Dimension incompatibility of NRRD files with ITK-snap

[Sebastien-PILUSO]

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.

[Sebastien-PILUSO]

In my opinion, providing a grayscale image (dimension: 3) at the output of the DAP seems more appropriate rather than RGB (dimension: 4) to avoid dimensionality problems later on. The input image is not in colour, so we could add an option (activated by default) that would convert the data directly into grayscale.