labeled with green arrows:
• Dura mater
• Superior sagittal sinus
• Inferior sagittal sinus
• Falx cerebri
Tip: Scroll 1 slice up and 1 slice down
from the slice to-be-traced in order to
determine brain matter from noise.
• If the area in question appears on
the slices above and below, it
should be included as brain matter
in the trace.
Dura
Inferior
Sagittal
Sinus
Falx cerebri
Superior Sagittal
Sinus
TCV Tracer: Example
Excluding Structures
Superior Sagittal Sinus
Continue tracing successive slices,
staying along the interior edge of the
dura mater and removing the
structures labeled with green arrows:
• Dura mater
• Superior sagittal sinus
•
•
•
Dura
3rd
Ventricle
Appears anteriorly and
posteriorly in this and
subsequent slices
Falx cerebri
Pineal gland
•
•
Often appears as bright signal
Trace just posterior to the Third
Ventricle
Pineal
Falx cerebri
Superior Sagittal
Sinus
TCV Tracer: Example
Excluding Structures
Continue tracing successive slices,
staying along the interior edge of the
dura mater and removing the
structures labeled with green arrows:
• Dura mater
• Superior sagittal sinus
•
•
•
Appears anteriorly and
posteriorly in this and
subsequent slices
Falx cerebri
Pineal gland
•
•
Often appears as bright signal
Trace just posterior to the Third
Ventricle
3rd
Ventricle
TCV Tracer: Example Excluding Structures
As slices progress ventrally, the trace contour complexity increases. Be sure to also remove:
• Cerebellar vermis
• Medially jutting dura mater
• Superior sagittal sinus
Here, the Third Ventricle is intact (compare with next slide). Thus, do NOT remove midbrain structures.
Original Image
Traced Image
Dura
Vermis
SSS
3rd Ventricle
TCV Tracer: Example
Excluding Midbrain Structures
Here, the Third Ventricle is NOT intact.
Thus, remove midbrain structures:
• Substantia nigra
• Red nucleus
• Pons
• Mammillary bodies
• Hypothalamus
• Cerebral peduncle
• Superior colliculus
Also, continue to remove:
• Cerebellar vermis
• Medially jutting dura mater
• Superior sagittal sinus
•
•
Anterior and posterior
Falx cerebri
3rd Ventricle
Dura
Vermis
Midbrain
Structures
TCV Tracer: Example
Excluding Midbrain Structures
Here, the Third Ventricle is NOT intact.
Thus, remove midbrain structures:
• Substantia nigra
• Red nucleus
• Pons
• Mammillary bodies
• Hypothalamus
• Cerebral peduncle
• Superior colliculus
Also, continue to remove:
• Cerebellar vermis
• Medially jutting dura mater
• Superior sagittal sinus
•
•
Anterior and posterior
Falx cerebri
TCV Tracer: Example
Excluding Ventral Structures
Cribiform plate
For slices approaching the foot, 2 or
more separate traces must be drawn.
This allows for the exclusion of:
• Optic nerves
•
•
•
•
•
Once the optic nerves have
crossed, do not include any
structures located anteriorly.
Amygdaloclaustral area
Cribiform plate
Midbrain structures
Cerebellum
Amygdaloclaustral
area
Optic
Nerve
Midbrain
Structures
Cerebellum
TCV Tracer: Example
Excluding Ventral Structures
For slices approaching the foot, 2 or
more separate traces must be drawn.
This allows for the exclusion of:
• Optic nerves
•
•
•
•
•
Cribiform plate
Amygdaloclaustral
area
Once the optic nerves have
crossed, do not include any
structures located anteriorly.
Amygdaloclaustral area
Cribiform plate
Midbrain structures
Cerebellum
Cerebellum
TCV Tracer: Example
Excluding Ventral Structures
For slices approaching the foot, 2 or
more separate traces must be drawn.
This allows for the exclusion of:
• Optic nerves
•
•
•
•
•
Once the optic nerves have
crossed, do not include any
structures located anteriorly.
Amygdaloclaustral area
Cribiform plate
Midbrain structures
Cerebellum
Completing the trace displays only the
structures within the trace line.
• Use “View Original” button to
plan your next trace.
• Remember to scroll up and down 1
slice to determine which
structures to include.
TCV Tracer: Example
Excluding Ventral Structures
For slices approaching the foot, 2 or
more separate traces must be drawn.
This allows for the exclusion of:
• Optic nerves
•
•
•
•
•
Cribiform plate
Amygdaloclaustral
area
Once the optic nerves have
crossed, do not include any
structures located anteriorly.
Amygdaloclaustral area
Cribiform plate
Midbrain structures
Cerebellum
Cerebellum
TCV Tracer: Example
Excluding Ventral Structures
For slices approaching the foot, 2 or
more separate traces must be drawn.
This allows for the exclusion of:
• Optic nerves
•
•
•
•
•
Once the optic nerves have
crossed, do not include any
structures located anteriorly.
Amygdaloclaustral area
Cribiform plate
Midbrain structures
Cerebellum
TCV Tracer: Example Dorsal Tracing
Slices toward the top of the head contain more noise and thicker dura mater.
• It is important to scroll between slices to determine brain matter.
If noise is accidentally included in the trace:
• Click the “Revert Slice” button to restore the original image.
• Then, “Begin Tracing” again.
Original Image
Dura
Traced Image
After tracing, save the TCV and close the tracing application. This will
launch the dialog box shown above.
Click “Continue” to launch TCV Filtering. This will remove image artifacts
like bias and inhomogeneity.
TCV Filtering
There is no graphical user interface
display on this step; you will only see
text output in the terminal, as shown.
CSF-BRAIN MODELING
• This section of the tutorial will detail
sequential modeling of brain matter and
Cerebrospinal Fluid (CSF).
 Quanta2 will separate brain matter voxels from CSF and
background voxels to calculate Gaussian curves.
 Intensity histograms of consecutive TCV-traced slices are
obtained using a user-defined statistical modeling type and
the presumption of underlying voxel intensities.
• CSF-Brain Modeling saves to the .ima file.
CSF-Brain Modeling
The pipeline dialog window will pop up. Click the “Continue” button and this selection
window will appear for CSF-Brain Modeling.
Shown above are the default settings, which can be user defined as needed.
• The Gaussian curves will show 2 segmentation domains (brain matter and CSF),
using an estimation sensitivity of 25 and the filtered TCV for intensity correction.
Click “Continue” to proceed.
CSF-Brain Modeling
Compare the Filtered TCV Image
(upper left) with the Threshold TCV
Image (bottom left) to infer if the
calculated threshold is acceptable: CSF
is being filtered out and brain matter
remains.
• The yellow line represents the
distribution intensity of the
Original TCV image. For a FLAIR
image, it should have 2 major
peaks.
• The blue curve represents CSF and
should contour a major peak of
the yellow line.
• The red curve represents brain
matter and should contour the
second major peak of the yellow
line.
• The point where the brain matter
(red) and CSF (blue) curves
intersect is the calculated
threshold.
CSF-Brain Modeling
Use the “>>” button to advance the
modeling slice.
The “<<” button allows viewing of
previous slices, but will discard any
changes.
CSF-Brain Modeling
Insufficient CSF to model:
Occasionally, the computed threshold
is unsatisfactory due to lack of
information. In that case, the user
must manually set the threshold. This
can be done by:
• Clicking “Change Threshold”
button
CSF-Brain Modeling
Insufficient CSF to model:
Occasionally, the computed threshold
is unsatisfactory due to lack of
information. In that case, the user
must manually set the threshold. This
can be done by:
• Clicking “Change Threshold”
button followed by using the
cursor to click at the desired
intensity location on the
histogram.
• Ideally, pick a point where the
brain matter and CSF curves would
intersect.
CSF-Brain Modeling
Manually set the threshold:
•
The filtering program often
presents unsatisfactory calculated
thresholds on the first and last
slices, especially when the CSF
curve is absent or is a straight line.
•
Be sure to manually set the
threshold.
On this slice, the Gaussian CSF curve
was calculated incorrectly due to large
fluctuations in the distribution
intensities of the yellow Original TCV
line.
•
•
The fluctuation changes could be
detected by lowering the
Estimation Sensitivity (from
default 25) at the start of the
CSF-Brain Modeling step.
Because this occurs on only a few
slices, there is no need to exit
this step to reset. The threshold
can easily be set manually.
CSF-Brain Modeling
After advancing through all slices, the
program will indicate “Insufficient data
to model”.
CSF-Brain Modeling
After advancing through all slices, the
program will indicate “Insufficient data
to model”.
Click “Exit And Save” button to
proceed to next stage of the pipeline.
WMHI MODELING
• This section of the tutorial will detail
sequential modeling of White Matter
Hyperintensities (WMHI).
 Quanta2 will calculate intensity histograms of the FLAIR
image to determine hyperintensities, e.g. voxels above the
user-defined threshold.
 The previously traced TCV image (.ima file) will be used.
Also, erosion of the created CSF mask is required because
FLAIRs have a bright lining, which skews threshold
calculations.
• WMHI Modeling creates a _WM.ROI file.
White Matter Modeling
The pipeline dialog will pop up. Click “Continue” to proceed to White Matter Modeling.
A selection window resembling the above will appear. Please select the options as shown
above for optimal resolution and click “Continue”.
• The Zmask, conversion of images using another statistical method, is not
necessary with FLAIRs.
White Matter Modeling
The red Gaussian curve generated is
used to compute the white matter
threshold to 3.5 (default), or userdefined, standard deviations from the
mean.
Compare the Thresholded Eroded TCV
Image (upper left) with the White
Matter Image (bottom left) to infer if
the calculated threshold is acceptable:
noise is being filtered out and white
matter remains.
White Matter Modeling
Although the computed threshold is
correct in many cases, noise appears in
undesired locations on the image.
These erroneous bright signals must
be manually removed by:
• Clicking “Edit WMHI” button.
Noise
White Matter Modeling
Although the computed threshold is
correct in many cases, noise appears in
undesired locations on the image.
These erroneous bright signals must
be manually removed by:
• Clicking “Edit WMHI” button. This
brings up a 3-paneled window
containing Scratch Pad Image,
Modeled Image, and TCV Image.
White Matter Modeling
•
Focusing on the Modeled and TCV
Images, use the “X” cursor to
locate bright signals:
•
•
•
•
•
Within ventricles
Around the outside edge of the
brain
Along motion lines.
• These are NOT WMHIs.
Holding and dragging the left
mouse button over the erroneous
signal erases (default).
Holding and dragging the right
mouse button over the area
restores, if you have made a
mistake.
White Matter Modeling
•
Focusing on the Modeled and TCV
Images, use the “X” cursor to
locate bright signals:
•
•
•
•
•
•
Within ventricles
Around the outside edge of the
brain
Along motion lines.
• These are NOT WMHIs.
Holding and dragging the left
mouse button over the erroneous
signal erases (default).
Holding and dragging the right
mouse button over the area
restores, if you have made a
mistake.
Finishing WMHI editing on the
slice by clicking “Save and Close
Window”, or middle mouse
button.
Corrected:
White Matter Modeling
•
Focusing on the Modeled and TCV
Images, use the “X” cursor to
locate bright signals:
•
•
•
•
•
•
•
Within ventricles
Around the outside edge of the
brain
Along motion lines.
• These are NOT WMHIs.
Holding and dragging the left
mouse button over the erroneous
signal erases (default).
Holding and dragging the right
mouse button over the area
restores, if you have made a
mistake.
Finishing WMHI editing on the
slice by clicking “Save and Close
Window”, or middle mouse
button.
Repeat this procedure with every
image slice.
Corrected:
White Matter Modeling
The “>>” button will advance you
through image slices.
The “<<” button will navigate to
previous slices, but will discard any
changes.
White Matter Modeling
The program often displays noise on
the first and last slices, especially
when the red Gaussian curve is not
smooth or cannot be calculated from
the large intensity differences.
Due to lack of information, the
threshold calculated is not accurate
and the user must manually mark the
threshold.
• Use the “Change Threshold”
button followed by using the cursor
to click at the desired intensity
location on the histogram.
• Ideally, pick a point where the
WMHI appears without displaying
noise.
Noise
White Matter Modeling
As an example, the top window
displays a manually set threshold
intensity that is too low.
• Tissue other than WMHIs are
displaying as bright signal.
• There is no way to distinguish and
erase erroneous WMHI.
• Use the “Change Threshold”
button to reset a higher threshold
intensity.
The bottom window displays a
manually set threshold intensity that is
too high.
• While some WHMIs are displayed
as bright signal, much of the tissue
is not.
• This will cause the WM burden to
appear lower than it actually is.
• Use the “Change Threshold”
button to reset a lower threshold
intensity.
White Matter Modeling
After changing the threshold, click the
“Edit WMHI” button to inspect and
erase erroneous signals.
Finish WMHI editing by clicking “Save
and Close Window”, or middle mouse
button.
White Matter Modeling
Once the last slice is reached, the
program will indicate “Last slice in
image. You must go back!” or
“Insufficient data to model”.
White Matter Modeling
Once the last slice is reached, the
program will indicate “Last slice in
image. You must go back!” or
“Insufficient data to model”.
•
•
•
Click “Save WMHI Array” button.
Then, click “Exit and Save” button.
Data will be lost if BOTH of these
commands are not initiated.
The next dialog window will ask if you wish to trace Regions Of Interest (ROIs).
If so, click “Continue”. Tracing ROIs will be explained in a separate tutorial.
If not, click “Skip Next Step”.
Par File
After skipping ROI trace, the last step in the
pipeline involves writing a Par File.
• This is a comma-separated text file that
stores volume data about the analyzed
brain.
Click “Write Report to File” button to write
all the analyzed volumes (in cubic
centimeters) to a .par file.
Close the dialog box to return to Quanta2
Main.
Par File Reader
To access analyzed volume data, the .par
file can be read using Parfile Reader
• This is located under the “Utilities”
menu in Quanta2 Main.
• Click the “Operations” menu to “Open”
and select a .par file to read.
The information displayed here can be
exported to a .csv file, which is compatible
with most spreadsheet programs.
• Click the “Operations” menu to “Export
as CSV”.
• The .csv file will be saved in the same
directory as the .par file.