Hello,
I have been trying to figure out how to transform a scan so that it aligns to the ACPC plane. I’ve tried using this module (https://www.slicer.org/wiki/Documentation/4.8/Modules/ACPCTransform ) and placing fiducial points on different slices to transform the scan, but have been unsuccessful. Can anyone explain how I can do this? Also, is there a way to overlay a grid on the scan or in some way calculate just horizontal distance with the ruler?
Thank you!
Hi Alexis,
You can try this code on the Python console:
import numpy as np
import SampleData
def getSampleVolume():
# Download MRHead
sampleDataLogic = SampleData.SampleDataLogic()
volumeNode = sampleDataLogic.downloadMRHead()
return volumeNode
def getMatrixToACPC(ac, pc, ih):
# Anteroposterior axis
pcAc = ac - pc
yAxis = pcAc / np.linalg.norm(pcAc)
# Lateral axis
acIhDir = ih - ac
xAxis = np.cross(yAxis, acIhDir)
xAxis /= np.linalg.norm(xAxis)
# Rostrocaudal axis
zAxis = np.cross(xAxis, yAxis)
# Rotation matrix
rotation = np.vstack([xAxis, yAxis, zAxis])
# AC in rotated space
translation = -np.dot(rotation, ac)
# Build homogeneous matrix
matrix = np.eye(4)
matrix[:3, :3] = rotation
matrix[:3, 3] = translation
return matrix
def getTransformNodeFromNumpyMatrix(matrix, name=None):
# Create VTK matrix object
vtkMatrix = vtk.vtkMatrix4x4()
for row in range(4):
for col in range(4):
vtkMatrix.SetElement(row, col, matrix[row, col])
# Create MRML transform node
transformNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLinearTransformNode')
if name is not None:
transformNode.SetName(name)
transformNode.SetAndObserveMatrixTransformToParent(vtkMatrix)
return transformNode
# I defined these on MRHead
ac = np.array([-0.0641399910762672, 17.61291529545006, 5.009494772024041])
pc = np.array([-0.5843405105866637, -10.4779127581112, 3.044020167647495])
ih = np.array([-1.1045410300970602, 1.746799450383008, 45.04402016764749])
volumeNode = getSampleVolume()
matrix = getMatrixToACPC(ac, pc, ih)
transformNode = getTransformNodeFromNumpyMatrix(matrix, name='World to ACPC')
# Create markups node with AC, PC and an interhemispheric point
markupsNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLMarkupsFiducialNode')
markupsNode.SetName('AC-PC-IH')
markupsNode.AddFiducialFromArray(ac, 'AC')
markupsNode.AddFiducialFromArray(pc, 'PC')
markupsNode.AddFiducialFromArray(ih, 'IH')
# Apply transform to volume node and markups node
volumeNode.SetAndObserveTransformNodeID(transformNode.GetID())
markupsNode.SetAndObserveTransformNodeID(transformNode.GetID())
# Fit image to slices
applicationLogic = slicer.app.applicationLogic()
applicationLogic.FitSliceToAll()
# Center views on AC
markupsLogic = slicer.modules.markups.logic()
acIndex = 0
markupsLogic.JumpSlicesToNthPointInMarkup(markupsNode.GetID(), acIndex)
By the way, looking forward to showing examples like these in a Jupyter Notebook
We worked hard with @jcfr during the during Slicer project week in Gran Canaria and we are excited to share one of the newest developments: Jupyter notebook support.
You can create interactive Python notebooks to run Slicer code and show resulting text data or slicer/3D view content in the notebook. Great for experimenting and sharing code and results with others.
[image]
See an example notebook here , which shows loading of a sample data set, display of a slice view, creation and display of a…
lassoan
(Andras Lasso)
July 20, 2018, 4:53am
3
shebaelena:
have been unsuccessful
These may help (they are accurate for Slicer 3.6, but the behavior is not that much different on Slicer 4.9):
If you still have problems, then please describe what you did exactly, what you expected to happen, and what happened instead.