reading segmentation file from Slicer (NRRD) with multiple segments with SimpleITK shows Exception

Engineering
,
22

If I change the NRRD kinds header in my files so the first dimension becomes of the type list (instead of complex) would that make that file readable by SimpleITK? @blowekamp @dzenanz

23

Have your u tried the outputPixelType option?

24

about to try it now…

25

@blowekamp This is what I got when I tried:

image = sitk.ReadImage(filename, sitk.sitkVectorUInt16)

(Notice that the outp pixel type is not a keyword argument)

  File "/Users/odin/anaconda/lib/python2.7/site-packages/SimpleITK/SimpleITK.py", line 8332, in ReadImage
    return _SimpleITK.ReadImage(*args)
RuntimeError: Exception thrown in SimpleITK ReadImage: /scratch/dashboards/SimpleITK-OSX10.6-intel-pkg/SimpleITK/Code/IO/src/sitkImageReaderBase.cxx:285:
sitk::ERROR: Only Complex image with float and double are supported!
26

This is the respective NRRD header dump

__len__ = {int} 10
u'dimension' (4867413600) = {int} 4
u'encoding' (4867413792) = {str} 'gzip'
u'keyvaluepairs' (4628472432) = {dict} # Slicer metadata about segments goes here
u'kinds' (4596423152) = {list} <type 'list'>: ['complex', 'domain', 'domain', 'domain']
u'measurement frame' (4867413984) = {list} <type 'list'>: [['1', '0', '0'], ['0', '1', '0'], ['0', '0', '1']]
u'sizes' (4867413696) = {list} <type 'list'>: [2, 41, 80, 9]
u'space' (4867413360) = {str} 'right-anterior-superior'
u'space directions' (4867413456) = {list} <type 'list'>: [u'none', ['-0.5', '1.01115573674059e-10', '1.7102395547300398e-11'], ['-1.0255169999999903e-10', '-0.492998018603237', '-0.08338437295609949'], ['-1.9387071799358836e-26', '-0.50030691366964397', '2.9579921079755898']]
u'space origin' (4867413888) = {list} <type 'list'>: ['-18.165176407702127', '-1.8838383685304463', '-70.585192304157161']
u'type' (4867413504) = {str} 'unsigned char'
27

That should make the file readable. I think that all the other metadata is OK, but you should try to be sure. You can also change it using a text editor (e.g. Notepad++) just to see if it works, you don’t have to do it programmatically.

28

Hi Dženan thanks! I will try that!

29

I agree with @lassoan that “list” is the right axis “kind” here: you know its a list when two things are true: it doesn’t make any sense to resample along this axis (as it would if this were a spatial or temporal axis), and, these values would not change in a predictable way with a change in the basis vectors used to span space (as they would if this were the coefficients of a vector or tensor).

But obviously a file format can’t teach software about how to handle meta-data. @lassoan is there ever a case where vtkTeemNRRDWriter might be used to save an actual vector field (like a displacement field from a non-rigid registration?)

2 Likes
30

vtkTeemNRRDWriter still uses different axis kinds for vector fields, tenors, etc. I’ve just changed it to use list kind for Segmentations.

3 Likes
31

Thank you @lassoan When do you think this change will be available in Slicer? I have another 900 images to go through with my radiologists… thanks!

32

It’s already available in the nightly version.

2 Likes
33

Hey Diego,

Would it be possible for you to share that code? Thank you in advance

1 Like