BlueBrain / BlueBrain/Deep-Atlas
Dimension incompatibility of NRRD files with ITK-snap
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- Python
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Description
The output NRRD files from the DeepAtlas pipeline cannot be read by ITK-snap visualization software.
The problem seems to be linked to the header setting.
Here is the error encountered:
`/data/hippogang/build/buildbot/Nightly/itk/v5.2.1/itk/Modules/IO/NRRD/src/itkNrrdImageIO.cxx:292:
itk::ERROR: NrrdImageIO(0x561df21fdfb0): ReadImageInformation: Error reading /gpfs/bbp.cscs.ch/project/proj137/piluso/atlas-densities/data/ccfv2/marker_volumes/ALDH1L1.nrrd:`
`[nrrd] nrrdLoad: trouble reading "/gpfs/bbp.cscs.ch/project/proj137/piluso/atlas-densities/data/ccfv2/marker_volumes/ALDH1L1.nrrd"`
`[nrrd] nrrdRead: trouble`
`[nrrd] _nrrdRead: trouble reading NRRD file`
`[nrrd] _nrrdFormatNRRD_read: trouble parsing space directions info |(25,0,0) (0,25,0) (0,0,25)|`
`[nrrd] _nrrdReadNrrdParse_space_directions: trouble getting space vector 4 of 4`
`[nrrd] _nrrdSpaceVectorParse: hit end of string before seeing (`
with the header being:
`OrderedDict([('type', 'float'), ('dimension', 4), ('space dimension', 3), ('sizes', array([528, 320, 456, 3])), ('space directions', array([[25., 0., 0.],
[ 0., 25., 0.],
[ 0., 0., 25.]])), ('endian', 'little'), ('encoding', 'gzip'), ('space origin', array([0., 0., 0.]))])`
When rewriting the raw data in modifying the header:
`OrderedDict([('type', 'float'), ('dimension', 3), ('sizes', array([528, 320, 456])), ('endian', 'little'), ('encoding', 'gzip')])`
ITK-snap is able to read the output NRRD file.
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