Centerlinesections and multiplanarresampling

Patricia Garcia Cañadilla

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Dec 1, 2017, 4:31:22 AM12/1/17

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Dear developers,

Firstable, thank you for your nice code. It's really useful :). I am very new to VMTK and I am trying to do a couple of things in MAC OS version:

- Compute the crossectional area in a tubular shape

- To the multiplanar resample following the centerline direction.

And I couldn't do any of the two. I managed to obtain the centerline, but when I execute:

vmtkcenterlinesections -ifile /Users/Patricia/Desktop/LADpaper/test_centerlines2.vtp -ocenterlinesfile /Users/Patricia/Desktop/LADpaper/AREAS.dat

It never finishes, it keeps running forever and I didn't get any results.

Regarding the MPR, when I execute that:

vmtkcenterlineresampling -ifile /Users/Patricia/Desktop/LADpaper/test_centerlines.vtp --pipe vmtkcenterlineattributes --pipe vmtkcenterlinegeometry --pipe vmtkimagecurvedmpr -ifile /Users/Patricia/Desktop/LADpaper/test.vti -ofile /Users/Patricia/Desktop/LADpaper/curved.vti --pipe vmtkimageviewer

I got the following error:

ERROR: In /Users/user133291/miniconda3/conda-bld/vtk_1509912335940/work/Common/DataModel/vtkImageData.cxx, line 1326

vtkImageData (0x7ff38cfb8a90): No Scalar Field has been specified - assuming 1 component!

test_centerlines.vtp

test_sm.vtp

test.vti

Patricia Garcia Cañadilla

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Dec 1, 2017, 8:31:05 AM12/1/17

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Dear again,

I tried with another cell that was smoother, and the crossectional area comptuing now works. However, I still have the same error when running the "vmtkimagecurvedmpr" as follows. I attached the new files also.

vmtkcenterlineresampling -ifile /Users/Patricia/Desktop/LADpaper/cell2_centerlines.vtp --pipe vmtkcenterlineattributes --pipe vmtkcenterlinegeometry --pipe vmtkimagecurvedmpr -ifile /Users/Patricia/Desktop/LADpaper/cell2.mha -ofile /Users/Patricia/Desktop/LADpaper/cell2_curved.mha --pipe vmtkimageviewer

ERROR: In /Users/user133291/miniconda3/conda-bld/vtk_1509912335940/work/Common/ExecutionModel/vtkExecutive.cxx, line 784

vtkCompositeDataPipeline (0x7f7f34b317c0): Algorithm vtkvmtkITKArchetypeImageSeriesScalarReader(0x7f7f27461bf0) returned failure for request: vtkInformation (0x7f7f37c06e10)

Debug: Off

Modified Time: 12362147

Reference Count: 1

Registered Events: (none)

Request: REQUEST_INFORMATION

FORWARD_DIRECTION: 0

ALGORITHM_AFTER_FORWARD: 1

Traceback (most recent call last):

File "/Users/Patricia/anaconda/lib/python2.7/site-packages/vmtk/pypeserver.py", line 46, in RunPypeProcess

pipe.Execute()

File "/Users/Patricia/anaconda/lib/python2.7/site-packages/vmtk/pype.py", line 280, in Execute

scriptObject.IORead()

File "/Users/Patricia/anaconda/lib/python2.7/site-packages/vmtk/pypescript.py", line 606, in IORead

reader.Execute()

File "/Users/Patricia/anaconda/lib/python2.7/site-packages/vmtk/vmtkimagereader.py", line 296, in Execute

self.ReadITKIO()

File "/Users/Patricia/anaconda/lib/python2.7/site-packages/vmtk/vmtkimagereader.py", line 225, in ReadITKIO

matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),

AttributeError: 'NoneType' object has no attribute 'GetElement'

ERROR: In /Users/user133291/miniconda3/conda-bld/vtk_1509912335940/work/Common/DataModel/vtkImageData.cxx, line 1326

vtkImageData (0x7f7f272d3180): No Scalar Field has been specified - assuming 1 component!

cell2_centerlines.vtp

cell2_sm.vtp

cell2.mha

Patricia Garcia Cañadilla

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Dec 6, 2017, 7:22:11 AM12/6/17

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Any idea why the multiplanar resampling is not working with my dataset?

El viernes, 1 de diciembre de 2017, 10:31:22 (UTC+1), Patricia Garcia Cañadilla escribió:

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