error reading nifti image: Image has an invalid orientation (code RIL)

[Markus Heller]

We are processing some relatively large CT data sets containing scans of multiple bones (non-human) where we extract regions of interest to be able to more easily process selected bones in detail. The location and orientation of the bones in the scans is rather arbitrary and random. We have used simple ITK to extract such regions and saved the results as nifti files. 

We would like to do some of the processing of the extracted regions in ITK-SNAP but noted that, depending on the orientation, ITK-SNAP would fail to read some files while e.g. slicer is quite happy to do so.

We also noted that c3d seems to be happy to read these files, and we could perform some manipulation (e.g. extract a region) using c3d - and the results seem ok; but again, whilst slicer will read the file produced by c3d here, ITK-SNAP does not (the orientation did not change).

I wonder if there is any scope to make ITK-SNAP more acceptable of such more "wild" orientations?

The error message in the specific case here was:     

Image has an invalid orientation (code RIL)

We tested this using a recent version of ITK-SNAP (4.2.0. rc1, 11th March 2024) and c3d ( 1.4.0; compile date: 16rth March 2024); I've included the print-out of a c3d  -info-full command below to provide an idea of the direction cosine matrix.

It would be lovely to get your thoughts here!

Best wishes, 
Markus

print-out of a c3d  -info-full command is as follows:
Image #1:
  Image Dimensions   : [525, 1284, 588]
  Bounding Box       : {[28.7262 -7.79078 179.673], [61.5636 72.5201 216.451]}
  Voxel Spacing      : [0.0625474, 0.0625474, 0.0625474]
  Intensity Range    : [0, 255]
  Mean Intensity     : 23.5149
  Canon. Orientation : Oblique, closest to RIL
  Direction Cos Mtx. :
    0.8030    -0.0105    -0.5958
   -0.4325     0.6775    -0.5949
    0.4099     0.7355     0.5395
  Voxel->RAS x-form  :
        -0.05023      0.00066      0.03727    -28.72616
         0.02705     -0.04237      0.03721      7.79078
         0.02564      0.04600      0.03374    179.67319
         0.00000      0.00000      0.00000      1.00000
  Image Metadata:
    ITK_original_direction of unsupported type class itk::Matrix<double,3,3>
    ITK_original_spacing of unsupported type class std::vector<double,class std::allocator<double> >
    bitpix = 8
    cal_max = 0
    cal_min = 0
    datatype = 2
    dim[0] = 3
    dim[1] = 525
    dim[2] = 1284
    dim[3] = 588
    dim[4] = 1
    dim[5] = 1
    dim[6] = 1
    dim[7] = 1
    dim_info = 0
    intent_code = 0
    intent_p1 = 0
    intent_p2 = 0
    intent_p3 = 0
    nifti_type = 1
    pixdim[0] = 0
    pixdim[1] = 0.0625474
    pixdim[2] = 0.0625474
    pixdim[3] = 0.0625474
    pixdim[4] = 0
    pixdim[5] = 0
    pixdim[6] = 0
    pixdim[7] = 0
    qform_code = 1
    qform_code_name = NIFTI_XFORM_SCANNER_ANAT
    qoffset_x = -28.7262
    qoffset_y = 7.79078
    qoffset_z = 179.673
    quatern_b = 0.289378
    quatern_c = 0.382784
    quatern_d = 0.868904
    scl_inter = 0
    scl_slope = 1
    sform_code = 1
    sform_code_name = NIFTI_XFORM_SCANNER_ANAT
    slice_code = 0
    slice_duration = 0
    slice_end = 0
    slice_start = 0
    srow_x = -0.0502278 0.000659004 0.0372681 -28.7262
    srow_y = 0.0270543 -0.0423739 0.0372115 7.79078
    srow_z = 0.02564 0.0460022 0.0337427 179.673
    toffset = 0
    vox_offset = 352
    xyzt_units = 2