NA-MIC
National Alliance for Medical Image Computing
http://na-mic.org
Slicer3 Tutorial:
Registration Library Case 15
AC-PC Alignment
Dominik Meier, Ron Kikinis
April 2010
Overview
1.
Introduction
2.
Prerequisites
3.
Modules Used
takes how long to do?
4.
Loading Example Dataset
2 min
5.
Viewing Input Data
3 min
6.
Selecting AC-PC Fiducials
5 min
7.
Selecting Midline Fiducials
2 min
8.
Align with ACPC module
1 min
9.
Resample & Save
3 min
National Alliance for Medical Image Computing
http://na-mic.org
Note: if wish to skip parts
of the tutorial, you will
find the data generated
by individual steps in the
Example Data Folder.
You may load these
individually via the
“File/Add Data…” menu.
The SlicerScene file that
comes with the tutorial
will only load the initial
volume data.
Introduction / Scenario
• We have a single MRI scan that we would
like to have rotationally aligned along the ACPC axis and the interhemispheral midline.
• This is a form of fiducial-based registration.
We will use the dedicated “ACPC Transform”
module for this.
• The line connecting the anterior- (AC) and
posterior commissure (PC) determines the
rotation around the left-right axis, such that
the AC-PC line becomes horizontal
• The interhemispheral midline determines the
rotation around the inferior-superior axis,
such that this plane becomes vertical in the
coronal and axial views.
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http://na-mic.org
Brain Orientation before/after AC-PC alignment
animated gif, view in presentation mode
Modules Used
• To accomplish this task we will use the
following modules:
– Fiducials Module
– “AC-PC Transform” Module
– Data Module
National Alliance for Medical Image Computing
http://na-mic.org
Prerequisites
• Slicer version 3.5 or later
• Example Dataset: download and extract the dataset for this tutorial:
RegLib_C14_BrainPET-MRI.zip, which should contain this tutorial and all original
and intermediate solution data files.
• Tutorials to complete first (optional):
– Slicer3Minute Tutorial
– Loading and Viewing Data
National Alliance for Medical Image Computing
http://na-mic.org
1. Loading Example Dataset
To get the Example Dataset loaded into Slicer:
Menu: File: Load Scene…
1.
–
Select the Slicer Scene file that comes with the downloaded example dataset,
called: RegLib_…_SlicerScene.mrml
–
This will load all the necessary images. If this fails, use the “Add Data…” menu
to load the files in the data directory.
2.
Select Layout: If loading the scene file, the proper
layout should be chosen automatically. To do this
manually, from the icon bar, click on the Layout menu
and select “Four-up Layout”.
3.
Link Views: Click on the Ring Icon in any of the slice
views to link all the views together. This will save you
the work of making selections for each slice window
separately.
4.
Choose Background: MRI_T1
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Build Fiducial List #1
1.
Click on the Fiducial Module Icon or
select “Fiducials” from the module
menu
2.
From the “Fiducial List” menu, select
“Create New Fiducial List”
3.
From the same menu, select
“Rename”
4.
Rename the new list something like
“fid_AC-PCLine”
(Note that the tutorial dataset already
contains such fiducial lists, so pick a
different name so you can keep them
apart)
National Alliance for Medical Image Computing
http://na-mic.org
Select AC & PC
1.
2.
3.
4.
5.
6.
7.
Navigate to the posterior
commissure
From the toolbar, click on the
“Fiducial Selection Tool”. This will
change the function of the left
mouse button to select fiducials in
the 2D and 3D views.
Left click on the location of the
anterior commissure, near the
midline. You may choose any
convenient view for this.
You should see a fiducial marker
being created. To adjust the position
(move it), first turn off the selection
tool, then place the mouse over the
marker until it changes color. You
can now drag it to a new location.
Switch back to the selection mode
Repeat the above for the posterior
commissure.
You should now have 2 entries in
your fiducial list. If you have more,
delete the extra ones by first
selecting them from the list and the
clicking on the left trash-can icon:
National Alliance for Medical Image Computing
http://na-mic.org
Build Fiducial List #2
1.
Create a second fiducial list for the
midline points.
2.
From the “Fiducial List” menu, select
“Create New Fiducial List”
3.
From the same menu, select
“Rename”
4.
Rename the new list something like
“fid_Midsagittal” or similar.
(Note that the tutorial dataset already
contains such fiducial lists, so pick a
different name so you can keep them
apart)
National Alliance for Medical Image Computing
http://na-mic.org
Select Midline fiducials
1.
Navigate to slices where the midsagittal
plane is well visible. Axial and coronal
views are recommended.
2.
From the toolbar, click on the “Fiducial
Selection Tool”. This will change the
function of the left mouse button to select
fiducials in the 2D and 3D views.
3.
Left click on a few locations of the midline.
More than 3 is recommended to get a
more robust result.
4.
For each click you should see a fiducial
marker being created. To adjust the
position (move it), first turn off the
selection tool, then place the mouse over
the marker until it changes color. You can
now drag it to a new location.
5.
You should now have >3 entries in your
fiducial list. To delete unwanted ones, first
select them from the list and the click on
the left trash-can icon:
National Alliance for Medical Image Computing
http://na-mic.org
AC-PC Module
1.
2.
3.
4.
5.
6.
Go to the “ACPC-Transform” module. You will find it in the alphabetical
list under “All Modules”
Under the “Transform” tab, select the two fiducial lists created for the
ACPC line and Midline
For “Output transform”, select “Create New Linear Transform” , then
select “Rename” again from same menu and rename as desired.
Click “Apply”.
In the space right above the “Transform” tab, you should see “Status
Completed” appear immediately after clicking Apply.
Go to the “Data” module. Drag the “MRI_T1” node onto the newly
created transform. You should see the display update as shown below.
animated gif, view in presentation mode
National Alliance for Medical Image Computing
http://na-mic.org
Apply & Save
1.
To apply the transform and create a new resampled
volume, right click on the “MRI-T1” node in the data
menu and select “Harden Transforms”. This will move
the node back to the root level and resample the
volume in the new orientation.
Alternatively you can use a resampling tool, such as
the “Resample Scalar/Vector/DTI Volume” for more
detailed control, e.g. to specify the interpolation
method.
2.
From the File menu, select “Save”
3.
In the dialog box, check the boxes for the resampled
MRI-T1 and the transform.
4.
Be careful when saving not to overwrite the original:
change the output filename.
5.
Ensure directories are as desired.
6.
Click on “Save Selected”.
National Alliance for Medical Image Computing
http://na-mic.org
What Next
•
Try the Manual Registration Tutorial or one of the tutorials from the
Registration Case Library.
– http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training
– http://namic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseI
nventory
– http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration#Registra
tion_in_3D_Slicer|Main
•
Feedback: anything amiss? If you have suggestions on how we
can improve this and other documentation, please let us know:
visit:
– http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation
National Alliance for Medical Image Computing
http://na-mic.org
Acknowledgements
Quic kT ime™ and a
T IFF (Uncompress ed) dec ompress or
are needed to s ee this pic ture.
National Alliance for Medical Image Computing
NIH U54EB005149
Neuroimage Analysis Center
NIH P41RR013218 -12S1 (ARRA Suppl)
National Alliance for Medical Image Computing
http://na-mic.org