Re: Image has an invalid orientation (code ...)

[Dorian P.]

The following command fixed the problem:

c3d input.nii -orient RAI -o output.nii

Thank you.

On Wed, Nov 5, 2014 at 2:15 PM, Dorian P. <alb...@gmail.com> wrote:

Hi Snappers,

I have a lesion mask for a subject that cannot be opened with ITKsnap. I receive the error: "Image has an invalid orientation (code ...)"

The image is regular nii.gz as many others, and I can open the same image in MRIcron. Note, ANTs  also failed to process this image correctly when doing some image math.

Any solutions how to fix this?

P.s. I can send you the location on CFN cluster if you need to have a look.

################# IMAGE HEADER ############### 

dpustina@chead:dpustina$ PrintHeader MR0047_M.nii

 Spacing [0.976562, 0.992063, 1]

 Origin [0, 0, 0]

 Direction 

1 0 0

0 -1 0

0 0 -1

 Size : 192 252  160

  Image Dimensions   : [192, 252, 160]

  Bounding Box       : {[0 0 0], [187.5 250 160]}

  Voxel Spacing      : [0.976562, 0.992063, 1]

  Intensity Range    : [0, 1]

  Mean Intensity     : 0.0171989

  Direction Cos Mtx. : 

1 0 0

0 -1 0

0 0 -1

  Voxel->RAS x-form  : 

  Image Metadata: 

    ITK_FileNotes = nifti 3D file produced by VoxBo

    bitpix = 8

    cal_max = 0

    cal_min = 0

    datatype = 2

    descrip = nifti 3D file produced by VoxBo

    dim[0] = 3

    dim[1] = 192

    dim[2] = 252

    dim[3] = 160

    dim[4] = 1

    dim[5] = 1

    dim[6] = 1

    dim[7] = 1

    intent_code = 0

    intent_p1 = 0

    intent_p2 = 0

    intent_p3 = 0

    pixdim[0] = 0

    pixdim[1] = 0.976562

    pixdim[2] = 0.992063

    pixdim[3] = 1

    pixdim[4] = 1

    pixdim[5] = 1

    pixdim[6] = 1

    pixdim[7] = 1

    qform_code = 8192

    qoffset_x = 0

    qoffset_y = 0

    qoffset_z = 0

    quatern_b = 9.80909e-45

    quatern_c = -1.01451e+34

    quatern_d = -nan

    scl_inter = 0

    scl_slope = 0

    sform_code = -2060

    slice_duration = 0

    slice_end = 0

    slice_start = 0

    srow_x = -1.01003e+34 -1.01451e+34 -9.90397e+33 1.4013e-45

    srow_y = 0 0 1.12104e-44 1.56945e-43

    srow_z = -1.01442e+34 -1.00702e+34 -1.01246e+34 0

    toffset = 0

    vox_offset = 352

[Dorian P.]

Also note, in Matlab:

volgood=spm_vol('MR0044_M.nii')

volbad=spm_vol('MR0047_M.nii')

>> volgood.private.mat0

ans =

   -0.9800         0         0   94.5700

         0    0.9956         0 -125.9378

         0         0    1.0000  -80.5000

         0         0         0    1.0000

volbad.private.mat0

ans =

   NaN   NaN   NaN   NaN

   NaN   NaN   NaN   NaN

   NaN   NaN   NaN   NaN

   NaN   NaN   NaN   NaN

Any solution?

Dorian

[Philip A Cook]

Something has wrecked the original header - the qform and sform are both nonsense. I suspect there was a bug involving wrong endianness when the header was written. Be careful that the image orientation after imposing RAI is correct.

On Nov 5, 2014, at 2:26 PM, Dorian P. <alb...@gmail.com> wrote:

> Also note, in Matlab:
> volgood=spm_vol('MR0044_M.nii')
> volbad=spm_vol('MR0047_M.nii')
>
>
> >> volgood.private.mat0
>
> ans =
>
> -0.9800 0 0 94.5700
> 0 0.9956 0 -125.9378
> 0 0 1.0000 -80.5000
> 0 0 0 1.0000
>
> volbad.private.mat0
>
> ans =
>
> NaN NaN NaN NaN
> NaN NaN NaN NaN
> NaN NaN NaN NaN
> NaN NaN NaN NaN
>
>
> Any solution?
>
> Dorian
>
>
> On Wed, Nov 5, 2014 at 2:15 PM, Dorian P. <alb...@gmail.com> wrote:
> Hi Snappers,
>
> I have a lesion mask for a subject that cannot be opened with ITKsnap. I receive the error: "Image has an invalid orientation (code ...)"
>

> <image.png>

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[Dorian P.]

Hi Snappers,

I have a lesion mask for a subject that cannot be opened with ITKsnap. I receive the error: "Image has an invalid orientation (code ...)"