Operating system: Ubuntu 16
Slicer version: 4.8
Expected behavior: Display volume information and an image
Actual behavior: Slicer displays a white image and crash when opening the “Volume” Module
Dear all,
I have a CD contains a DICOM of MRI T2 Map Volume. I converted the contents to nrrd to do some experience. This produces 9 volumes: imgT2MAP_0 to imgT2MAP_7 (8 separate files nrrd files) and one nrrd file imgT2MAP of type vtkMRMLMultiVolumeNode.
When I open the last file in Slicer it display an image but it does not show voxel values in the Data Probe. Instead it displays “8 components”. My question is how this image is represented with these 8 values? what are the gray values in the shown image?
I tried to do some computation e.g. generate the first image imgT2MAP_0 from imgT2MAP by taking only the first value from the vector. The code runs but I got a white image, when I open the resulted volume in “Volume” Slicer crashes. Here is the code (forgive my dirty coding as I wrote in a hurry):
v = self.inputSelector.currentNode()
# get image properties
vd=v.GetImageData()
sz=vd.GetDimensions()
sp= v.GetSpacing()
og= v.GetOrigin()
dm = vtk.vtkMatrix4x4()
v.GetIJKToRASDirectionMatrix(dm)
va = slicer.util.array(v.GetID())
tp = vd.GetScalarType()
img=vtk.vtkImageData()
img.SetDimensions(sz)
img.AllocateScalars(tp, 1)
thresholder=vtk.vtkImageThreshold()
thresholder.SetInputData(img)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
vn=slicer.vtkMRMLScalarVolumeNode()
vn.SetSpacing(sp)
vn.SetOrigin(og)
vn.SetIJKToRASDirectionMatrix(dm)
vn.SetImageDataConnection(thresholder.GetOutputPort())
vn.SetName("imgT2MapOutput")
# Add volume to scene
slicer.mrmlScene.AddNode(vn)
displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.util.getNode('Grey')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
vn.SetAndObserveDisplayNodeID(displayNode.GetID())
vn.CreateDefaultStorageNode()
vm = slicer.util.getNode("imgT2MapOutPut")
vmd=vm.GetImageData()
vma = slicer.util.array(vm.GetID())
for k in xrange(0, sz[0]):
for j in xrange(0,sz[1]):
for i in xrange(0, sz[2]):
vc= va[i,j,k]
vma [i,j,k] = vc[0]
vm.Modified()
Please help me to find out what makes this strange output and slicer crash in the previous code. Also, I would like to know if there is a better way to do the same thing e.g. using iterators instead of loops.
Thanks!
You can load 4D nrrd files if Sequences module is installed. In Add data dialog, choose Volume sequence for the data set. If you use .seq.nrrd extension instead of just .nrrd then Volume sequence will be selected by default.
I changed the file by adding .seq and load the volume as you described.
In Volume Module. The volume type is changed.
This is helpful for viewing but I still can not do computations e.g. generate different nodes from the sequence or compute T2 mapping. Could you please check the code I wrote and help with mentioned issues.
Thanks for the reply and the info.
I didn’t know that there is already such an extension, why it does not appear in Slicer’s extension manager?
I was planning to use Scipy to do the fitting so at the end I have only one file python code to make a simple portable Slicer plugin.
I will check the links today.
Still (for the sake of knowledge), I don’t know what cause the issues in the code above. If I change this line:
vma [i,j,k] = vc[0]
To be something like
vma [i,j,k] = 0
or
vma [i,j,k] = 4000
In both situations, Slicer does not crash when I load the resulted volume in “Volume” module. It crashes only when I try to assign voxel value from the multi volume. I printed the value of vc[0] and it looks like a single scalar value (not a vector).
When you copy between numpy arrays, numpy tries to do shallow copies. During shallow copying, numpy reallocates memory and shares it between arrays, which is a prohibited operation on the VTK-managed array that slicer.util.array returns. See more information here.
T2Mapping extension was only added to the latest master version of Slicer, which currently in a transitioning phase and so not all extensions are available.
I’ve now added T2mapping to the latest stable (4.8.1) extension index, so the T2mapping extension should show up tomorrow in stable version’s extension manager.
Thanks for your concern. The extension is useful. but there is only one issue that the result is not shown after computation, something like this should be added to the end of the python file (in my case, I am interested in the Spine sagittal view):
yellow_logic = slicer.app.layoutManager().sliceWidget("Yellow").sliceLogic()
yellow_cn = yellow_logic.GetSliceCompositeNode()
yellow_cn.SetBackgroundVolumeID(T2outputVolume.GetID())
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpYellowSliceView)
# Fit slice to window
sliceNodes = slicer.util.getNodes('vtkMRMLSliceNode*')
layoutManager = slicer.app.layoutManager()
for sliceNode in sliceNodes.values():
sliceWidget = layoutManager.sliceWidget(sliceNode.GetLayoutName())
if sliceWidget:
sliceWidget.sliceLogic().FitSliceToAll()
logging.info('Processing completed')
return True
