Sorry I can’t find such a display as this one:
I tried to copy, as suggested , the above script, and paste it in the console, but I got an error message : hereafter you’ll find the log
import slicer
import ants
import os
import time
Function to create a Slicer node from an ANTSImage
def nodeFromANTSImage(antsImage, name):
import ants
imageNode = slicer.mrmlScene.AddNewNodeByClass(‘vtkMRMLScalarVolumeNode’, name)
tempFilePath = os.path.join(
slicer.app.temporaryPath,
“tempImage_{0}.nii.gz”.format(time.time()),
)
ants.image_write(antsImage, tempFilePath)
storageNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
storageNode.SetFileName(tempFilePath)
storageNode.ReadData(imageNode, True)
os.remove(tempFilePath)
return imageNode
Input directory of aligned images (such as from ANTs Registraion Groupwise Registration)
input_directory = “D:/ANTsData/MouseOutputs”
End pattern for selecting the transformed images from the input directory
filename_end_pattern = “transformed.nii.gz”
filePaths =
for file in os.listdir(input_directory):
if file.endswith(filename_end_pattern):
filePaths.append(os.path.join(input_directory, file))
averagedANTSImage = ants.math.average_images(filePaths)
averagedImageNode = nodeFromANTSImage(averagedANTSImage, “AverageImage”)
slicer.util.setSliceViewerLayers(background=averagedImageNode, fit=True)
Traceback (most recent call last):
File “”, line 2, in
ModuleNotFoundError: No module named ‘ants’
philippe pellerin
philippepellerin@me.com
