Calculate a transformation that aligns brain images to Talairach coordinate system (also known as stereotaxic or ACPC coordinate system) based on anatomical landmarks.
Compute ACPC transform¶
- Begin by opening the
ACPC Transformmodule. In
Input landmarkssection, click on the
ACPC Lineselector and select
Create a new markups line.
- Use this line to define the posterior border of the anterior commissure as well as the anterior border of the posterior commissure in the axial slice. To place a line end-point, click
Placebutton on the toolbar then click in the image. Click on a point to show it in all slice views. You will need to toggle between slices before you place the second point to do this. Verify in the sagittal slice that this line is accurate.
- To create the midline, click on the
Midlineselector and select
Create New MarkupsFiducialfrom the dropdown.
- Select at least 5 points along reliable midline structures, (e.g. third ventricle, cerebral aqueduct, etc) ideally on different slices.
- Click on
Output transformselector and choose
Create New Transform, and then click
Applyto compute the transform.
Apply the computed transform to a volume¶
- Option A: Change image orientation information in the image header (image data is not changed, therefore there is no image quality loss):
Datamodule to navigate to the Subject hierarchy.
- Right-click on the
Transformcolumn of your original MRI scan and select
- Right-click there again and select
Harden transformto permanently modify the image with this transform.
- Option B: Resample the volume to align the voxel array’s axes with ACPC axes (it is useful if the image needs to be segmented or processed along ACPC axes directions, but may result in slight image quality degradation). Go to
Resample Scalar/Vector/DWI Volume, then choose:
Input volume-> original volume
Output Volume-> create a new volume node
Reference volume-> the original volume (should work well if
Center volumeoption is disabled) or a standard Talairach volume (recommended if
Center volumeis enabled). Alternatively, output volume geometry can be specified using
Manual Output Parameterssection.
Transfrom Nodeoutput transform of ACPC module as
Panels and their use¶
- ACPC Line: markups line specified by the user, connecting a point at the anterior commissure with a point at the posterior commissure.
- Midline: series of markups points (at least 3) placed by the user on the mid sagittal plane (the division between the hemispheres of the brain).
- Center volume: If this option is enabled then the output transform will translate the AC point to the origin. If this option is disabled then the position of the volume will be preserved and transform will only change the orientation.
- Output transform: transformation matrix (rigid translation and rotation) that the module computes from the input landmarks. If this transformation is applied to the volume then it will make the ACPC line “horizontal” (be in AP axis of the patient coordinate system), line up the mid sagittal plane “vertical” (fit on the AS plane of the patient coordinate system), and (if centering is enabled) then make the AC point the origin (the (0,0,0) coordinate in the patient coordiante system).
- Nicole Aucoin (SPL, BWH)
- Ron Kikinis (SPL, BWH)
- Andras Lasso (PerkLab, Queen’s University)
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.